Mercurial > repos > yufei-luo > s_mart

diff SMART/galaxy/CountReadGCPercent.xml @ 38:2c0c0a89fad7

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author m-zytnicki
date Thu, 02 May 2013 09:56:47 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/galaxy/CountReadGCPercent.xml	Thu May 02 09:56:47 2013 -0400
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+<tool id="CountReadGCPercent" name="count read GC percent">
+    <description>Count GC percent for each read against a genome.</description>
+	<requirements>
+		<requirement type="set_environment">PYTHONPATH</requirement>
+	</requirements>
+    <command interpreter="python"> ../Java/Python/CountReadGCPercent.py -i $inputFastaFile -j $inputGffFile -o $outputFile</command>
+  <inputs>
+      <param name="inputFastaFile" type="data" label="Input reference fasta File" format="fasta"/>
+      <param name="inputGffFile" type="data" label="Input File" format="gff3"/>
+  </inputs>
+
+  <outputs>
+    <data format="gff3" name="outputFile" label="[count read GC percent] Output File"/>
+   </outputs>
+
+  <help>
+Count the GC% of a FASTA file.
+  </help>
+</tool>
+