# HG changeset patch
# User iuc
# Date 1466437490 14400
# Node ID 1b7800489efbbc76cfbb8b841a8264f5da9d5180
# Parent  f7564c3f9dc0bb58eb2b69e33256abe0e0f52c85
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 6dad4ca6483946af64f484feaff78ac9d1d87352

diff -r f7564c3f9dc0 -r 1b7800489efb abundance_estimates_to_matrix.xml
--- a/abundance_estimates_to_matrix.xml	Wed Jun 08 06:49:31 2016 -0400
+++ b/abundance_estimates_to_matrix.xml	Mon Jun 20 11:44:50 2016 -0400
@@ -2,11 +2,7 @@
     <description>for a de novo assembly of RNA-Seq data by Trinity</description>
     <requirements>
         <requirement type="package" version="2.1.1">trinity</requirement>
-        <requirement type="package" version="1.1.2">bowtie</requirement>
-        <requirement type="package" version="1.2">samtools</requirement>
-        <requirement type="package" version="3.12.0">edger</requirement>
-        <requirement type="package" version="3.12.0">bioconductor-edger</requirement>
-        <requirement type="package" version="1.2.28">rsem</requirement>
+        <requirement type="package" version="3.14.0">bioconductor-edger</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:"/>
diff -r f7564c3f9dc0 -r 1b7800489efb align_and_estimate_abundance.xml
--- a/align_and_estimate_abundance.xml	Wed Jun 08 06:49:31 2016 -0400
+++ b/align_and_estimate_abundance.xml	Mon Jun 20 11:44:50 2016 -0400
@@ -6,7 +6,7 @@
         <requirement type="package" version="2.2.6">bowtie2</requirement>
         <requirement type="package" version="1.2">samtools</requirement>
         <requirement type="package" version="1.2.28">rsem</requirement>
-        <requirement type="package" version="1.5.1">express</requirement>
+        <requirement type="package" version="1.5.1">eXpress</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:"/>
diff -r f7564c3f9dc0 -r 1b7800489efb run_DE_analysis.xml
--- a/run_DE_analysis.xml	Wed Jun 08 06:49:31 2016 -0400
+++ b/run_DE_analysis.xml	Mon Jun 20 11:44:50 2016 -0400
@@ -5,10 +5,8 @@
         <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 -->
         <requirement type="package" version="1.10.0">deseq2</requirement>
         <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="3.28.2">limma</requirement>
-        <requirement type="package" version="3.27.4">bioconductor-limma</requirement>
+        <requirement type="package" version="3.14.0">bioconductor-edger</requirement>
+        <requirement type="package" version="3.28.10">bioconductor-limma</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:"/>
diff -r f7564c3f9dc0 -r 1b7800489efb tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jun 08 06:49:31 2016 -0400
+++ b/tool_dependencies.xml	Mon Jun 20 11:44:50 2016 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="trinity" version="2.1.1">
-        <repository changeset_revision="7a745f45e753" name="package_trinity_2_1_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="cec8b7f159c5" name="package_trinity_2_1_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="bowtie" version="1.1.2">
         <repository changeset_revision="a1c1a92e13a6" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
@@ -12,22 +12,22 @@
     <package name="samtools" version="1.2">
         <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="edger" version="3.12.0">
-        <repository changeset_revision="bb14bf1e4535" name="package_r_edger_3_12_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="bioconductor-edger" version="3.14.0">
+        <repository changeset_revision="8ed6cfd2b21f" name="package_bioconductor_edger_3_14_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="rsem" version="1.2.28">
         <repository changeset_revision="4567331d510a" name="package_rsem_1_2_28" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="express" version="1.5.1">
+    <package name="eXpress" version="1.5.1">
         <repository changeset_revision="93017e8743e5" name="package_express_1_5_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="limma" version="3.28.2">
-        <repository changeset_revision="4fa8ed0ffea1" name="package_r_limma_3_28_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="bioconductor-limma" version="3.28.10">
+        <repository changeset_revision="fc78b4bbe0ab" name="package_bioconductor_limma_3_28_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="deseq2" version="1.10.0">
        <repository changeset_revision="e4a11a7d33d6" name="package_deseq2_1_10_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <set_environment version="1.0">
-        <environment_variable action="set_to" name="TRINITY_MEM_OPTIONS">--max_memory 30G --bflyHeapSpaceMax 30G</environment_variable>
+        <environment_variable action="set_to" name="TRINITY_MEM_OPTIONS">'--max_memory 30G --bflyHeapSpaceMax 30G'</environment_variable>
     </set_environment>
 </tool_dependency>