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1 <tool id="seedGff" name="seedGff">
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2 <description>Creates the seed from -15 to -25 bp before ATG</description>
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3 <command interpreter="perl"> seedGff.pl -i $inputFile -p $startPosFromAtg -e $endPosSeed
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4 #if $optionSeedSize.seedSize == "Yes":
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5 -l $optionSeedSize.seedLength
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6 #end if
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7 -o $outputFile
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8 </command>
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9 <inputs>
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10 <param name="inputFile" type="data" label="Input File" format="gff"/>
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11 <param name="startPosFromAtg" type="integer" value="25" help="greather positive number for the start position of the seed from Atg "/>
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12 <param name="endPosSeed" type="integer" value="15" help="end of the seed (smaller than the sart of the seed, positive number)"/>
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13 <conditional name="optionSeedSize">
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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.">
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15 <option value="Yes">Yes</option>
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16 <option value="No" selected="true">No</option>
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17 </param>
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18 <when value="Yes">
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19 <param name="seedLength" type="integer" value="4" label="The length of seed, default: 4nt" />
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20 </when>
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21 <when value="No">
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22 </when>
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23 </conditional>
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24
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25
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26 </inputs>
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27
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28 <outputs>
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29 <data format="gff" name="outputFile" label="[seedGff] Output File"/>
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30 </outputs>
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31
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32 <help>
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33 command example: perl seedGff.pl -i input_annot.gff -p 25 -e 15 -o output_cis_seed.gff
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34 </help>
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35 </tool>
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