Mercurial > repos > iuc > trinity_abundance_estimates_to_matrix

diff abundance_estimates_to_matrix.xml @ 5:8b5039bdf1f6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
author iuc
date Fri, 31 Mar 2017 11:37:24 -0400
parents fba77b1f69b4
children 74217fbfba4d
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--- a/abundance_estimates_to_matrix.xml	Thu Mar 23 10:18:33 2017 -0400
+++ b/abundance_estimates_to_matrix.xml	Fri Mar 31 11:37:24 2017 -0400
@@ -1,17 +1,17 @@
-<tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@.1">
+<tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@.0">
     <description>for a de novo assembly of RNA-Seq data by Trinity</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="3.14.0">bioconductor-edger</requirement>
-        <requirement type="package" version="0.7.2">salmon</requirement>
+        <requirement type="package" version="3.16.5">bioconductor-edger</requirement>
+        <!-- Cannot update to salmon 0.8.2 because in Bioconda it requires icu 58, while r-base 3.3.1 requires icu 54 -->
+        <requirement type="package" version="0.8.1">salmon</requirement>
     </expand>
-    <expand macro="stdio"/>
-    <command><![CDATA[
+    <command detect_errors="aggressive"><![CDATA[
         #import re
         #for $entry in $samples:
-            ln -s '${entry}' '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' &&
+            ln -f -s '${entry}' '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' &&
         #end for
 
         abundance_estimates_to_matrix.pl