Mercurial > repos > yufei-luo > s_mart

diff smart_toolShed/SMART/galaxy/testArgum.xml @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/galaxy/testArgum.xml	Thu Jan 17 10:52:14 2013 -0500
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+<tool id="test_argument" name="test_argu" version="1.0.0">
+  <description>To test the arguments from shell.</description>
+  <command> 
+../testArgu.sh $test_out 
+#for $i in $replicate_groups
+#for $j in $i.replicates
+$j.bam_alignment:#slurp
+#end for
+#end for
+    >> $Log_File </command>
+  <inputs>
+	<param format="gff3" name="anno_input_selected" type="data" label="Genome annotation in GFF3 file" help="A tab delimited format for storing sequence features and annotations"/>
+   <repeat name="replicate_groups" title="Replicate group" min="2">
+     <repeat name="replicates" title="Replicate">
+      <param format="fastq" name="bam_alignment" type="data" label="BAM alignment file" help="BAM alignment file. Can be generated from SAM files using the SAM Tools."/>
+     </repeat>
+   </repeat>
+  </inputs>
+
+  <outputs>
+    <data format="txt" name="test_out" label="DESeq result"/>
+	<data format="txt" name="Log_File" label="DESeq result"/>
+  </outputs>
+</tool>