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diff LINKYX_reformat_trinity_header.xml @ 22:7997c93ee479

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last attempt to install perl as part of linkyx
author biomonika <biomonika@psu.edu>
date Thu, 11 Sep 2014 19:40:01 -0400
parents
children ba6849a9389e
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LINKYX_reformat_trinity_header.xml	Thu Sep 11 19:40:01 2014 -0400
@@ -0,0 +1,27 @@
+<tool id="reformat_trinity_header" name="reformat_trinity_header">
+      <description>Reformat Trinity header</description>
+      <requirements>
+        <requirement type="set_environment">LINKYX_PATH</requirement>
+        <requirement type="set_environment">SAMTOOLS</requirement>
+        <requirement type="package" version="0.1.19">samtools</requirement>
+        <requirement type="package" version="1.6.922">bioperl</requirement>
+      </requirements>
+      <command interpreter="bash">LINKYX_reformat_trinity_header.sh $output $input1</command>
+      <inputs>
+        <param format="fasta" name="input1" type="data" label="Trinity.fasta"/>
+      </inputs>
+      <outputs>
+        <data format="fasta" name="output" />
+      </outputs>
+  
+     <tests>
+       <test>
+        <output name="out_file1" file="Trinity.fasta"/>
+       </test>
+     </tests>
+   
+     <help>
+   Reformat Trinity header, keep only part until first space.
+     </help>
+   
+   </tool>
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