From a194cc90304f85acf572e9a55eb6b11a06a82eb4 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Thu, 6 Jul 2017 12:01:08 +0100
Subject: [PATCH] Fix default values for some hisat2 options

Also add some `argument` attributes.

Fix https://github.com/galaxyproject/tools-iuc/issues/1406 .
---
 tools/hisat2/hisat2.xml        | 59 +++++++++++++++++++++++++++---------------
 tools/hisat2/hisat2_macros.xml | 10 -------
 2 files changed, 38 insertions(+), 31 deletions(-)

diff --git a/tools/hisat2/hisat2.xml b/tools/hisat2/hisat2.xml
index f81d37bb6..ff55f34a7 100644
--- a/tools/hisat2/hisat2.xml
+++ b/tools/hisat2/hisat2.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="hisat2" name="HISAT2" version="2.0.5.1" profile="17.01">
+<tool id="hisat2" name="HISAT2" version="2.0.5.2" profile="17.01">
     <description>A fast and sensitive alignment program</description>
     <macros>
         <import>hisat2_macros.xml</import>
@@ -86,10 +86,13 @@
         #end if
         #if str($alignment_options.alignment_options_selector) == "advanced":
             --n-ceil ${alignment_options.function_type},${alignment_options.constant_term},${alignment_options.coefficient}
-            ${alignment_options.skip_forward} ${alignment_options.skip_reverse} ${alignment_options.ignore_quals}
+            ${alignment_options.ignore_quals}
+            ${alignment_options.skip_forward}
+            ${alignment_options.skip_reverse}
         #end if
         #if str($spliced_options.spliced_options_selector) == "advanced":
-            --pen-cansplice ${spliced_options.canonical_penalty} --pen-noncansplice ${spliced_options.noncanonical_penalty}
+            --pen-cansplice ${spliced_options.canonical_penalty}
+            --pen-noncansplice ${spliced_options.noncanonical_penalty}
             --pen-canintronlen ${spliced_options.function_type},${spliced_options.constant_term},${spliced_options.coefficient}
             --pen-noncanintronlen ${spliced_options.nc_function_type},${spliced_options.nc_constant_term},${spliced_options.nc_coefficient}
             #if str($spliced_options.known_splice_gtf) != 'None':
@@ -167,7 +170,14 @@
             </param>
             <when value="defaults" />
             <when value="advanced">
-                <expand macro="function" helptext="Sets a function governing the maximum number of ambiguous characters" />
+                <param name="function_type" argument="--n-ceil" type="select" display="radio" label="Function governing the maximum number of ambiguous characters (usually Ns and/or .s) allowed in a read as a function of read length" help="Reads exceeding this ceiling are filtered out">
+                    <option value="C">Constant [f(x) = B]</option>
+                    <option value="L" selected="true">Linear [f(x) = B + A * x]</option>
+                    <option value="S">Square root [f(x) = B + A * x&#178;]</option>
+                    <option value="G">Natural logarithm [f(x) = B + A * log(x)]</option>
+                </param>
+                <param name="constant_term" type="float" value="0" label="Constant term (B)" help="Constant term for the above function" />
+                <param name="coefficient" type="float" value="0.15" label="Coefficient (A)" help="Coefficient for the above function" />
                 <param argument="--ignore-quals" name="ignore_quals" type="boolean" truevalue="--ignore-quals" falsevalue="" label="Ignore quality values" help="When calculating a mismatch penalty, always consider the quality value at the mismatched position to be the highest possible, regardless of the actual value. I.e. input is treated as though all quality values are high. This is also the default behavior when the input doesn't specify quality values" />
                 <param argument="--nofw" name="skip_forward" type="boolean" truevalue="--nofw" falsevalue="" label="Skip forward strand of reference" help="If --nofw is specified, hisat2 will not attempt to align unpaired reads to the forward (Watson) reference strand. In paired-end mode, --nofw and --norc pertain to the fragments; i.e. specifying --nofw causes hisat2 to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand" />
                 <param argument="--norc" name="skip_reverse" type="boolean" truevalue="--norc" falsevalue="" label="Skip reverse strand of reference" help="If --norc is specified, hisat2 will not attempt to align unpaired reads against the reverse-complement (Crick) reference strand. In paired-end mode, --nofw and --norc pertain to the fragments; i.e. specifying --norc causes hisat2 to explore only those paired-end configurations corresponding to fragments from the forward-complement (Watson) strand" />
@@ -193,7 +203,14 @@
             </param>
             <when value="defaults" />
             <when value="advanced">
-                <expand macro="function" helptext="Sets a function governing the minimum alignment score needed for an alignment to be considered &quot;valid&quot; (i.e. good enough to report)" />
+                <param name="function_type" argument="--score-min" type="select" display="radio" label="Function governing the minimum alignment score needed for an alignment to be considered &quot;valid&quot; (i.e. good enough to report)" help="This is a function of read length">
+                    <option value="C">Constant [f(x) = B]</option>
+                    <option value="L" selected="true">Linear [f(x) = B + A * x]</option>
+                    <option value="S">Square root [f(x) = B + A * x&#178;]</option>
+                    <option value="G">Natural logarithm [f(x) = B + A * log(x)]</option>
+                </param>
+                <param name="constant_term" type="float" value="0" label="Constant term (B)" help="Constant term for the above function" />
+                <param name="coefficient" type="float" value="-0.2" label="Coefficient (A)" help="Coefficient for the above function" />
                 <param argument="--ma" name="match_bonus" type="integer" value="2" label="Set match bonus" help="In local mode N is added to the alignment score for each position where a read character aligns to a reference character and the characters match. Not used in end-to-end mode" />
                 <param argument="--mp" name="max_mismatch" type="integer" value="6" label="Maximum mismatch penalty" help="Sets the maximum mismatch penalty. A number less than or equal to MX and greater than or equal to MN is subtracted from the alignment score for each position where a read character aligns to a reference character, the characters do not match, and neither is an N. If --ignore-quals is specified, the number subtracted quals MX. Otherwise, the number subtracted is MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) ) where Q is the Phred quality value" />
                 <param argument="--mp" name="min_mismatch" type="integer" value="2" label="Minimum mismatch penalty" help="Sets the minimum mismatch penalty. A number less than or equal to MX and greater than or equal to MN is subtracted from the alignment score for each position where a read character aligns to a reference character, the characters do not match, and neither is an N. If --ignore-quals is specified, the number subtracted quals MX. Otherwise, the number subtracted is MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) ) where Q is the Phred quality value" />
@@ -214,24 +231,24 @@
             </param>
             <when value="defaults" />
             <when value="advanced">
-                <param name="canonical_penalty" type="integer" value="0" label="Penalty for canonical splice sites" />
-                <param name="noncanonical_penalty" type="integer" value="3" label="Penalty for non-canonical splice sites" />
-                <param name="function_type" type="select" display="radio" label="Penalty for long introns with canonical splice sites">
-                    <option value="C">Constant</option>
-                    <option value="L">Linear [f(x) = y + z * x]</option>
-                    <option value="S">Square root [f(x) = y + z * x&#178;]</option>
-                    <option value="G">Natural logarithm [f(x) = y + z * log(x)]</option>
+                <param name="canonical_penalty" argument="--pen-cansplice" type="integer" value="0" label="Penalty for canonical splice sites" />
+                <param name="noncanonical_penalty" argument="--pen-noncansplice" type="integer" value="12" label="Penalty for non-canonical splice sites" />
+                <param name="function_type" argument="--pen-canintronlen" type="select" display="radio" label="Penalty function for long introns with canonical splice sites" help="Alignments with shorter introns are preferred to those with longer ones">
+                    <option value="C">Constant [f(x) = B]</option>
+                    <option value="L">Linear [f(x) = B + A * x]</option>
+                    <option value="S">Square root [f(x) = B + A * x&#178;]</option>
+                    <option value="G" selected="true">Natural logarithm [f(x) = B + A * log(x)]</option>
                 </param>
-                <param name="constant_term" type="integer" value="0" label="Constant term (y)" help="Constant term for long canonical introns" />
-                <param name="coefficient" type="integer" value="0" label="Coefficient (z)" help="Coefficient for long canonical introns" />
-                <param name="nc_function_type" type="select" display="radio" label="Penalty for long introns with noncanonical splice sites">
-                    <option value="C">Constant</option>
-                    <option value="L">Linear [f(x) = y + z * x]</option>
-                    <option value="S">Square root [f(x) = y + z * x&#178;]</option>
-                    <option value="G" selected="True">Natural logarithm [f(x) = y + z * log(x)]</option>
+                <param name="constant_term" type="float" value="-8" label="Constant term (B)" help="Constant term for the above function" />
+                <param name="coefficient" type="float" value="1" label="Coefficient (A)" help="Coefficient for the above function" />
+                <param name="nc_function_type" argument="--pen-noncanintronlen" type="select" display="radio" label="Penalty function for long introns with non-canonical splice sites" help="Alignments with shorter introns are preferred to those with longer ones">
+                    <option value="C">Constant [f(x) = B]</option>
+                    <option value="L">Linear [f(x) = B + A * x]</option>
+                    <option value="S">Square root [f(x) = B + A * x&#178;]</option>
+                    <option value="G" selected="true">Natural logarithm [f(x) = B + A * log(x)]</option>
                 </param>
-                <param name="nc_constant_term" type="integer" value="-8" label="Constant term (y)" help="Constant term for long non-canonical introns" />
-                <param name="nc_coefficient" type="integer" value="1" label="Coefficient (z)" help="Coefficient for long non-canonical introns" />
+                <param name="nc_constant_term" type="float" value="-8" label="Constant term (B)" help="Constant term for the above function" />
+                <param name="nc_coefficient" type="float" value="1" label="Coefficient (A)" help="Coefficient for the above function" />
                 <param name="min_intron" type="integer" value="20" label="Minimum intron length" />
                 <param name="max_intron" type="integer" value="500000" label="Maximum intron length" />
                 <param argument="--rna-strandness" name="rna_strandness" type="select" label="Specify strand-specific information"
diff --git a/tools/hisat2/hisat2_macros.xml b/tools/hisat2/hisat2_macros.xml
index 4a227df3b..ee191664e 100644
--- a/tools/hisat2/hisat2_macros.xml
+++ b/tools/hisat2/hisat2_macros.xml
@@ -1,15 +1,5 @@
 <?xml version="1.0"?>
 <macros>
-    <xml name="function" tokens="helptext">
-        <param display="radio" help="@HELPTEXT@" label="Function type" name="function_type" type="select">
-            <option value="C">Constant</option>
-            <option value="L">Linear [f(x) = y + z * x]</option>
-            <option value="S">Square root [f(x) = y + z * x&#178;]</option>
-            <option value="G">Natural logarithm [f(x) = y + z * log(x)]</option>
-        </param>
-        <param help="@HELPTEXT@" label="Constant term (y)" name="constant_term" type="integer" value="0" />
-        <param help="@HELPTEXT@" label="Coefficient (z)" name="coefficient" type="integer" value="0" />
-    </xml>
     <xml name="single_paired_selector">
         <param label="Single end or paired reads?" name="paired_selector" type="select">
             <option value="paired_collection">Collection of paired reads</option>