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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