Mercurial > repos > yufei-luo > s_mart

diff SMART/bacteriaRegulatoryRegion_Detection/coverageGff.xml @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/bacteriaRegulatoryRegion_Detection/coverageGff.xml	Mon Apr 29 03:20:15 2013 -0400
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+<tool id="coverageGff" name="coverage Gff">
+  <description>Computes reads coverage form a "nbElements" tag and writes the calculated coverage in a gff3 out file.</description>
+  <command interpreter="perl"> coverageGff.pl -i $inputFile -l $readSize > $outputFile  </command>
+  <inputs>
+    <param name="inputFile" type="data" label="Input File" format="gff"/>
+    <param name="readSize" type="integer" value="38" help="The size of read, default: 38nt"/>
+
+  </inputs>
+
+  <outputs>
+    <data format="gff3" name="outputFile" label="[coveragePl] Output File"/>
+  </outputs>
+
+  <help>
+	command example: perl coverageGff.pl -i *_trans_inIG.gff > *_trans_inIG_cov.gff
+  </help>
+</tool>