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comparison bedclean.xml @ 11:b7f1d9f8f3bc

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author xuebing
date Sat, 10 Mar 2012 07:59:27 -0500
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10:1558594a3c2e 11:b7f1d9f8f3bc
1 <tool id="bedclean" name="clean interval">
2 <description>remove off-chromosome lines</description>
3 <command interpreter="python">bedclean.py $input $genome $output > $log </command>
4 <inputs>
5 <param name="input" type="data" format="interval" label="Original interval file"/>
6 <param name="genome" type="select" label="Select genome">
7 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm9.genome" selected="true">mm9</option>
8 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm8.genome">mm8</option>
9 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg18.genome">hg18</option>
10 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg19.genome">hg19</option>
11 </param>
12 </inputs>
13 <outputs>
14 <data format="input" name="output" label="${tool.name} on ${on_string} (interval)"/>
15 <data format="txt" name="log" label="${tool.name} on ${on_string} (log)"/>
16 </outputs>
17 <help>
18
19 **Description**
20
21 remove lines that are
22
23 1. comment or track name lines
24
25 2. on chr*_random
26
27 3. or have negative coordinates
28
29 4. or the end is larger than chromosome size
30
31
32 </help>
33 </tool>