From 974b56635b229becf7984f899dd15b93c3d3309c Mon Sep 17 00:00:00 2001
From: Ignacio Eguinoa <igegu@psb.ugent.be>
Date: Fri, 9 Jun 2017 16:17:57 +0200
Subject: [PATCH 01/18] all_gff sample loc file

---
 tools/bedtools/all_gff.loc.sample | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)
 create mode 100644 tools/bedtools/all_gff.loc.sample

diff --git a/tools/bedtools/all_gff.loc.sample b/tools/bedtools/all_gff.loc.sample
new file mode 100644
index 000000000..b3b8c1c57
--- /dev/null
+++ b/tools/bedtools/all_gff.loc.sample
@@ -0,0 +1,16 @@
+#This file lists the locations and dbkeys of all the GFF files
+#This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>      <dbkey> <display_name>  <file_path>
+#
+#So, all_gff.loc could look something like this:
+#
+#apiMel3        apiMel3 Honeybee (Apis mellifera): apiMel3      /path/to/annotation/apiMel3/apiMel3.gff
+#hg19canon      hg19    Human (Homo sapiens): hg19 Canonical    /path/to/annotation/hg19/hg19canon.gff
+#hg19full       hg19    Human (Homo sapiens): hg19 Representative transcripts /path/to/annotation/hg19/hg19_representative_tx.gff
+#
+#Your all_gff.loc file should contain an entry for each different annotation.
+#So there can be multiple gff files for each build,
+#such as with hg19 above.
+#

From 246b59ff7d6ed6bbbe70aa3bcf0c564e681aaa4a Mon Sep 17 00:00:00 2001
From: Ignacio Eguinoa <igegu@psb.ugent.be>
Date: Fri, 9 Jun 2017 16:58:01 +0200
Subject: [PATCH 02/18] add different source options

---
 tools/bedtools/closestBed.xml | 27 ++++++++++++++++++++++++---
 1 file changed, 24 insertions(+), 3 deletions(-)

diff --git a/tools/bedtools/closestBed.xml b/tools/bedtools/closestBed.xml
index d51258352..964387aa4 100644
--- a/tools/bedtools/closestBed.xml
+++ b/tools/bedtools/closestBed.xml
@@ -7,7 +7,6 @@
     <expand macro="stdio" />
     <command>
 <![CDATA[
-        #set inputBs = "' '".join([str( $file ) for $file in $inputB])
 
         closestBed
         $strand
@@ -24,13 +23,35 @@
             -k $k
         #end if
         -a '$inputA'
-        -b '$inputBs'
+        #if str($overlap_with.source) == "data_table":
+		-b '$overlap_with.table.fields.path'
+	#else	
+		#set inputBs = "' '".join([str( $file ) for $file in $overlap_with.history.own_file])
+		-b '$inputBs'
+	#end if 
         > '$output'
 ]]>
     </command>
     <inputs>
         <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
-        <param format="bed,gff,vcf,gff3" name="inputB" type="data" multiple="True" label="overlap intervals in this BED/VCF/GFF file?"/>
+        <!-- overlap with file (inputB) -->
+        <conditional name="overlap_with">
+          <param name="source" type="select" label="Overlap with: will you select a BED/VCF/GFF file from your history or use a built-in GFF file?" help="Built-in GFF files contain full annotation of a reference genome">
+            <option value="history" selected="True">Use a BED/VCF/GFF file from the history</option>
+            <option value="data_table">Use a built-in GFF file</option>
+          </param>
+          <when value="data_table">
+            <param name="table" type="select" label="Select reference GFF" help="If your genome of interest is not listed, contact the Galaxy team">
+              <options from_data_table="all_gff">
+                <filter type="sort_by" column="2"/>
+                <validator type="no_options" message="No files are available"/>
+              </options>
+            </param>
+          </when>
+          <when value="history">
+            <param name="own_file" type="data" format="bed,gff,vcf,gff3" multiple="True" label="Select a BED/VCF/GFF file" />
+          </when>
+        </conditional>
 
         <param name="ties" type="select"
             label="How ties for closest feature should be handled"

From e70806d55a75c6638e50530db1e7572c2b4042b6 Mon Sep 17 00:00:00 2001
From: Ignacio Eguinoa <igegu@psb.ugent.be>
Date: Fri, 9 Jun 2017 16:59:32 +0200
Subject: [PATCH 03/18] add all_gff tool_data_table conf entry

---
 tools/bedtools/tool_data_table_conf.xml.sample | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/tools/bedtools/tool_data_table_conf.xml.sample b/tools/bedtools/tool_data_table_conf.xml.sample
index d5c59b96f..afad1d472 100644
--- a/tools/bedtools/tool_data_table_conf.xml.sample
+++ b/tools/bedtools/tool_data_table_conf.xml.sample
@@ -4,4 +4,9 @@
         <columns>value, dbkey, name, path</columns>
         <file path="tool-data/all_fasta.loc" />
     </table>
+    <!-- Locations of all gff files with annotations of genome builds -->
+    <table name="all_gff" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_gff.loc" />
+    </table>	
 </tables>

From 05df476173b25adff4ac6c318afbc7ce98c531fe Mon Sep 17 00:00:00 2001
From: Ignacio Eguinoa <igegu@psb.ugent.be>
Date: Fri, 9 Jun 2017 17:50:01 +0200
Subject: [PATCH 04/18] correct input name

---
 tools/bedtools/closestBed.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/bedtools/closestBed.xml b/tools/bedtools/closestBed.xml
index 964387aa4..d16f642bb 100644
--- a/tools/bedtools/closestBed.xml
+++ b/tools/bedtools/closestBed.xml
@@ -26,7 +26,7 @@
         #if str($overlap_with.source) == "data_table":
 		-b '$overlap_with.table.fields.path'
 	#else	
-		#set inputBs = "' '".join([str( $file ) for $file in $overlap_with.history.own_file])
+		#set inputBs = "' '".join([str( $file ) for $file in $overlap_with.own_file])
 		-b '$inputBs'
 	#end if 
         > '$output'

From 3eb230ccb050d1ddf54ae7c40d01aa9713fcfbed Mon Sep 17 00:00:00 2001
From: Ignacio <ignacio.eguinoa@gmail.com>
Date: Sat, 10 Jun 2017 14:34:05 +0200
Subject: [PATCH 05/18] fix names in tests

---
 tools/bedtools/closestBed.xml | 20 +++++++++++++-------
 1 file changed, 13 insertions(+), 7 deletions(-)

diff --git a/tools/bedtools/closestBed.xml b/tools/bedtools/closestBed.xml
index d16f642bb..6b4d81bb4 100644
--- a/tools/bedtools/closestBed.xml
+++ b/tools/bedtools/closestBed.xml
@@ -110,37 +110,43 @@
     <tests>
         <test>
             <param name="inputA" value="closestBedA.bed" ftype="bed" />
-            <param name="inputB" value="closestBedB.bed" ftype="bed" />
+            <param name="source" value="history" />
+            <param name="own_file" value="closestBedB.bed" ftype="bed" />
             <output name="output" file="closestBed_result1.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="closestBed_a.bed" ftype="bed" />
-            <param name="inputB" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" />
+            <param name="source" value="history" />
+            <param name="own_file" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" />
             <param name="addition" value="True" />
             <output name="output" file="closestBed_result2.bed" ftype="bed" />
         </test>
         <test>
-            <param name="inputA" value="closestBed_a.bed" ftype="bed" />
-            <param name="inputB" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" />
+            <param name="inputA" value="closestBed_a.bed" ftype="bed" /> 
+            <param name="source" value="history" />
+            <param name="own_file" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" />
             <param name="addition" value="True" />
             <param name="mdb" value="all" />
             <output name="output" file="closestBed_result3.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="closestBed_c.bed" ftype="bed" />
-            <param name="inputB" value="closestBed_d.bed" ftype="bed" />
+            <param name="source" value="history" /> 
+            <param name="own_file" value="closestBed_d.bed" ftype="bed" />
             <param name="addition2_select" value="ref" />
             <output name="output" file="closestBed_result4.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="closestBed_c.bed" ftype="bed" />
-            <param name="inputB" value="closestBed_d.bed" ftype="bed" />
+            <param name="source" value="history" />  
+            <param name="own_file" value="closestBed_d.bed" ftype="bed" />
             <param name="addition2_select" value="a" />
             <output name="output" file="closestBed_result5.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="closestBedA.bed" ftype="bed" />
-            <param name="inputB" value="a.bed" ftype="bed" />
+            <param name="source" value="history" />
+            <param name="own_file" value="a.bed" ftype="bed" />
             <param name="k" value="3" />
             <output name="output" file="closestBed_result6.bed" ftype="bed" />
         </test>

From 87e65e905e4ac3dc20e252bbc7307aed36bd568c Mon Sep 17 00:00:00 2001
From: Ignacio <ignacio.eguinoa@gmail.com>
Date: Sun, 11 Jun 2017 18:28:00 +0200
Subject: [PATCH 06/18] correct indentation

---
 tools/bedtools/closestBed.xml | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/tools/bedtools/closestBed.xml b/tools/bedtools/closestBed.xml
index 6b4d81bb4..28fe5439c 100644
--- a/tools/bedtools/closestBed.xml
+++ b/tools/bedtools/closestBed.xml
@@ -24,10 +24,10 @@
         #end if
         -a '$inputA'
         #if str($overlap_with.source) == "data_table":
-		-b '$overlap_with.table.fields.path'
+	    -b '$overlap_with.table.fields.path'
 	#else	
-		#set inputBs = "' '".join([str( $file ) for $file in $overlap_with.own_file])
-		-b '$inputBs'
+	    #set inputBs = "' '".join([str( $file ) for $file in $overlap_with.own_file])
+	    -b '$inputBs'
 	#end if 
         > '$output'
 ]]>
@@ -36,20 +36,20 @@
         <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
         <!-- overlap with file (inputB) -->
         <conditional name="overlap_with">
-          <param name="source" type="select" label="Overlap with: will you select a BED/VCF/GFF file from your history or use a built-in GFF file?" help="Built-in GFF files contain full annotation of a reference genome">
+            <param name="source" type="select" label="Overlap with: will you select a BED/VCF/GFF file from your history or use a built-in GFF file?" help="Built-in GFF files contain full annotation of a reference genome">
             <option value="history" selected="True">Use a BED/VCF/GFF file from the history</option>
             <option value="data_table">Use a built-in GFF file</option>
-          </param>
-          <when value="data_table">
-            <param name="table" type="select" label="Select reference GFF" help="If your genome of interest is not listed, contact the Galaxy team">
-              <options from_data_table="all_gff">
-                <filter type="sort_by" column="2"/>
-                <validator type="no_options" message="No files are available"/>
-              </options>
             </param>
+            <when value="data_table">
+                <param name="table" type="select" label="Select reference GFF" help="If your genome of interest is not listed, contact the Galaxy team">
+                    <options from_data_table="all_gff">
+                        <filter type="sort_by" column="2"/>
+                        <validator type="no_options" message="No files are available"/>
+                    </options>
+                </param>
           </when>
           <when value="history">
-            <param name="own_file" type="data" format="bed,gff,vcf,gff3" multiple="True" label="Select a BED/VCF/GFF file" />
+              <param name="own_file" type="data" format="bed,gff,vcf,gff3" multiple="True" label="Select a BED/VCF/GFF file" />
           </when>
         </conditional>
 

From 536fd5c4187fe536fc6a69a3d998ddf2b9fe85c2 Mon Sep 17 00:00:00 2001
From: Ignacio <ignacio.eguinoa@gmail.com>
Date: Sun, 11 Jun 2017 19:35:52 +0200
Subject: [PATCH 07/18] fix tab indentation

---
 tools/bedtools/closestBed.xml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tools/bedtools/closestBed.xml b/tools/bedtools/closestBed.xml
index 28fe5439c..c83b4d928 100644
--- a/tools/bedtools/closestBed.xml
+++ b/tools/bedtools/closestBed.xml
@@ -24,11 +24,11 @@
         #end if
         -a '$inputA'
         #if str($overlap_with.source) == "data_table":
-	    -b '$overlap_with.table.fields.path'
-	#else	
-	    #set inputBs = "' '".join([str( $file ) for $file in $overlap_with.own_file])
-	    -b '$inputBs'
-	#end if 
+            -b '$overlap_with.table.fields.path'
+        #else	
+        #set inputBs = "' '".join([str( $file ) for $file in $overlap_with.own_file])
+            -b '$inputBs'
+        #end if 
         > '$output'
 ]]>
     </command>

From ef35c61fc41556aa7700de970650c78a9a7e55cf Mon Sep 17 00:00:00 2001
From: Ignacio <ignacio.eguinoa@gmail.com>
Date: Mon, 26 Jun 2017 11:04:35 +0200
Subject: [PATCH 08/18] add samtools requirements in tools that use it

---
 tools/bedtools/bedToBam.xml   | 4 +++-
 tools/bedtools/bedpeToBam.xml | 4 +++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/tools/bedtools/bedToBam.xml b/tools/bedtools/bedToBam.xml
index c5af342c1..b8f761f8f 100644
--- a/tools/bedtools/bedToBam.xml
+++ b/tools/bedtools/bedToBam.xml
@@ -3,7 +3,9 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="requirements">
+        <requirement type="package" version="1.2">samtools</requirement>
+    </expand>
     <expand macro="stdio" />
     <command>
 <![CDATA[
diff --git a/tools/bedtools/bedpeToBam.xml b/tools/bedtools/bedpeToBam.xml
index 000cda7c5..7a236997f 100644
--- a/tools/bedtools/bedpeToBam.xml
+++ b/tools/bedtools/bedpeToBam.xml
@@ -3,7 +3,9 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="requirements">
+        <requirement type="package" version="1.2">samtools</requirement>
+    </expand>
     <expand macro="stdio" />
     <command>
 <![CDATA[

From fe03f78f155bd02fd081c2298442933b1e1f6f19 Mon Sep 17 00:00:00 2001
From: Ignacio <ignacio.eguinoa@gmail.com>
Date: Mon, 26 Jun 2017 11:42:09 +0200
Subject: [PATCH 09/18] add samtools as general requirement

---
 tools/bedtools/bamToBed.xml   | 4 +---
 tools/bedtools/bedToBam.xml   | 4 +---
 tools/bedtools/bedpeToBam.xml | 4 +---
 tools/bedtools/macros.xml     | 1 +
 4 files changed, 4 insertions(+), 9 deletions(-)

diff --git a/tools/bedtools/bamToBed.xml b/tools/bedtools/bamToBed.xml
index fe4ccec24..9e56de898 100644
--- a/tools/bedtools/bamToBed.xml
+++ b/tools/bedtools/bamToBed.xml
@@ -3,9 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <requirement type="package" version="1.2">samtools</requirement>
-    </expand>
+    <expand macro="requirements"/>
     <expand macro="stdio" />
     <command>
 <![CDATA[
diff --git a/tools/bedtools/bedToBam.xml b/tools/bedtools/bedToBam.xml
index b8f761f8f..c0cd2bce2 100644
--- a/tools/bedtools/bedToBam.xml
+++ b/tools/bedtools/bedToBam.xml
@@ -3,9 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <requirement type="package" version="1.2">samtools</requirement>
-    </expand>
+    <expand macro="requirements"/>
     <expand macro="stdio" />
     <command>
 <![CDATA[
diff --git a/tools/bedtools/bedpeToBam.xml b/tools/bedtools/bedpeToBam.xml
index 7a236997f..37fe51cbd 100644
--- a/tools/bedtools/bedpeToBam.xml
+++ b/tools/bedtools/bedpeToBam.xml
@@ -3,9 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <requirement type="package" version="1.2">samtools</requirement>
-    </expand>
+    <expand macro="requirements"/>
     <expand macro="stdio" />
     <command>
 <![CDATA[
diff --git a/tools/bedtools/macros.xml b/tools/bedtools/macros.xml
index 2257be94b..1b0589e3c 100644
--- a/tools/bedtools/macros.xml
+++ b/tools/bedtools/macros.xml
@@ -2,6 +2,7 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="2.26.0gx">bedtools</requirement>
+            <requirement type="package" version="1.2">samtools</requirement>
             <yield/>
         </requirements>
     </xml>

From 0f9d184164c53f7828ab9892faa2ecfc2a84b932 Mon Sep 17 00:00:00 2001
From: Ignacio <ignacio.eguinoa@gmail.com>
Date: Mon, 26 Jun 2017 13:51:13 +0200
Subject: [PATCH 10/18] install samtools in travis environment

---
 .travis.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.travis.yml b/.travis.yml
index cf3dd8029..e9abfd57b 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -58,6 +58,7 @@ before_install:
   - unset JAVA_HOME
 
 install:
+  - apt-get -y install samtools	  #required to convert test output format
   - pip install planemo
   - planemo conda_init
   - export PATH="$PLANEMO_CONDA_PREFIX/bin:$PATH"

From b827ca5bd1d88c4e9b40afb87dd3c14dfca2fc86 Mon Sep 17 00:00:00 2001
From: Ignacio <ignacio.eguinoa@gmail.com>
Date: Mon, 26 Jun 2017 14:01:32 +0200
Subject: [PATCH 11/18] fix samtools installs

---
 .travis.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index e9abfd57b..20fa53ac6 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -58,7 +58,8 @@ before_install:
   - unset JAVA_HOME
 
 install:
-  - apt-get -y install samtools	  #required to convert test output format
+  #samtools is required to parse test outputs
+  - apt-get -y install samtools	  
   - pip install planemo
   - planemo conda_init
   - export PATH="$PLANEMO_CONDA_PREFIX/bin:$PATH"

From fbbd173d3fd58c9dd22f4a5293f33909950e5005 Mon Sep 17 00:00:00 2001
From: Ignacio <ignacio.eguinoa@gmail.com>
Date: Mon, 26 Jun 2017 14:10:56 +0200
Subject: [PATCH 12/18] correct syntax to install samtools

---
 .travis.yml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 20fa53ac6..4efc531b0 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -57,9 +57,12 @@ before_install:
   - export PLANEMO_CONDA_PREFIX="$HOME/conda"
   - unset JAVA_HOME
 
+addons:
+  apt:
+    packages:
+    - samtools
+
 install:
-  #samtools is required to parse test outputs
-  - apt-get -y install samtools	  
   - pip install planemo
   - planemo conda_init
   - export PATH="$PLANEMO_CONDA_PREFIX/bin:$PATH"

From 1827e6e806791aa101a3ea0560b08e548cc863c8 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Mon, 26 Jun 2017 14:40:55 +0100
Subject: [PATCH 13/18] Skip samtools install in lint and deploy stages

---
 .travis.yml | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 4efc531b0..68ce736a0 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -8,6 +8,7 @@ python: 2.7
 jobs:
   include:
     - stage: lint
+      addons: {}
       before_install: skip
       install:
         - pip install flake8 flake8-import-order planemo
@@ -33,6 +34,7 @@ jobs:
       env: CHUNK=2
 
     - stage: deploy
+      addons: {}
       before_install: skip
       install:
         - pip install planemo
@@ -51,17 +53,17 @@ jobs:
               while read -r DIR; do planemo shed_update --shed_target toolshed --shed_email "$SHED_EMAIL" --shed_password "$SHED_PASSWORD" --force_repository_creation "$DIR" || exit 1; done < changed_repositories.list
           fi
 
+addons:
+  apt:
+    packages:
+    - samtools
+
 before_install:
   - export GALAXY_REPO=https://github.com/galaxyproject/galaxy
   - export GALAXY_RELEASE=release_17.05
   - export PLANEMO_CONDA_PREFIX="$HOME/conda"
   - unset JAVA_HOME
 
-addons:
-  apt:
-    packages:
-    - samtools
-
 install:
   - pip install planemo
   - planemo conda_init

From 38a45ebf42b45aa6cd10ff76a9b1605ccdd38b54 Mon Sep 17 00:00:00 2001
From: Ignacio <ignacio.eguinoa@gmail.com>
Date: Mon, 26 Jun 2017 17:03:10 +0200
Subject: [PATCH 14/18] remove global samtools dependency

---
 tools/bedtools/macros.xml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tools/bedtools/macros.xml b/tools/bedtools/macros.xml
index 1b0589e3c..2257be94b 100644
--- a/tools/bedtools/macros.xml
+++ b/tools/bedtools/macros.xml
@@ -2,7 +2,6 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="2.26.0gx">bedtools</requirement>
-            <requirement type="package" version="1.2">samtools</requirement>
             <yield/>
         </requirements>
     </xml>

From fa058dae96fad2b719d2a0a88bea02863c47974d Mon Sep 17 00:00:00 2001
From: Ignacio <ignacio.eguinoa@gmail.com>
Date: Mon, 26 Jun 2017 17:10:28 +0200
Subject: [PATCH 15/18] add samtools dependency

---
 tools/bedtools/bamToBed.xml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tools/bedtools/bamToBed.xml b/tools/bedtools/bamToBed.xml
index 9e56de898..a27541d3d 100644
--- a/tools/bedtools/bamToBed.xml
+++ b/tools/bedtools/bamToBed.xml
@@ -3,6 +3,9 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="1.2">samtools</requirement>
+    </expand>
     <expand macro="requirements"/>
     <expand macro="stdio" />
     <command>

From bca54f1f9d7818bd41ba7b023a481d02923e6455 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Mon, 26 Jun 2017 17:23:24 +0200
Subject: [PATCH 16/18] Remove doubled expand macro

---
 tools/bedtools/bamToBed.xml   | 1 -
 tools/bedtools/bedToBam.xml   | 2 +-
 tools/bedtools/bedpeToBam.xml | 2 +-
 3 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/tools/bedtools/bamToBed.xml b/tools/bedtools/bamToBed.xml
index a27541d3d..fe4ccec24 100644
--- a/tools/bedtools/bamToBed.xml
+++ b/tools/bedtools/bamToBed.xml
@@ -6,7 +6,6 @@
     <expand macro="requirements">
         <requirement type="package" version="1.2">samtools</requirement>
     </expand>
-    <expand macro="requirements"/>
     <expand macro="stdio" />
     <command>
 <![CDATA[
diff --git a/tools/bedtools/bedToBam.xml b/tools/bedtools/bedToBam.xml
index c0cd2bce2..c5af342c1 100644
--- a/tools/bedtools/bedToBam.xml
+++ b/tools/bedtools/bedToBam.xml
@@ -3,7 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
+    <expand macro="requirements" />
     <expand macro="stdio" />
     <command>
 <![CDATA[
diff --git a/tools/bedtools/bedpeToBam.xml b/tools/bedtools/bedpeToBam.xml
index 37fe51cbd..000cda7c5 100644
--- a/tools/bedtools/bedpeToBam.xml
+++ b/tools/bedtools/bedpeToBam.xml
@@ -3,7 +3,7 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
+    <expand macro="requirements" />
     <expand macro="stdio" />
     <command>
 <![CDATA[

From 22a906b9a832a35307277f5f5b00a4f0b517b03e Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Tue, 4 Jul 2017 14:16:29 +0100
Subject: [PATCH 17/18] Move loc files in tool-data/ and use tabs

---
 tools/bedtools/all_gff.loc.sample                   | 16 ----------------
 tools/bedtools/{ => tool-data}/all_fasta.loc.sample |  0
 tools/bedtools/tool-data/all_gff.loc.sample         | 14 ++++++++++++++
 3 files changed, 14 insertions(+), 16 deletions(-)
 delete mode 100644 tools/bedtools/all_gff.loc.sample
 rename tools/bedtools/{ => tool-data}/all_fasta.loc.sample (100%)
 create mode 100644 tools/bedtools/tool-data/all_gff.loc.sample

diff --git a/tools/bedtools/all_gff.loc.sample b/tools/bedtools/all_gff.loc.sample
deleted file mode 100644
index b3b8c1c57..000000000
--- a/tools/bedtools/all_gff.loc.sample
+++ /dev/null
@@ -1,16 +0,0 @@
-#This file lists the locations and dbkeys of all the GFF files
-#This file has the format (white space characters are
-#TAB characters):
-#
-#<unique_build_id>      <dbkey> <display_name>  <file_path>
-#
-#So, all_gff.loc could look something like this:
-#
-#apiMel3        apiMel3 Honeybee (Apis mellifera): apiMel3      /path/to/annotation/apiMel3/apiMel3.gff
-#hg19canon      hg19    Human (Homo sapiens): hg19 Canonical    /path/to/annotation/hg19/hg19canon.gff
-#hg19full       hg19    Human (Homo sapiens): hg19 Representative transcripts /path/to/annotation/hg19/hg19_representative_tx.gff
-#
-#Your all_gff.loc file should contain an entry for each different annotation.
-#So there can be multiple gff files for each build,
-#such as with hg19 above.
-#
diff --git a/tools/bedtools/all_fasta.loc.sample b/tools/bedtools/tool-data/all_fasta.loc.sample
similarity index 100%
rename from tools/bedtools/all_fasta.loc.sample
rename to tools/bedtools/tool-data/all_fasta.loc.sample
diff --git a/tools/bedtools/tool-data/all_gff.loc.sample b/tools/bedtools/tool-data/all_gff.loc.sample
new file mode 100644
index 000000000..5df48e3f3
--- /dev/null
+++ b/tools/bedtools/tool-data/all_gff.loc.sample
@@ -0,0 +1,14 @@
+#This file lists the locations and dbkeys of all the GFF files
+#This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>	<display_name>	<file_path>
+#
+#So, all_gff.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/annotation/apiMel3/apiMel3.gff
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/annotation/hg19/hg19canon.gff
+#hg19full	hg19	Human (Homo sapiens): hg19 Representative transcripts	/path/to/annotation/hg19/hg19_representative_tx.gff
+#
+#Your all_gff.loc file should contain an entry for each different annotation.
+#So there can be multiple gff files for each build, such as with hg19 above.

From 95a238b916d01e7fffc3fbf417ea79fe7595dde9 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Tue, 4 Jul 2017 15:13:58 +0100
Subject: [PATCH 18/18] IUC code style and indentation fixes. Use `argument`
 attribute

---
 tools/bedtools/closestBed.xml | 121 ++++++++++++++++++++----------------------
 1 file changed, 57 insertions(+), 64 deletions(-)

diff --git a/tools/bedtools/closestBed.xml b/tools/bedtools/closestBed.xml
index c83b4d928..b2b2545bb 100644
--- a/tools/bedtools/closestBed.xml
+++ b/tools/bedtools/closestBed.xml
@@ -5,40 +5,37 @@
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-
-        closestBed
-        $strand
-        $addition
-        #if $addition2.addition2_select:
-            -D $addition2.addition2_select
-            $addition2.iu
-            $addition2.id
-        #end if
-        $io
-        -mdb $mdb
-        -t $ties
-        #if $k:
-            -k $k
-        #end if
-        -a '$inputA'
-        #if str($overlap_with.source) == "data_table":
-            -b '$overlap_with.table.fields.path'
-        #else	
-        #set inputBs = "' '".join([str( $file ) for $file in $overlap_with.own_file])
-            -b '$inputBs'
-        #end if 
-        > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+closestBed
+$strand
+$addition
+#if $addition2.addition2_select:
+    -D $addition2.addition2_select
+    $addition2.iu
+    $addition2.id
+#end if
+$io
+-mdb $mdb
+-t $ties
+#if str($k):
+    -k $k
+#end if
+-a '$inputA'
+#if str($overlap_with.source) == "data_table":
+    -b '$overlap_with.table.fields.path'
+#else
+    #set inputBs = "' '".join([str( $file ) for $file in $overlap_with.inputB])
+    -b '$inputBs'
+#end if
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
+        <param name="inputA" type="data" format="bed,vcf,gff,gff3" label="BED/VCF/GFF file"/>
         <!-- overlap with file (inputB) -->
         <conditional name="overlap_with">
             <param name="source" type="select" label="Overlap with: will you select a BED/VCF/GFF file from your history or use a built-in GFF file?" help="Built-in GFF files contain full annotation of a reference genome">
-            <option value="history" selected="True">Use a BED/VCF/GFF file from the history</option>
-            <option value="data_table">Use a built-in GFF file</option>
+                <option value="history" selected="true">Use a BED/VCF/GFF file from the history</option>
+                <option value="data_table">Use a built-in GFF file</option>
             </param>
             <when value="data_table">
                 <param name="table" type="select" label="Select reference GFF" help="If your genome of interest is not listed, contact the Galaxy team">
@@ -47,31 +44,31 @@
                         <validator type="no_options" message="No files are available"/>
                     </options>
                 </param>
-          </when>
-          <when value="history">
-              <param name="own_file" type="data" format="bed,gff,vcf,gff3" multiple="True" label="Select a BED/VCF/GFF file" />
-          </when>
+            </when>
+            <when value="history">
+                <param name="inputB" type="data" format="bed,gff,vcf,gff3" multiple="true" label="Select a BED/VCF/GFF file" />
+            </when>
         </conditional>
 
         <param name="ties" type="select"
             label="How ties for closest feature should be handled"
             help="This occurs when two features in B have exactly the same overlap with a feature in A.">
-            <option value="all" selected="True">all - Report all ties (default)</option>
+            <option value="all" selected="true">all - Report all ties (default)</option>
             <option value="first">first - Report the first tie that occurred in the B file</option>
             <option value="last">last - Report the last tie that occurred in the B file</option>
         </param>
 
         <expand macro="strand2" />
 
-        <param name="addition" type="boolean" checked="false" truevalue="-d" falsevalue=""
+        <param name="addition" argument="-d" type="boolean" truevalue="-d" falsevalue="" checked="false"
             label="In addition to the closest feature in B, report its distance to A as an extra column"
-            help="The reported distance for overlapping features will be 0. (-d)" />
+            help="The reported distance for overlapping features will be 0" />
 
         <conditional name="addition2">
-            <param name="addition2_select" type="select"
+            <param name="addition2_select" argument="-D" type="select"
                 label="Add additional columns to report distance to upstream feature. Distance defintion"
-                help="Like -d, report the closest feature in B, and its distance to A as an extra column. However unlike -d, use negative distances to report upstream features. (-D)">
-                <option value="" selected="True">Do not report the distance et all.</option>
+                help="Like -d, report the closest feature in B, and its distance to A as an extra column. However unlike -d, use negative distances to report upstream features">
+                <option value="" selected="true">Do not report the distance et all.</option>
                 <option value="ref">Report distance with respect to the reference genome. B features with a lower (start, stop) are upstream. (-ref)</option>
                 <option value="a">Report distance with respect to A. When A is on the - strand, "upstream" means B has a higher (start,stop). (-a)</option>
                 <option value="b">Report distance with respect to B. When B is on the - strand, "upstream" means A has a higher (start,stop). (-b)</option>
@@ -88,80 +85,76 @@
             </when>
         </conditional>
 
-        <param name="k" type="integer" value="1" optional="True" min="1"
-            label="Report the k closest hits" help="(-k)"/>
+        <param argument="-k" type="integer" min="1" value="1" optional="true"
+            label="Report the k closest hits" />
 
-        <param name="io" type="boolean" checked="false" truevalue="-io" falsevalue=""
+        <param argument="-io" type="boolean" truevalue="-io" falsevalue="" checked="false"
             label="Ignore features in B that overlap A"
-            help="That is, we want close, yet not touching features only. (-io)" />
+            help="That is, we want close, yet not touching features only" />
 
-        <param name="mdb" type="select" optional="True"
-            label="How multiple databases are resolved"
-            help="(-mdb)">
-            <option value="each" selected="True">Report closest records for each database. (-each)</option>
+        <param argument="-mdb" type="select"
+            label="How multiple databases are resolved">
+            <option value="each" selected="true">Report closest records for each database. (-each)</option>
             <option value="all">Report closest records among all databases. (-all)</option>
         </param>
     </inputs>
     <outputs>
         <!-- Would like to use a nicer name, but since there are possibly many inputB datasets, falling back to ${on_string} -->
         <!-- <data format_source="inputA" name="output" metadata_source="inputA" label="Closest regions from ${inputB[0].name} to ${inputA.name}"/> -->
-        <data format_source="inputA" name="output" metadata_source="inputA" label="Closest regions from ${on_string}"/>
+        <data name="output" format_source="inputA" metadata_source="inputA" label="Closest regions from ${on_string}" />
     </outputs>
     <tests>
         <test>
             <param name="inputA" value="closestBedA.bed" ftype="bed" />
             <param name="source" value="history" />
-            <param name="own_file" value="closestBedB.bed" ftype="bed" />
+            <param name="inputB" value="closestBedB.bed" ftype="bed" />
             <output name="output" file="closestBed_result1.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="closestBed_a.bed" ftype="bed" />
             <param name="source" value="history" />
-            <param name="own_file" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" />
-            <param name="addition" value="True" />
+            <param name="inputB" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" />
+            <param name="addition" value="true" />
             <output name="output" file="closestBed_result2.bed" ftype="bed" />
         </test>
         <test>
-            <param name="inputA" value="closestBed_a.bed" ftype="bed" /> 
+            <param name="inputA" value="closestBed_a.bed" ftype="bed" />
             <param name="source" value="history" />
-            <param name="own_file" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" />
+            <param name="inputB" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" />
             <param name="addition" value="True" />
             <param name="mdb" value="all" />
             <output name="output" file="closestBed_result3.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="closestBed_c.bed" ftype="bed" />
-            <param name="source" value="history" /> 
-            <param name="own_file" value="closestBed_d.bed" ftype="bed" />
+            <param name="source" value="history" />
+            <param name="inputB" value="closestBed_d.bed" ftype="bed" />
             <param name="addition2_select" value="ref" />
             <output name="output" file="closestBed_result4.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="closestBed_c.bed" ftype="bed" />
-            <param name="source" value="history" />  
-            <param name="own_file" value="closestBed_d.bed" ftype="bed" />
+            <param name="source" value="history" />
+            <param name="inputB" value="closestBed_d.bed" ftype="bed" />
             <param name="addition2_select" value="a" />
             <output name="output" file="closestBed_result5.bed" ftype="bed" />
         </test>
         <test>
             <param name="inputA" value="closestBedA.bed" ftype="bed" />
             <param name="source" value="history" />
-            <param name="own_file" value="a.bed" ftype="bed" />
+            <param name="inputB" value="a.bed" ftype="bed" />
             <param name="k" value="3" />
             <output name="output" file="closestBed_result6.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Similar to intersectBed, closestBed searches for overlapping features in A and B. In the event that no feature in B overlaps the current feature in A, closestBed will report the closest (that is, least genomic distance from the start or end of A) feature in B. For example, one might want to find which is the closest gene to a significant GWAS polymorphism. Note that closestBed will report an overlapping feature as the closest—that is, it does not restrict to closest non-overlapping feature.
 
 .. image:: $PATH_TO_IMAGES/closest-glyph.png
 
-
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>