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1 <tool id="from_imgt_clonal_pairs" name="IMGT to Paired Clonal Sequences" version="1.0">
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2 <description>Comparison of clonal sequences in paired samples</description>
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3 <command interpreter="bash">
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4 from_imgt.sh $out_file
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5 #for $i, $f in enumerate($patients)
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6 "$f.name" "$f.cellcount" "$f.receptor" "$len($f.samples)"
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7 #for $j, $g in enumerate($f.samples)
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8 "${g.sname}" "${g.file}"
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9 #end for
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10 #end for
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11 </command>
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12 <inputs>
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13 <repeat name="patients" title="Patient" min="1" default="1">
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14 <param name="name" type="text" label="Patient name" />
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15 <param name="cellcount" type="text" label="Cell Count" />
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16 <param name="receptor" type="text" label="Receptor" />
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17 <repeat name="samples" title="Sample" min="1" max="2" default="1">
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18 <param name="sname" type="text" label="Sample name" />
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19 <param name="file" type="data" label="Data to Process" />
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20 </repeat>
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21 </repeat>
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22
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23 </inputs>
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24 <outputs>
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25 <data format="tabular" name="out_file" />
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26 </outputs>
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27 <help>
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28 </help>
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29 </tool>
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