Mercurial > repos > davidvanzessen > imgt_locus_split

comparison imgt_locus_split.xml @ 1:418b7dbc8947 draft

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author davidvanzessen
date Mon, 17 Jul 2017 08:54:02 -0400
parents b00c257f0a67
children 4bb8f6523130
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0:b00c257f0a67 1:418b7dbc8947
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.4.13">python-magic</requirement> 3 <requirement type="package" version="0.4.13">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 --loci $loci 8 --output-ig ${output_ig}
9 --output $output 9 --output-igh ${output_igh}
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 ${output_trg}
10 ]]></command> 17 ]]></command>
11 <inputs> 18 <inputs>
12 <param name="input" type="data" format="data" label="The IMGT zip file to be split"/> 19 <param name="input" type="data" format="data" label="The IMGT zip file to be split"/>
13 <param name="loci" type="select" label="Loci" multiple="true" display="checkboxes"> 20 <param name="loci" type="select" label="Loci" multiple="true" display="checkboxes">
14 <option value="IG" selected="true">IG</option> 21 <option value="IG" selected="true">IG</option>
21 <option value="TRD">TRD</option> 28 <option value="TRD">TRD</option>
22 <option value="TRG">TRG</option> 29 <option value="TRG">TRG</option>
23 </param> 30 </param>
24 </inputs> 31 </inputs>
25 <outputs> 32 <outputs>
26 <data format="imgt_archive" name="output" label="${input.name} $loci" /> 33 <data format="imgt_archive" name="output_ig" label="Filtered IMGT IG: ${input.name}">
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>
27 </outputs> 60 </outputs>
28 <help><![CDATA[ 61 <help><![CDATA[
29 Creates a new IMGT zip file for every checked locus with sequences from only that locus. 62 Creates a new IMGT zip file for every checked locus with sequences from only that locus.
30 ]]></help> 63 ]]></help>
31 <citations> 64 <citations>