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1 <tool id="immunerepertoirecombined" name="Immunerepertoire combined" version="1.0">
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2 <description>pipeline</description>
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3 <command interpreter="bash">
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4 combined.sh
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5 #for $i, $f in enumerate($files)
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6 ${f.file}
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7 ${f.id}
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8 #end for
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9 "$clonaltype_select" $out_file $out_file.files_path
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10 </command>
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11 <inputs>
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12 <repeat name="files" title="File" min="1" default="1">
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13 <param name="file" format="fasta" type="data" label="Data to Process" />
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14 <param name="id" type="text" label="ID" />
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15 </repeat>
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16 <param name="clonaltype_select" type="select" label="Clonal Type Definition">
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17 <option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3.Seq</option>
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18 <option value="Top.V.Gene,CDR3.Seq.DNA">Top.V.Gene, CDR3.Seq.DNA</option>
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19 <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.J.Gene, CDR3.Seq</option>
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20 <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.J.Gene, CDR3.Seq.DNA</option>
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21 <option value="Top.V.Gene,Top.D.Gene,Top.J.Gene,CDR3.Seq.DNA">Top.V.Gene, Top.D.Gene, Top.J.Gene, CDR3.Seq.DNA</option>
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22 </param>
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23 </inputs>
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24 <outputs>
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25 <data format="html" name="out_file" />
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26 </outputs>
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27 <help>
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28 The entire Immune Repertoire pipeline as a single tool, input several FASTA files, give them an ID and it will BLAST, parse, merge and plot them.
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29 </help>
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30 <requirements>
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31 <requirement type="package" version="1.0.0">igBlastn</requirement>
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32 </requirements>
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33 </tool>
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34
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