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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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