Mercurial > repos > davidvanzessen > imgt_locus_split

comparison imgt_locus_split.xml @ 2:4bb8f6523130 draft

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author davidvanzessen
date Tue, 05 Mar 2019 04:41:47 -0500
parents 418b7dbc8947
children 9aa036caa8e9
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1:418b7dbc8947 2:4bb8f6523130
1 <tool id="imgt_locus_split" name="IMGT Locus Split" version="0.1"> 1 <tool id="imgt_locus_split" name="IMGT Locus Split" version="0.1">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.4.13">python-magic</requirement> 3 <requirement type="package" version="0.4.15">python-magic</requirement>
4 </requirements> 4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[ 5 <command detect_errors="exit_code"><![CDATA[
6 python3 $__tool_directory__/imgt_locus_split.py 6 python3 $__tool_directory__/imgt_locus_split.py
7 --input $input 7 --input $input
8 --output-ig ${output_ig} 8 --loci $loci
9 --output-igh ${output_igh} 9 --output $output
10 --output-igk ${output_igk}
11 --output-igl ${output_igl}
12 --output-tr ${output_tr}
13 --output-tra ${output_tra}
14 --output-trb ${output_trb}
15 --output-trd ${output_trd}
16 --output-trg ${output_trg}
17 ]]></command> 10 ]]></command>
18 <inputs> 11 <inputs>
19 <param name="input" type="data" format="data" label="The IMGT zip file to be split"/> 12 <param name="input" type="data" format="data" label="The IMGT zip file to be split"/>
20 <param name="loci" type="select" label="Loci" multiple="true" display="checkboxes"> 13 <param name="loci" type="select" label="Loci" multiple="true" display="checkboxes">
21 <option value="IG" selected="true">IG</option> 14 <option value="IG" selected="true">IG</option>
28 <option value="TRD">TRD</option> 21 <option value="TRD">TRD</option>
29 <option value="TRG">TRG</option> 22 <option value="TRG">TRG</option>
30 </param> 23 </param>
31 </inputs> 24 </inputs>
32 <outputs> 25 <outputs>
33 <data format="imgt_archive" name="output_ig" label="Filtered IMGT IG: ${input.name}"> 26 <data format="imgt_archive" name="output" label="${input.name} $loci" />
34 <filter>loci.__contains__('IG')</filter>
35 </data>
36 <data format="imgt_archive" name="output_igh" label="Filtered IMGT IGH: ${input.name}">
37 <filter>loci.__contains__('IGH')</filter>
38 </data>
39 <data format="imgt_archive" name="output_igk" label="Filtered IMGT IGK: ${input.name}">
40 <filter>loci.__contains__('IGK')</filter>
41 </data>
42 <data format="imgt_archive" name="output_igl" label="Filtered IMGT IGL: ${input.name}">
43 <filter>loci.__contains__('IGL')</filter>
44 </data>
45 <data format="imgt_archive" name="output_tr" label="Filtered IMGT TR: ${input.name}">
46 <filter>loci.__contains__('TR')</filter>
47 </data>
48 <data format="imgt_archive" name="output_tra" label="Filtered IMGT TRA: ${input.name}">
49 <filter>loci.__contains__('TRA')</filter>
50 </data>
51 <data format="imgt_archive" name="output_trb" label="Filtered IMGT TRB: ${input.name}">
52 <filter>loci.__contains__('TRB')</filter>
53 </data>
54 <data format="imgt_archive" name="output_trd" label="Filtered IMGT TRD: ${input.name}">
55 <filter>loci.__contains__('TRD')</filter>
56 </data>
57 <data format="imgt_archive" name="output_trg" label="Filtered IMGT TRG: ${input.name}">
58 <filter>loci.__contains__('TRG')</filter>
59 </data>
60 </outputs> 27 </outputs>
61 <help><![CDATA[ 28 <help><![CDATA[
62 Creates a new IMGT zip file for every checked locus with sequences from only that locus. 29 Creates a new IMGT zip file for every checked locus with sequences from only that locus.
63 ]]></help> 30 ]]></help>
64 <citations> 31 <citations>