# HG changeset patch
# User iuc
# Date 1463049814 14400
# Node ID dfe891be734c3330b8a7ff0894943f733bc0c533
# Parent  001b655b2db3a499aef85c09889b57dd2ddb79e4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 91515eb8b87ca2399f556369d6112b0cf3a78617

diff -r 001b655b2db3 -r dfe891be734c run_DE_analysis.xml
--- a/run_DE_analysis.xml	Mon May 02 09:03:02 2016 -0400
+++ b/run_DE_analysis.xml	Thu May 12 06:43:34 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="run_DE_analysis" name="Differential expression analysis" version="2.1.1">
+<tool id="run_DE_analysis" name="Differential expression analysis" version="2.1.1.1">
     <description>using a Trinity assembly</description>
     <requirements>
         <requirement type="package" version="2.1.1">trinity</requirement>
@@ -7,52 +7,52 @@
         <requirement type="package" version="1.10.0">bioconductor-deseq2</requirement>
         <requirement type="package" version="3.12.0">edger</requirement>
         <requirement type="package" version="3.12.0">bioconductor-edger</requirement>
-        <requirement type="package" version="3.27.4">limma</requirement>
+        <requirement type="package" version="3.28.2">limma</requirement>
         <requirement type="package" version="3.27.4">bioconductor-limma</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:"/>
     </stdio>
     <command><![CDATA[
-        
+
         ln -s "${matrix}" "input.matrix"
-        
+
         &&
-        
+
         run_DE_analysis.pl
-        
+
         --matrix "input.matrix"
 
         --samples_file "${samples}"
-        
+
         --method ${method_choice.method}
-        
+
         #if $method_choice.method == "edgeR":
             --dispersion ${method_choice.edger_dispersion}
         #end if
-        
+
         #if $method_choice.method == "ROTS":
             --ROTS_B ${method_choice.rots_b}
             --ROTS_K ${method_choice.rots_k}
         #end if
-        
+
         --min_rowSum_counts ${additional_params.min_rowSum_counts}
-        
+
         #if $additional_params.reference_sample:
             --reference_sample ${additional_params.reference_sample}
         #end if
-        
+
         #if $additional_params.contrasts:
             --contrasts ${additional_params.contrasts}
         #end if
-        
+
         --output results
-        
+
     ]]></command>
     <inputs>
         <param format="tabular" name="matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/>
         <param format="tabular" name="samples" type="data" label="Sample description" help="file describing samples and replicates"/>
-        
+
         <conditional name="method_choice">
             <param type="select" name="method" label="Differential analysis method">
                 <option value="edgeR">edgeR</option>
@@ -72,7 +72,7 @@
             <when value="DESeq2">
             </when>
         </conditional>
-        
+
         <section name="additional_params" title="Additional Options" expanded="False">
             <param name="min_rowSum_counts" type="integer" value="2" label="Minimum count" help="Only those rows of matrix meeting requirement will be tested"/>
             <param name="reference_sample" type="text" optional="true" value="" label="Name of a sample to which all other samples should be compared" help="default is doing all pairwise-comparisons among samples"/>
@@ -138,7 +138,7 @@
 .. _Trinity: http://trinityrnaseq.github.io
 ]]>
     </help>
-    
+
      <citations>
         <citation type="doi">doi:10.1038/nbt.1883</citation>
     </citations>
diff -r 001b655b2db3 -r dfe891be734c tool_dependencies.xml
--- a/tool_dependencies.xml	Mon May 02 09:03:02 2016 -0400
+++ b/tool_dependencies.xml	Thu May 12 06:43:34 2016 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="trinity" version="2.1.1">
-        <repository changeset_revision="bfd7596eecbe" name="package_trinity_2_1_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="74d616d566f3" name="package_trinity_2_1_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="bowtie" version="1.1.2">
         <repository changeset_revision="8584a4574ab1" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
@@ -13,7 +13,7 @@
         <repository changeset_revision="5b7172f9b230" name="package_samtools_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="edger" version="3.12.0">
-        <repository changeset_revision="09793dbcaf78" name="package_r_edger_3_12_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="c0e0ef144301" name="package_r_edger_3_12_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="rsem" version="1.2.28">
         <repository changeset_revision="987ca85aead4" name="package_rsem_1_2_28" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
@@ -21,8 +21,8 @@
     <package name="express" version="1.5.1">
         <repository changeset_revision="690e3e7d202b" name="package_express_1_5_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="limma" version="3.27.4">
-        <repository changeset_revision="956b99cc83e7" name="package_r_limma_3_27_4" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="limma" version="3.28.2">
+        <repository changeset_revision="4ae6642b634f" name="package_r_limma_3_28_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="deseq2" version="1.10.0">
        <repository changeset_revision="b771de3e4f63" name="package_deseq2_1_10_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />