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1 <tool id="mutation_analysis_shm" name="Mutation Analysis" version="1.0">
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2 <description></description>
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3 <command interpreter="bash">
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22
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4 wrapper.sh $in_file $method $out_file $out_file.files_path ${in_file.name} ${include_fr1}
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5 </command>
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6 <inputs>
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7 <param name="in_file" type="data" label="IMGT zip file to be analysed" />
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19
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8 <param name="method" type="select" label="Identification method" help="" >
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9 <option value="custom" selected="true">custom</option>
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10 <option value="blastn">blastn</option>
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11 </param>
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22
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12 <param name="include_fr1" type="select" label="Include mutations in FR1 region" help="" >
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13 <option value="yes">yes</option>
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14 <option value="no" selected="true">no</option>
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15 </param>
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16 </inputs>
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17 <outputs>
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18 <data format="html" name="out_file" label = "Mutation analysis on ${in_file.name}"/>
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19 </outputs>
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20 <help>
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21 Takes an IMGT zip (http://www.imgt.org/HighV-QUEST/search.action) file and creates a summarization of the mutation analysis.
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22 </help>
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23 <requirements>
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24 <requirement type="package" version="1.0">blastn</requirement>
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25 </requirements>
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26 </tool>
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