# HG changeset patch
# User iuc
# Date 1467130960 14400
# Node ID 258c64019e506f5aae71f62b5576f077297ae0d0
# Parent  1b7800489efbbc76cfbb8b841a8264f5da9d5180
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 811337eaab815f54f0fd93a3dd23a1153993ea2a

diff -r 1b7800489efb -r 258c64019e50 abundance_estimates_to_matrix.xml
--- a/abundance_estimates_to_matrix.xml	Mon Jun 20 11:44:50 2016 -0400
+++ b/abundance_estimates_to_matrix.xml	Tue Jun 28 12:22:40 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="abundance_estimates_to_matrix" name="Build expression matrix" version="2.1.1">
+<tool id="abundance_estimates_to_matrix" name="Build expression matrix" version="2.1.1.1">
     <description>for a de novo assembly of RNA-Seq data by Trinity</description>
     <requirements>
         <requirement type="package" version="2.1.1">trinity</requirement>
@@ -9,7 +9,7 @@
     </stdio>
     <command><![CDATA[
         #for $entry in $samples:
-            ln -s "${entry.file}" "${entry.sample_name}.tsv" &&
+            ln -s "${entry.file}" "${entry.sample_name}" &&
         #end for
 
         abundance_estimates_to_matrix.pl
@@ -18,7 +18,7 @@
         --cross_sample_norm ${additional_params.cross_sample_norm}
 
         #for $entry in $samples:
-            "${entry.sample_name}.tsv"
+            "${entry.sample_name}"
         #end for
     ]]></command>
     <inputs>
diff -r 1b7800489efb -r 258c64019e50 run_DE_analysis.xml
--- a/run_DE_analysis.xml	Mon Jun 20 11:44:50 2016 -0400
+++ b/run_DE_analysis.xml	Tue Jun 28 12:22:40 2016 -0400
@@ -79,10 +79,10 @@
     </inputs>
     <outputs>
         <collection name="DE_results" type="list" label="Differential expression results on ${on_string}">
-            <discover_datasets pattern="(?P&lt;name&gt;.+)\.DE_results" ext="tabular" directory="results" visible="true" />
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.DE_results$" ext="tabular" directory="results" />
         </collection>
         <collection name="PDF_results" type="list" label="Differential expression plots on ${on_string}">
-            <discover_datasets pattern="(?P&lt;name&gt;.+)\.pdf" ext="pdf" directory="results" visible="true" />
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.pdf$" ext="pdf" directory="results" />
         </collection>
     </outputs>
     <tests>
diff -r 1b7800489efb -r 258c64019e50 samples_qccheck.xml
--- a/samples_qccheck.xml	Mon Jun 20 11:44:50 2016 -0400
+++ b/samples_qccheck.xml	Tue Jun 28 12:22:40 2016 -0400
@@ -9,41 +9,41 @@
         <exit_code range="1:"/>
     </stdio>
     <command><![CDATA[
-        
+
         ln -s "${matrix}" "input.matrix"
-        
+
         &&
-        
+
         PtR
         --matrix "input.matrix"
-        
+
         --samples "${samples}"
-        
+
         --CPM --log2 --compare_replicates
-        
+
         &&
-        
+
         PtR
         --matrix "input.matrix"
-        
+
         --samples "${samples}"
-        
+
         --CPM --log2 --sample_cor_matrix
-        
+
         &&
-        
+
         PtR
         --matrix "input.matrix"
-        
+
         --samples "${samples}"
-        
+
         --CPM --log2 --prin_comp 3
-        
+
         && mkdir out_pdf
         && mv *rep_compare.pdf out_pdf/
         && mv *sample_cor_matrix.pdf out_pdf/
         && mv *principal_components.pdf out_pdf/
-        
+
     ]]></command>
     <inputs>
         <param format="tabular" name="matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/>
@@ -51,7 +51,7 @@
     </inputs>
     <outputs>
         <collection name="reports" type="list" label="Quality check result files on ${on_string}">
-            <discover_datasets pattern="__name__" ext="pdf" directory="out_pdf" visible="true" />
+            <discover_datasets pattern="__name__" ext="pdf" directory="out_pdf" />
         </collection>
     </outputs>
     <tests>
@@ -106,7 +106,7 @@
 .. _Trinity: http://trinityrnaseq.github.io
 ]]>
     </help>
-    
+
      <citations>
         <citation type="doi">10.1038/nbt.1883</citation>
     </citations>