Mercurial > repos > devteam > filter_transcripts_via_tracking
view filter_transcripts_via_tracking.xml @ 0:31154ff9f5e1 draft
Imported from capsule None
author | devteam |
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date | Mon, 27 Jan 2014 09:28:51 -0500 |
parents | |
children | 45f89dcf0b4c |
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<tool id="filter_combined_via_tracking" name="Filter Combined Transcripts" version="0.1"> <description>using tracking file</description> <command interpreter="python"> filter_transcripts_via_tracking.py $tracking_file $transcripts_file $filtered_transcripts $sample_num </command> <inputs> <param format="gtf" name="transcripts_file" type="data" label="Cufflinks assembled transcripts" help=""/> <param format="tabular" name="tracking_file" type="data" label="Cuffcompare tracking file" help=""/> <param name="sample_num" type="select" label="Sample Number"> <option value="1">1</option> <option value="2">2</option> </param> </inputs> <outputs> <data format="gtf" name="filtered_transcripts"/> </outputs> <tests> </tests> <help> Uses a tracking file (produced by cuffcompare) to filter a GTF file of transcripts (usually the transcripts produced by cufflinks). Filtering is done by extracting transcript IDs from tracking file and then filtering the GTF so that the output GTF contains only transcript found in the tracking file. Because a tracking file has multiple samples, a sample number is used to filter transcripts for a particular sample. </help> </tool>