annotate draw_variants.xml @ 26:91e835060ad2

Updates to Admixture, Aggregate Individuals, and Restore Attributes to support gd_genotype
author Richard Burhans <burhans@bx.psu.edu>
date Mon, 03 Jun 2013 12:29:29 -0400
parents 248b06e86022
children 8997f2ca8c7a
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1 <tool id="gd_draw_variants" name="Draw" version="1.0.0">
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2 <description>variants</description>
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3
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4 <command interpreter="python">
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5 draw_variants.py "$input" "$indel_input" "$coverage_input" "$annotation_input" "$indiv_input" "$ref_name" "$min_coverage" "$output"
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6 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
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7 #set $arg = '%s:%s' % ($individual_col, $individual)
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8 "$arg"
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9 #end for
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10 </command>
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11
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12 <inputs>
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13 <param name="input" type="data" format="gd_snp" label="SNP dataset" />
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14 <param name="indel_input" type="data" format="gd_snp" label="Indel dataset" />
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15 <param name="coverage_input" type="data" format="interval" label="Coverage dataset" />
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16 <param name="annotation_input" type="data" format="interval" label="Annotation dataset" />
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17 <param name="indiv_input" type="data" format="gd_indivs" label="Population Individuals" />
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18
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19 <param name="ref_name" type="select" label="Ref name">
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20 <options from_dataset="indiv_input">
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21 <column name="name" index="1"/>
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22 <column name="value" index="1"/>
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23 <filter type="add_value" name="default" value="default" index="0" />
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24 </options>
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25 </param>
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26
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27 <param name="min_coverage" type="integer" min="1" value="1" label="Minimum coverage" />
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28 </inputs>
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29
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30 <outputs>
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31 <data name="output" format="svg" />
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32 </outputs>
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33
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34 <help>
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35 </help>
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36 </tool>