|
11
|
1 <tool id="bedclean" name="clean interval">
|
|
|
2 <description>remove off-chromosome lines</description>
|
|
12
|
3 <command interpreter="python">bedClean.py $input $genome $output > $log </command>
|
|
|
4 <inputs>
|
|
|
5 <param name="input" type="data" format="interval" label="Original interval file"/>
|
|
|
6 <param name="genome" type="select" label="Select genome">
|
|
|
7 <option value="/media/data/Research/Project/galaxy/data/chrsize/mouse.mm9.genome" selected="true">mm9</option>
|
|
|
8 <option value="/media/data/Research/Project/galaxy/data/chrsize/mouse.mm8.genome">mm8</option>
|
|
|
9 <option value="/media/data/Research/Project/galaxy/data/chrsize/human.hg18.genome">hg18</option>
|
|
|
10 <option value="/media/data/Research/Project/galaxy/data/chrsize/human.hg19.genome">hg19</option>
|
|
11
|
11 </param>
|
|
|
12 </inputs>
|
|
|
13 <outputs>
|
|
12
|
14 <data format="input" name="output" label="${tool.name} on ${on_string} (interval)"/>
|
|
11
|
15 <data format="txt" name="log" label="${tool.name} on ${on_string} (log)"/>
|
|
|
16 </outputs>
|
|
|
17 <help>
|
|
|
18
|
|
12
|
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
|
|
11
|
31
|
|
|
32 </help>
|
|
|
33 </tool>
|
