Mercurial > repos > yufei-luo > s_mart
comparison SMART/bacteriaRegulatoryRegion_Detection/seedGff.xml @ 18:94ab73e8a190
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| author | m-zytnicki |
|---|---|
| date | Mon, 29 Apr 2013 03:20:15 -0400 |
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| 17:b0e8584489e6 | 18:94ab73e8a190 |
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| 1 <tool id="seedGff" name="seedGff"> | |
| 2 <description>Creates the seed from -15 to -25 bp before ATG</description> | |
| 3 <command interpreter="perl"> seedGff.pl -i $inputFile -p $startPosFromAtg -e $endPosSeed | |
| 4 #if $optionSeedSize.seedSize == "Yes": | |
| 5 -l $optionSeedSize.seedLength | |
| 6 #end if | |
| 7 -o $outputFile | |
| 8 </command> | |
| 9 <inputs> | |
| 10 <param name="inputFile" type="data" label="Input File" format="gff"/> | |
| 11 <param name="startPosFromAtg" type="integer" value="25" help="greather positive number for the start position of the seed from Atg "/> | |
| 12 <param name="endPosSeed" type="integer" value="15" help="end of the seed (smaller than the sart of the seed, positive number)"/> | |
| 13 <conditional name="optionSeedSize"> | |
| 14 <param name="seedSize" type="select" label="The length of seed." help="If you have choosed the value of start/end position of seed, you don't need to fill this option."> | |
| 15 <option value="Yes">Yes</option> | |
| 16 <option value="No" selected="true">No</option> | |
| 17 </param> | |
| 18 <when value="Yes"> | |
| 19 <param name="seedLength" type="integer" value="4" label="The length of seed, default: 4nt" /> | |
| 20 </when> | |
| 21 <when value="No"> | |
| 22 </when> | |
| 23 </conditional> | |
| 24 | |
| 25 | |
| 26 </inputs> | |
| 27 | |
| 28 <outputs> | |
| 29 <data format="gff" name="outputFile" label="[seedGff] Output File"/> | |
| 30 </outputs> | |
| 31 | |
| 32 <help> | |
| 33 command example: perl seedGff.pl -i input_annot.gff -p 25 -e 15 -o output_cis_seed.gff | |
| 34 </help> | |
| 35 </tool> |