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
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>