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comparison draw_variants.xml @ 24:248b06e86022

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Added gd_genotype datatype. Modified tools to support new datatype.
author Richard Burhans <burhans@bx.psu.edu>
date Tue, 28 May 2013 16:24:19 -0400
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children 8997f2ca8c7a
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23:66a183c44dd5 24:248b06e86022
1 <tool id="gd_draw_variants" name="Draw" version="1.0.0">
2 <description>variants</description>
3
4 <command interpreter="python">
5 draw_variants.py "$input" "$indel_input" "$coverage_input" "$annotation_input" "$indiv_input" "$ref_name" "$min_coverage" "$output"
6 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
7 #set $arg = '%s:%s' % ($individual_col, $individual)
8 "$arg"
9 #end for
10 </command>
11
12 <inputs>
13 <param name="input" type="data" format="gd_snp" label="SNP dataset" />
14 <param name="indel_input" type="data" format="gd_snp" label="Indel dataset" />
15 <param name="coverage_input" type="data" format="interval" label="Coverage dataset" />
16 <param name="annotation_input" type="data" format="interval" label="Annotation dataset" />
17 <param name="indiv_input" type="data" format="gd_indivs" label="Population Individuals" />
18
19 <param name="ref_name" type="select" label="Ref name">
20 <options from_dataset="indiv_input">
21 <column name="name" index="1"/>
22 <column name="value" index="1"/>
23 <filter type="add_value" name="default" value="default" index="0" />
24 </options>
25 </param>
26
27 <param name="min_coverage" type="integer" min="1" value="1" label="Minimum coverage" />
28 </inputs>
29
30 <outputs>
31 <data name="output" format="svg" />
32 </outputs>
33
34 <help>
35 </help>
36 </tool>