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1 <tool id="imgt_locus_split" name="IMGT Locus Split" version="0.1">
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2 <requirements>
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3 <requirement type="package" version="0.4.13">python-magic</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 python3 $__tool_directory__/imgt_locus_split.py
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1
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7 --input $input
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8 --output-ig ${output_ig}
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9 --output-igh ${output_igh}
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10 --output-igk ${output_igk}
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11 --output-igl ${output_igl}
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12 --output-tr ${output_tr}
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13 --output-tra ${output_tra}
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14 --output-trb ${output_trb}
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15 --output-trd ${output_trd}
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16 --output-trg ${output_trg}
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17 ]]></command>
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18 <inputs>
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19 <param name="input" type="data" format="data" label="The IMGT zip file to be split"/>
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20 <param name="loci" type="select" label="Loci" multiple="true" display="checkboxes">
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21 <option value="IG" selected="true">IG</option>
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22 <option value="IGH">IGH</option>
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23 <option value="IGK">IGK</option>
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24 <option value="IGL">IGL</option>
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25 <option value="TR" selected="true">TR</option>
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26 <option value="TRA">TRA</option>
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27 <option value="TRB">TRB</option>
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28 <option value="TRD">TRD</option>
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29 <option value="TRG">TRG</option>
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30 </param>
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31 </inputs>
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32 <outputs>
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33 <data format="imgt_archive" name="output_ig" label="Filtered IMGT IG: ${input.name}">
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34 <filter>loci.__contains__('IG')</filter>
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35 </data>
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36 <data format="imgt_archive" name="output_igh" label="Filtered IMGT IGH: ${input.name}">
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37 <filter>loci.__contains__('IGH')</filter>
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38 </data>
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39 <data format="imgt_archive" name="output_igk" label="Filtered IMGT IGK: ${input.name}">
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40 <filter>loci.__contains__('IGK')</filter>
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41 </data>
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42 <data format="imgt_archive" name="output_igl" label="Filtered IMGT IGL: ${input.name}">
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43 <filter>loci.__contains__('IGL')</filter>
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44 </data>
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45 <data format="imgt_archive" name="output_tr" label="Filtered IMGT TR: ${input.name}">
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46 <filter>loci.__contains__('TR')</filter>
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47 </data>
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48 <data format="imgt_archive" name="output_tra" label="Filtered IMGT TRA: ${input.name}">
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49 <filter>loci.__contains__('TRA')</filter>
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50 </data>
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51 <data format="imgt_archive" name="output_trb" label="Filtered IMGT TRB: ${input.name}">
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52 <filter>loci.__contains__('TRB')</filter>
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53 </data>
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54 <data format="imgt_archive" name="output_trd" label="Filtered IMGT TRD: ${input.name}">
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55 <filter>loci.__contains__('TRD')</filter>
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56 </data>
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57 <data format="imgt_archive" name="output_trg" label="Filtered IMGT TRG: ${input.name}">
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58 <filter>loci.__contains__('TRG')</filter>
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59 </data>
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60 </outputs>
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61 <help><![CDATA[
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62 Creates a new IMGT zip file for every checked locus with sequences from only that locus.
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63 ]]></help>
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64 <citations>
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65 <citation type="doi">10.1093/nar/gku1056</citation>
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66 </citations>
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67 </tool> |
