Mercurial > repos > iuc > trinity_run_de_analysis

diff run_de_analysis.xml @ 9:48537273a30b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
author iuc
date Thu, 14 Jun 2018 03:13:26 -0400
parents 2be382e6918a
children 55cf05b65ad5
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line diff
--- a/run_de_analysis.xml	Mon Jan 22 11:29:32 2018 -0500
+++ b/run_de_analysis.xml	Thu Jun 14 03:13:26 2018 -0400
@@ -1,16 +1,16 @@
-<tool id="trinity_run_de_analysis" name="Differential expression analysis" version="@WRAPPER_VERSION@.0">
+<tool id="trinity_run_de_analysis" name="Differential expression analysis" version="@WRAPPER_VERSION@">
     <description>using a Trinity assembly</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="3.16.5">bioconductor-edger</requirement>
-        <requirement type="package" version="3.30.13">bioconductor-limma</requirement>
-        <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
+        <requirement type="package" version="3.20.7">bioconductor-edger</requirement>
+        <requirement type="package" version="3.34.9">bioconductor-limma</requirement>
+        <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement>
     </expand>
     <command detect_errors="aggressive"><![CDATA[
 
-        ln -f -s "${matrix}" "input.matrix"
+        ln -f -s '${matrix}' "input.matrix"
 
         &&
 
@@ -18,7 +18,7 @@
 
         --matrix "input.matrix"
 
-        --samples_file "${samples}"
+        --samples_file '${samples}'
 
         --method ${method_choice.method}
 
@@ -103,7 +103,7 @@
             </output_collection>
             <output_collection name="PDF_results">
                 <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf"/>
-                <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/>
+                <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="200" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/>
                 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/>
             </output_collection>
         </test>