Mercurial > repos > xuebing > sharplabtool
comparison tools/mytools/bedclean.xml @ 0:9071e359b9a3
Uploaded
| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:9071e359b9a3 |
|---|---|
| 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> |