Mercurial > repos > yqiancolumbia > ctk_test
comparison bedExt.xml @ 0:0475e4175855 draft default tip
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
author | yqiancolumbia |
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date | Mon, 30 Apr 2018 05:25:11 -0400 |
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1 <tool id="bedExt" name="Get the position before the start site"> | |
2 <description>as a potential cross link site that causes truncation</description> | |
3 <command interpreter="perl"> | |
4 /home/galaxy/tools/CTK/bedExt.pl -n $NeighborRegion -l $LeftExtension -r $RightExtension -v $input $output | |
5 </command> | |
6 | |
7 <inputs> | |
8 <param name="input" type="data" format="bed" label="Input BED file in which CLIP tags with deletions were removed"/> | |
9 <param name="NeighborRegion" type="text" value="up" label="Get neighbor region relative to up|down|r=100"/> | |
10 <param name="LeftExtension" type="integer" value="-1" label="Extension on the left, with sign 0"/> | |
11 <param name="RightExtension" type="integer" value="-1" label="Extension on the right, with sign 0"/> | |
12 </inputs> | |
13 | |
14 <outputs> | |
15 <data name="output" format="bed" label="Output file in BED format extended around start site as a potential cross link site that causes truncation" /> | |
16 </outputs> | |
17 <help> | |
18 | |
19 .. class:: infomark | |
20 | |
21 **What this tool does** | |
22 | |
23 This tool will extract sequences specied by a bed file. | |
24 | |
25 Here it will take as input files in BED format in which CLIP tags with deletions were removed and output files in BED format extended around start site as a potential cross link site that causes truncation. | |
26 </help> | |
27 </tool> | |
28 |