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6
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1 <tool id="modifySequenceList" name="modify sequence list">
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2 <description>Extend or shring a list of sequences. </description>
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18
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3 <requirements>
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4 <requirement type="set_environment">PYTHONPATH</requirement>
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5 </requirements>
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6
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6 <command interpreter="python"> ../Java/Python/modifySequenceList.py -i $inputFile -f fasta
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7 #if $OptionStart.Start == "Yes":
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8 -s $OptionStart.StartVal
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9 #end if
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10 #if $OptionEnd.End == "Yes":
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11 -e $OptionEnd.EndVal
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12 #end if
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13 -o $outputFile
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14 </command>
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15
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16
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17 <inputs>
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18 <param name="inputFile" type="data" format="fasta" label="input file"/>
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19
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20 <conditional name="OptionStart">
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21 <param name="Start" type="select" label="keep first nucleotides">
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22 <option value="Yes">Yes</option>
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23 <option value="No" selected="true">No</option>
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24 </param>
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25 <when value="Yes">
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26 <param name="StartVal" type="integer" value="0" />
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27 </when>
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28 <when value="No">
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29 </when>
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30 </conditional>
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31
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32 <conditional name="OptionEnd">
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33 <param name="End" type="select" label="keep last nucleotides">
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34 <option value="Yes">Yes</option>
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35 <option value="No" selected="true">No</option>
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36 </param>
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37 <when value="Yes">
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38 <param name="EndVal" type="integer" value="0"/>
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39 </when>
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40 <when value="No">
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41 </when>
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42 </conditional>
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43 </inputs>
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44
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45 <outputs>
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46 <data format="fasta" name="outputFile" label="[modify sequence list] output file"/>
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6
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47 </outputs>
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48
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49 <help>
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50 This tool reads a list of sequences (in multi-FASTA/Q format) that you provide and shrinks each sequence to the *n* first nucleotides or the *n* last nucleotides.
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51 </help>
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6
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52 </tool>
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