From 34ebb22edc81a6b4cc9f9a8cda11613ce855d3ef Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Loraine=20Gu=C3=A9guen?=
 <loraine-gueguen@users.noreply.github.com>
Date: Thu, 27 Apr 2017 14:49:21 +0200
Subject: [PATCH 1/4] DE_matrices needed only if running go_enrichment.

---
 tools/trinity/analyze_diff_expr.xml | 33 ++++++++++++++-------------------
 1 file changed, 14 insertions(+), 19 deletions(-)

diff --git a/tools/trinity/analyze_diff_expr.xml b/tools/trinity/analyze_diff_expr.xml
index c611d7db9..c07c8809a 100644
--- a/tools/trinity/analyze_diff_expr.xml
+++ b/tools/trinity/analyze_diff_expr.xml
@@ -15,10 +15,12 @@
         ln -s "${input}" "${re.sub('[^\w\-_.]', '_', input.element_identifier)}.DE_results"
         &&
     #end for
-    #for $DE_matrix in $DE_matrices
-        ln -s "${DE_matrix}" "${re.sub('[^\w\-_.]', '_', DE_matrix.element_identifier)}.count_matrix"
-        &&
-    #end for
+    #if str( $additional_params.GO_enrichment.examine_GO_enrichment ) == "yes":
+        #for $DE_matrix in $DE_matrices
+            ln -s "${DE_matrix}" "${re.sub('[^\w\-_.]', '_', DE_matrix.element_identifier)}.count_matrix"
+            &&
+        #end for
+    #end if
 
     analyze_diff_expr.pl
         --matrix "${matrix}"
@@ -48,7 +50,6 @@
         <param format="tabular" name="matrix" argument="--matrix" type="data" label="Expression matrix" help="Raw counts matrix produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool"/>
         <param format="tabular" name="samples" argument="--samples" type="data" label="Sample description" help="File describing samples and replicates"/>
         <param format="tabular" name="DE_results" type="data_collection" collection_type="list" label="Differential expression results" help="Generated by 'Differential expression analysis using a Trinity assembly' tool"/>
-        <param format="tabular" name="DE_matrices" type="data_collection" collection_type="list" label="Differential expression count matrices" help="Generated by 'Differential expression analysis using a Trinity assembly' tool"/>
         <param name="p" type="float" argument="-P" value="0.001" label="p-value cutoff for FDR"/>
         <param name="c" type="float" argument="-C" value="2" label="min abs(log2(a/b)) fold change" help="Default: 2 (meaning 2^(2) or 4-fold"/>
         <section name="additional_params" title="Additional Options" expanded="False">
@@ -63,6 +64,7 @@
                 <when value="no">
                 </when>
                 <when value="yes">
+                    <param format="tabular" name="DE_matrices" type="data_collection" collection_type="list" label="Differential expression count matrices" help="Generated by 'Differential expression analysis using a Trinity assembly' tool"/>
                     <param format="tabular" name="GO_annots" argument="--GO_annots" type="data" label="Extracted GO assignments file" help="Generated by the Trinotate script extract_GO_assignments_from_Trinotate_xls.pl. Must have 2 columns: feature_id GO:000001,GO:00002,..."/>
                     <param format="tabular" name="gene_lengths" argument="--gene_lengths" type="data" label="Gene length file" help="Must have 2 columns: feature_id length"/>
                 </when>
@@ -98,13 +100,6 @@
                     <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" />
               </collection>
             </param>
-            <param name="DE_matrices">
-                <collection type="list">
-                    <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2" value="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.count_matrix" ftype="tabular" />
-                    <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.count_matrix" ftype="tabular" />
-                    <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix" ftype="tabular" />
-              </collection>
-            </param>
             <output_collection name="extracted_DE_genes">
                 <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.0.wt_37-UP" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset"/>
                 <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.0.wt_GSNO-UP" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset"/>
@@ -133,16 +128,16 @@
                     <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" />
                 </collection>
             </param>
-            <param name="DE_matrices">
-                <collection type="list">
-                    <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2" value="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.count_matrix" ftype="tabular" />
-                    <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.count_matrix" ftype="tabular" />
-                    <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix" ftype="tabular" />
-                </collection>
-            </param>
             <section name="additional_params">
                 <conditional name="GO_enrichment">
                     <param name="examine_GO_enrichment" value="yes"/>
+                    <param name="DE_matrices">
+                        <collection type="list">
+                            <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2" value="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.count_matrix" ftype="tabular" />
+                            <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.count_matrix" ftype="tabular" />
+                            <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix" ftype="tabular" />
+                        </collection>
+                    </param>
                     <param name="GO_annots" value="count/trinotate/go_annotations.txt"/>
                     <param name="gene_lengths" value="count/trinotate/genes.lengths.txt"/>
                 </conditional>

From 5fe7b47489146178533f2dcf00812ed75ccf1a29 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Loraine=20Gu=C3=A9guen?=
 <loraine-gueguen@users.noreply.github.com>
Date: Thu, 27 Apr 2017 15:56:08 +0200
Subject: [PATCH 2/4] DE_matrices needed only if running go_enrichment. Tests
 passed.

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

diff --git a/tools/trinity/analyze_diff_expr.xml b/tools/trinity/analyze_diff_expr.xml
index c07c8809a..7fe8c34e0 100644
--- a/tools/trinity/analyze_diff_expr.xml
+++ b/tools/trinity/analyze_diff_expr.xml
@@ -16,7 +16,7 @@
         &&
     #end for
     #if str( $additional_params.GO_enrichment.examine_GO_enrichment ) == "yes":
-        #for $DE_matrix in $DE_matrices
+        #for $DE_matrix in $additional_params.GO_enrichment.DE_matrices
             ln -s "${DE_matrix}" "${re.sub('[^\w\-_.]', '_', DE_matrix.element_identifier)}.count_matrix"
             &&
         #end for

From 35998623fe7dbd4ab05db98d192dc2fac69d2683 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Loraine=20Gu=C3=A9guen?=
 <loraine-gueguen@users.noreply.github.com>
Date: Thu, 11 May 2017 10:56:19 +0200
Subject: [PATCH 3/4] Improve handling of input file names for DE_results and
 count_matrix files. Adjust file names in tests consequently. Add test for
 DE_results input files with non-standard names. Keep '.subset' in the name
 generated for extracted_DE_genes output files.

---
 tools/trinity/analyze_diff_expr.xml | 73 ++++++++++++++++++++++++++++---------
 1 file changed, 56 insertions(+), 17 deletions(-)

diff --git a/tools/trinity/analyze_diff_expr.xml b/tools/trinity/analyze_diff_expr.xml
index 7fe8c34e0..5124d11c9 100644
--- a/tools/trinity/analyze_diff_expr.xml
+++ b/tools/trinity/analyze_diff_expr.xml
@@ -1,4 +1,4 @@
-<tool id="trinity_analyze_diff_expr" name="Extract and cluster differentially expressed transcripts" version="@WRAPPER_VERSION@.1">
+<tool id="trinity_analyze_diff_expr" name="Extract and cluster differentially expressed transcripts" version="@WRAPPER_VERSION@.2">
     <description>from a Trinity assembly</description>
     <macros>
         <import>macros.xml</import>
@@ -12,12 +12,20 @@
     ## DE results input files must be in the working directory and have suffix .DE_results
     #import re
     #for $input in $DE_results
-        ln -s "${input}" "${re.sub('[^\w\-_.]', '_', input.element_identifier)}.DE_results"
+        #if re.search('.DE_results$',input.element_identifier)
+            ## General case, where DE results files have been previously generated by run_de_analysis.pl
+            ln -s "${input}" "${re.sub('[^\w\-_.]', '_', input.element_identifier)}"
+        #else
+            ## Particular case, where DE results files have non-standard names
+            ln -s "${input}" "${re.sub('[^\w\-_.]', '_', input.element_identifier)}.DE_results"
+        #end if
         &&
     #end for
     #if str( $additional_params.GO_enrichment.examine_GO_enrichment ) == "yes":
+        ## DE matrix input files must be in the working directory and have the same name as DE results input files, but replacing suffix .DE_results by suffix .count_matrix
         #for $DE_matrix in $additional_params.GO_enrichment.DE_matrices
-            ln -s "${DE_matrix}" "${re.sub('[^\w\-_.]', '_', DE_matrix.element_identifier)}.count_matrix"
+            ## Handle general case, where DE results files and DE matrix files have been previously generated by run_de_analysis.pl
+            ln -s "${DE_matrix}" "${re.sub('[^\w\-_.]', '_', DE_matrix.element_identifier)}"
             &&
         #end for
     #end if
@@ -64,7 +72,7 @@
                 <when value="no">
                 </when>
                 <when value="yes">
-                    <param format="tabular" name="DE_matrices" type="data_collection" collection_type="list" label="Differential expression count matrices" help="Generated by 'Differential expression analysis using a Trinity assembly' tool"/>
+                    <param format="tabular" name="DE_matrices" type="data_collection" collection_type="list" label="Differential expression count matrices" help="Generated by 'Differential expression analysis using a Trinity assembly' tool. If not, be careful that the file names are identical to the file names of differential expression results, with extension '.count_matrix' instead of '.DE_results'."/>
                     <param format="tabular" name="GO_annots" argument="--GO_annots" type="data" label="Extracted GO assignments file" help="Generated by the Trinotate script extract_GO_assignments_from_Trinotate_xls.pl. Must have 2 columns: feature_id GO:000001,GO:00002,..."/>
                     <param format="tabular" name="gene_lengths" argument="--gene_lengths" type="data" label="Gene length file" help="Must have 2 columns: feature_id length"/>
                 </when>
@@ -73,7 +81,7 @@
     </inputs>
     <outputs>
         <collection name="extracted_DE_genes" type="list" label="${tool.name} on ${on_string}: extracted differentially expressed genes">
-            <discover_datasets pattern="(?P&lt;name&gt;.+)\.subset$" ext="tabular" />
+            <discover_datasets pattern="(?P&lt;name&gt;.+\.subset)$" ext="tabular" />
         </collection>
         <collection name="summary_files" type="list" label="${tool.name} on ${on_string}: summary files">
             <data format="tabular" name="results_matrix" from_work_dir="results.matrix"/>
@@ -90,23 +98,24 @@
         </collection>
     </outputs>
     <tests>
+        <!-- Test without GO enrichment analysis -->
         <test>
             <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
             <param name="samples" value="count/samples.txt"/>
             <param name="DE_results">
                 <collection type="list">
-                    <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2" value="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results" ftype="tabular" />
-                    <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" />
-                    <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" />
+                    <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results" value="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results" ftype="tabular" />
+                    <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results" value="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" />
+                    <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results" value="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" />
               </collection>
             </param>
             <output_collection name="extracted_DE_genes">
-                <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.0.wt_37-UP" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset"/>
-                <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.0.wt_GSNO-UP" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset"/>
-                <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_37-UP" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset"/>
-                <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_ph8-UP" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset"/>
-                <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_GSNO-UP" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset"/>
-                <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_ph8-UP" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset"/>
+                <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.0.wt_37-UP.subset" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset"/>
+                <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.0.wt_GSNO-UP.subset" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset"/>
+                <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_37-UP.subset" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset"/>
+                <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_ph8-UP.subset" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset"/>
+                <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_GSNO-UP.subset" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset"/>
+                <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_ph8-UP.subset" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset"/>
             </output_collection>
             <output_collection name="summary_files">
                 <element name="results_matrix" compare="sim_size" file="count/analyze_diff_expr/results.matrix"/>
@@ -118,6 +127,7 @@
             </output_collection>
             <output name="rdata" compare="sim_size" file="count/analyze_diff_expr/results.matrix.RData"/>
         </test>
+        <!-- Test without GO enrichment analysis, test name of DE_results input files different from those generated by tool run_de_analysis.pl -->
         <test>
             <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
             <param name="samples" value="count/samples.txt"/>
@@ -126,6 +136,35 @@
                     <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2" value="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results" ftype="tabular" />
                     <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" />
                     <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" />
+              </collection>
+            </param>
+            <output_collection name="extracted_DE_genes">
+                <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.0.wt_37-UP.subset" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset"/>
+                <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.0.wt_GSNO-UP.subset" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset"/>
+                <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_37-UP.subset" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset"/>
+                <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_ph8-UP.subset" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset"/>
+                <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_GSNO-UP.subset" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset"/>
+                <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_ph8-UP.subset" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset"/>
+            </output_collection>
+            <output_collection name="summary_files">
+                <element name="results_matrix" compare="sim_size" file="count/analyze_diff_expr/results.matrix"/>
+                <element name="results_matrix_log2_centered" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.centered.dat"/>
+                <element name="results_matrix_log2_centered_heatmap" delta="100" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/>
+                <element name="results_matrix_log2" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.dat"/>
+                <element name="results_matrix_log2_sample_cor" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.sample_cor.dat"/>
+                <element name="results_matrix_log2_sample_cor_matrix" delta="100" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.sample_cor_matrix.pdf"/>
+            </output_collection>
+            <output name="rdata" compare="sim_size" file="count/analyze_diff_expr/results.matrix.RData"/>
+        </test>
+        <!-- Test with GO enrichment analysis -->
+        <test>
+            <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
+            <param name="samples" value="count/samples.txt"/>
+            <param name="DE_results">
+                <collection type="list">
+                    <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results" value="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results" ftype="tabular" />
+                    <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results" value="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" />
+                    <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results" value="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" />
                 </collection>
             </param>
             <section name="additional_params">
@@ -133,9 +172,9 @@
                     <param name="examine_GO_enrichment" value="yes"/>
                     <param name="DE_matrices">
                         <collection type="list">
-                            <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2" value="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.count_matrix" ftype="tabular" />
-                            <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.count_matrix" ftype="tabular" />
-                            <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix" ftype="tabular" />
+                            <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.count_matrix" value="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.count_matrix" ftype="tabular" />
+                            <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.count_matrix" value="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.count_matrix" ftype="tabular" />
+                            <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix" value="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix" ftype="tabular" />
                         </collection>
                     </param>
                     <param name="GO_annots" value="count/trinotate/go_annotations.txt"/>

From bd508175724d134aa147fd3a11e89741b370db85 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Loraine=20Gu=C3=A9guen?=
 <loraine-gueguen@users.noreply.github.com>
Date: Thu, 11 May 2017 11:56:39 +0200
Subject: [PATCH 4/4] Remove unnecessary bioconductor-go.db requirement. This
 conda package is already installed with bioconductor-goseq.

---
 tools/trinity/analyze_diff_expr.xml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tools/trinity/analyze_diff_expr.xml b/tools/trinity/analyze_diff_expr.xml
index 5124d11c9..c1a1df143 100644
--- a/tools/trinity/analyze_diff_expr.xml
+++ b/tools/trinity/analyze_diff_expr.xml
@@ -6,7 +6,6 @@
     <expand macro="requirements">
         <requirement type="package" version="2.6.0">bioconductor-qvalue</requirement>
         <requirement type="package" version="1.26.0">bioconductor-goseq</requirement>
-        <requirement type="package" version="3.4.0">bioconductor-go.db</requirement>
     </expand>
     <command detect_errors="aggressive"><![CDATA[
     ## DE results input files must be in the working directory and have suffix .DE_results