Mercurial > repos > yusuf > extend_bed_regions
comparison ExtendBedRegions.xml @ 0:cb1c17dddc14 default tip
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| author | Yusuf Ali <ali@yusuf.email> |
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| date | Wed, 25 Mar 2015 13:32:42 -0600 |
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| -1:000000000000 | 0:cb1c17dddc14 |
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| 1 <?xml version="1.0"?> | |
| 2 | |
| 3 <tool id="extend_bed_regions_1" name="Expand or contract regions"> | |
| 4 <description>in a BED file by a fixed number of bases</description> | |
| 5 <version_string>echo 1.0.0</version_string> | |
| 6 <command interpreter="perl">extend_bed_regions $in_bed $extent $strand $out_bed</command> | |
| 7 <inputs> | |
| 8 <param format="bed" name="in_bed" type="data" label="BED file whose regions should be modified"/> | |
| 9 <param name="extent" type="integer" value="50" label="Number of bases to extend each BED region (negative values cause contraction)"/> | |
| 10 <param name="strand" type="select" display="radio" label="Which end to extend?" help="If the BED file contains strand info, extension will be strand specific. Otherwise, the positive strand is assumed"> | |
| 11 <option value="5">5'</option> | |
| 12 <option value="3">3'</option> | |
| 13 <option value="both" selected="true">Both</option> | |
| 14 </param> | |
| 15 </inputs> | |
| 16 <outputs> | |
| 17 <data name="out_bed" format="bed" type="data" label="BED file with extended/contracted regions"/> | |
| 18 </outputs> | |
| 19 | |
| 20 <tests/> | |
| 21 | |
| 22 <help> | |
| 23 This tool expands each regions defined in a BED file by the specified amount, at the specified end(s). If expanded regions overlap, they are merged. | |
| 24 </help> | |
| 25 | |
| 26 </tool> |