Mercurial > repos > yufei-luo > s_mart

annotate SMART/bacteriaRegulatoryRegion_Detection/splitTranscriptGff.xml @ 18:94ab73e8a190

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
parents
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="splitTranscriptGff" name="splitTranscriptGff">
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
2 <description> Define UTRs and intergenic operonic regions from a transcript file and following a reference file </description>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
3 <command interpreter="perl">
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
4 splitTranscriptGff.pl -i $referenciesFile -j $transcriptsFile > $outputFile
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
5 </command>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
6
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
7 <inputs>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
8 <param name="referenciesFile" type="data" label="Referencies Input File" format="gff" />
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
9 <param name="transcriptsFile" type="data" label="Transcripts Input File" format="gff" />
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
10 </inputs>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
11
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
12 <outputs>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
13 <data format="gff3" name="outputFile" label="[splitTranscript] Output File"/>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
14 </outputs>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
15
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
16 <help>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
17 Note that iputs files should be sorted by increasing positions and that expressed referencies should be included in transcripts.
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
18
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
19 Command example: perl splitTranscriptGff.pl -i annotations.gff -j transcripts.gff > TUTag.gff3
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
20 </help>
94ab73e8a190 Uploaded
m-zytnicki
parents:
diff changeset
21 </tool>