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1 <tool id="baseline_fasta_generator" name="Baseline generator" version="1.0">
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2 <description>Generate baseline fasta file</description>
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3
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3 <command interpreter="bash">
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5
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4 wrapper.sh "
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5 #for $i, $input in enumerate($inputs)
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6 ${input.in_file}
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7 #end for
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8 "
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9 "
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10 #for $i, $input in enumerate($inputs)
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11 ${input.id}
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12 #end for
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13 "
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14 $reference $out_file
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15 </command>
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16 <inputs>
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5
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17 <repeat name="inputs" title="inputs" min="1" default="1">
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18 <param name="in_file" type="data" label="Input excel or IMGT zip file" />
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19 <param name="id" type="text" label="ID (alpha-numeric, no spaces)" />
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20 </repeat>
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21 <param name="reference" type="data" format="fasta" label="Reference fasta file" />
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22 </inputs>
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23 <outputs>
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5
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24 <data format="fasta" name="out_file" label = "Baseline generator on ${on_string} with $reference.name"/>
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25 </outputs>
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26 <help>
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27 Gur Yaari; Mohamed Uduman; Steven H. Kleinstein. Quantifying selection in high-throughput Immunoglobulin sequencing data sets. Nucleic Acids Res. 2012 May 27.
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28
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29 Mohamed Uduman; Gur Yaari; Uri Hershberg; Mark J. Shlomchik; Steven H. Kleinstein. Detecting selection in immunoglobulin sequences. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W499-504.
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30 </help>
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31 </tool>
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