Mercurial > repos > devteam > filter_transcripts_via_tracking
annotate filter_transcripts_via_tracking.xml @ 1:45f89dcf0b4c draft default tip
planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author | devteam |
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date | Tue, 21 Jul 2015 14:21:36 -0400 |
parents | 31154ff9f5e1 |
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rev | line source |
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0 | 1 <tool id="filter_combined_via_tracking" name="Filter Combined Transcripts" version="0.1"> |
2 <description>using tracking file</description> | |
3 <command interpreter="python"> | |
4 filter_transcripts_via_tracking.py | |
5 $tracking_file | |
6 $transcripts_file | |
7 $filtered_transcripts | |
8 $sample_num | |
9 </command> | |
10 <inputs> | |
11 <param format="gtf" name="transcripts_file" type="data" label="Cufflinks assembled transcripts" help=""/> | |
12 <param format="tabular" name="tracking_file" type="data" label="Cuffcompare tracking file" help=""/> | |
13 <param name="sample_num" type="select" label="Sample Number"> | |
14 <option value="1">1</option> | |
15 <option value="2">2</option> | |
16 </param> | |
17 </inputs> | |
18 | |
19 <outputs> | |
20 <data format="gtf" name="filtered_transcripts"/> | |
21 </outputs> | |
22 | |
23 <tests> | |
24 </tests> | |
25 | |
26 <help> | |
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planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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27 **What it does** |
45f89dcf0b4c
planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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28 |
0 | 29 Uses a tracking file (produced by cuffcompare) to filter a GTF file of transcripts (usually the transcripts produced by |
30 cufflinks). Filtering is done by extracting transcript IDs from tracking file and then filtering the | |
31 GTF so that the output GTF contains only transcript found in the tracking file. Because a tracking file has multiple | |
32 samples, a sample number is used to filter transcripts for a particular sample. | |
33 </help> | |
34 </tool> |