Mercurial > repos > yufei-luo > s_mart

annotate SMART/bacteriaRegulatoryRegion_Detection/coverageGff.xml @ 31:0ab839023fe4

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
18
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
1 <tool id="coverageGff" name="coverage Gff">
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
2 <description>Computes reads coverage form a "nbElements" tag and writes the calculated coverage in a gff3 out file.</description>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
3 <command interpreter="perl"> coverageGff.pl -i $inputFile -l $readSize > $outputFile </command>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
4 <inputs>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
5 <param name="inputFile" type="data" label="Input File" format="gff"/>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
6 <param name="readSize" type="integer" value="38" help="The size of read, default: 38nt"/>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
7
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
8 </inputs>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
9
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
10 <outputs>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
11 <data format="gff3" name="outputFile" label="[coveragePl] Output File"/>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
12 </outputs>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
13
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
14 <help>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
15 command example: perl coverageGff.pl -i *_trans_inIG.gff > *_trans_inIG_cov.gff
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
16 </help>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
17 </tool>