[2] | 1 | <tool id="filter_combined_via_tracking" name="Filter Combined Transcripts" version="0.1"> |
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| 2 | <description>using tracking file</description> |
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| 3 | <command interpreter="python"> |
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| 4 | filter_transcripts_via_tracking.py |
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| 5 | $tracking_file |
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| 6 | $transcripts_file |
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| 7 | $filtered_transcripts |
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| 8 | $sample_num |
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| 9 | </command> |
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| 10 | <inputs> |
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| 11 | <param format="gtf" name="transcripts_file" type="data" label="Cufflinks assembled transcripts" help=""/> |
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| 12 | <param format="tabular" name="tracking_file" type="data" label="Cuffcompare tracking file" help=""/> |
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| 13 | <param name="sample_num" type="select" label="Sample Number"> |
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| 14 | <option value="1">1</option> |
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| 15 | <option value="2">2</option> |
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| 16 | </param> |
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| 17 | </inputs> |
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| 18 | |
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| 19 | <outputs> |
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| 20 | <data format="gtf" name="filtered_transcripts"/> |
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| 21 | </outputs> |
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| 22 | |
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| 23 | <tests> |
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| 24 | </tests> |
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| 25 | |
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| 26 | <help> |
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| 27 | Uses a tracking file (produced by cuffcompare) to filter a GTF file of transcripts (usually the transcripts produced by |
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| 28 | cufflinks). Filtering is done by extracting transcript IDs from tracking file and then filtering the |
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| 29 | GTF so that the output GTF contains only transcript found in the tracking file. Because a tracking file has multiple |
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| 30 | samples, a sample number is used to filter transcripts for a particular sample. |
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| 31 | </help> |
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| 32 | </tool> |
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