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comparison bed_clean.xml @ 9:5236cb10885a default tip

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author xuebing
date Sat, 31 Mar 2012 13:08:38 -0400
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1 <tool id="bed_clean" name="bed_clean">
2 <description>clean up BED files</description>
3 <command interpreter="python">bed_clean.py $input $genome $output > $log </command>
4 <inputs>
5 <param name="input" type="data" format="interval" label="Original interval file"/>
6
7 <param name="genome" type="select" label="Select chromsome size file" >
8 <options from_file="chrsize.loc">
9 <column name="name" index="0"/>
10 <column name="value" index="1"/>
11 </options>
12 </param>
13
14 </inputs>
15 <outputs>
16 <data format="input" name="output" label="${tool.name} on ${on_string} (interval)"/>
17 <data format="txt" name="log" label="${tool.name} on ${on_string} (log)"/>
18 </outputs>
19 <help>
20
21 **Description**
22
23 remove lines that are
24
25 1. comment or track name lines
26
27 2. on chr*_random
28
29 3. or have negative coordinates
30
31 4. or the end is larger than chromosome size
32
33 5. convert strand * to +
34
35
36 </help>
37 </tool>