Mercurial > repos > jfb > blosum_toolshed

diff blosum4galaxy/Blosum.xml @ 5:81da7e8c5ad1 draft

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Uploaded
author jfb
date Tue, 30 Oct 2018 14:25:24 -0400
parents 0c6cffd4393f
children ff689372d877
line wrap: on
line diff
--- a/blosum4galaxy/Blosum.xml	Mon Oct 29 16:38:58 2018 -0400
+++ b/blosum4galaxy/Blosum.xml	Tue Oct 30 14:25:24 2018 -0400
@@ -4,13 +4,13 @@
        <requirement type="package">openjdk</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[        
-        java -Djava.awt.headless=true -jar '$__tool_directory__/blosum2.jar'
+        java -Djava.awt.headless=true -jar '$__tool_directory__/blosum2.jar' '$INPUT' output.csv
     ]]></command>
     <inputs>
-        <param format="csv" name="INPUT.csv" type="data" label="Peptide Sequences"/>
+        <param format="csv" name="INPUT" type="data" label="Peptide Sequences"/>
     </inputs>      
     <outputs>
-        <data format="csv" name="BlosumOutput.csv" from_work_dir="BlosumOutput.csv" label="BlosumOutput.csv"/>
+        <data format="csv" name="BlosumOutput.csv" from_work_dir="output.csv" label="BlosumOutput.csv"/>
     </outputs>
     <tests>
         <test>