# HG changeset patch
# User iuc
# Date 1466437469 14400
# Node ID 3cc94f4d58aec240c9079eabf3b74bd6bf6aa7e2
# Parent  c6bebb3b396270cdca6beff8c0deb0290a1e3cb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 6dad4ca6483946af64f484feaff78ac9d1d87352

diff -r c6bebb3b3962 -r 3cc94f4d58ae abundance_estimates_to_matrix.xml
--- a/abundance_estimates_to_matrix.xml	Tue Jun 07 10:25:45 2016 -0400
+++ b/abundance_estimates_to_matrix.xml	Mon Jun 20 11:44:29 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 c6bebb3b3962 -r 3cc94f4d58ae align_and_estimate_abundance.xml
--- a/align_and_estimate_abundance.xml	Tue Jun 07 10:25:45 2016 -0400
+++ b/align_and_estimate_abundance.xml	Mon Jun 20 11:44:29 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 c6bebb3b3962 -r 3cc94f4d58ae run_DE_analysis.xml
--- a/run_DE_analysis.xml	Tue Jun 07 10:25:45 2016 -0400
+++ b/run_DE_analysis.xml	Mon Jun 20 11:44:29 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 c6bebb3b3962 -r 3cc94f4d58ae tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jun 07 10:25:45 2016 -0400
+++ b/tool_dependencies.xml	Mon Jun 20 11:44:29 2016 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="trinity" version="2.1.1">
-        <repository changeset_revision="c550c572d8b8" name="package_trinity_2_1_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="cc51a3467ff1" 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" />
@@ -12,22 +12,22 @@
     <package name="samtools" version="1.2">
         <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="c0e0ef144301" name="package_r_edger_3_12_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="bioconductor-edger" version="3.14.0">
+        <repository changeset_revision="d1ebebe12abc" name="package_bioconductor_edger_3_14_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" />
     </package>
-    <package name="express" version="1.5.1">
+    <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="3.28.2">
-        <repository changeset_revision="4ae6642b634f" name="package_r_limma_3_28_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="bioconductor-limma" version="3.28.10">
+        <repository changeset_revision="90b7c39ce562" name="package_bioconductor_limma_3_28_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="deseq2" version="1.10.0">
        <repository changeset_revision="5d9def29ff0b" name="package_deseq2_1_10_0" owner="iuc" toolshed="https://testtoolshed.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>