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1 <tool id="complete_immunerepertoire_igg" name="Complete ImmuneRepertoire" version="1.0">
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2 <description> </description>
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3 <command interpreter="bash">
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4 complete.sh "
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5 #for $i, $f in enumerate($patients)
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6 ${f.id}
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7 #for $j, $g in enumerate($f.samples)
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8 ${g.sample}
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9 #end for
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10 #end for
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11 " $out_file $out_file.files_path "$clonaltype" $species $locus $filterproductive
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12 </command>
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13 <inputs>
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14 <repeat name="patients" title="Patients" min="1" default="1">
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15 <repeat name="samples" title="Sample" min="1" default="1">
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16 <param name="sample" type="data" label="Sample to Process" />
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17 </repeat>
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18 <param name="id" type="text" label="ID" />
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19 </repeat>
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20 <param name="clonaltype" type="select" label="Clonal Type Definition">
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21 <option value="none">Don't remove duplicates based on clonaltype</option>
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22 <option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3.Seq</option>
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23 <option value="Top.V.Gene,CDR3.Seq.DNA">Top.V.Gene, CDR3.Seq.DNA</option>
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24 <option value="Top.V.Gene,Top.J.Gene,CDR3.Seq">Top.V.Gene, Top.J.Gene, CDR3.Seq</option>
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25 <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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26 <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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27 </param>
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28
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29 <param name="species" type="select" label="Species">
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30 <option value="human">Human</option>
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31 <option value="mouse">Mouse</option>
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32 </param>
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33
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34 <param name="locus" type="select" label="Locus">
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35 <option value="igh">IGH</option>
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36 <option value="igk">IGK</option>
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37 <option value="igl">IGL</option>
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38 <option value="trb">TRB</option>
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39 <option value="tra">TRA</option>
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40 <option value="trg">TRG</option>
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41 <option value="trd">TRD</option>
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42 </param>
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43
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44 <param name="filterproductive" type="select" label="Filter out the unproductive sequences">
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45 <option value="yes">Yes</option>
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46 <option value="no">No</option>
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47 </param>
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48 </inputs>
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49 <outputs>
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50 <data format="html" name="out_file" />
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51 </outputs>
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52 <help>
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53 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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54 </help>
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55 </tool>
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