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24
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1 <tool id="gd_select_individuals" name="Select" version="1.0.0">
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2 <description>individuals from a SNP table</description>
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3
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4 <command interpreter="bash">
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5 echo.bash "$input" "$output"
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6 #for $individual in str($individuals).split(',')
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7 #set $individual_idx = $input.dataset.metadata.individual_names.index($individual)
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8 #set $individual_col = str( $input.dataset.metadata.individual_columns[$individual_idx] )
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9 #set $arg = '\t'.join([$individual_col, $individual, ''])
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10 "$arg"
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11 #end for
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12 </command>
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13
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14 <inputs>
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15 <param name="input" type="data" format="wsf"/>
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16 <param name="individuals" type="select" display="checkboxes" multiple="true" label="Individuals to include">
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17 <options>
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18 <filter type="data_meta" ref="input" key="individual_names" />
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19 </options>
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20 <validator type="no_options" message="You must select at least one individual"/>
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21 </param>
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22 </inputs>
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23
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24 <outputs>
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25 <data name="output" format="ind" label="Individuals from ${input.hid}" />
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26 </outputs>
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27
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28 <tests>
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29 <test>
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30 <param name="input" value="genome_diversity/test_in/sample.wsf" ftype="wsf" />
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31 <param name="individuals" value="PB1,PB2" />
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32 <output name="output" file="genome_diversity/test_in/a.ind" />
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33 </test>
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34 </tests>
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35
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36 <help>
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37 **What it does**
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38
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39 The user selects a SNP table and a set of individuals from the table.
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40 The command saves that list of individuals for use by other Galaxy tools.
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41 </help>
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42 </tool>
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