Mercurial > repos > rico > test_single_file
changeset 24:81edc38bf5b1
Uploaded
author | rico |
---|---|
date | Thu, 05 Apr 2012 15:22:09 -0400 |
parents | 2d4aac68471a |
children | deae8671505e |
files | select_individuals.xml |
diffstat | 1 files changed, 42 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/select_individuals.xml Thu Apr 05 15:22:09 2012 -0400 @@ -0,0 +1,42 @@ +<tool id="gd_select_individuals" name="Select" version="1.0.0"> + <description>individuals from a SNP table</description> + + <command interpreter="bash"> + echo.bash "$input" "$output" + #for $individual in str($individuals).split(',') + #set $individual_idx = $input.dataset.metadata.individual_names.index($individual) + #set $individual_col = str( $input.dataset.metadata.individual_columns[$individual_idx] ) + #set $arg = '\t'.join([$individual_col, $individual, '']) + "$arg" + #end for + </command> + + <inputs> + <param name="input" type="data" format="wsf"/> + <param name="individuals" type="select" display="checkboxes" multiple="true" label="Individuals to include"> + <options> + <filter type="data_meta" ref="input" key="individual_names" /> + </options> + <validator type="no_options" message="You must select at least one individual"/> + </param> + </inputs> + + <outputs> + <data name="output" format="ind" label="Individuals from ${input.hid}" /> + </outputs> + + <tests> + <test> + <param name="input" value="genome_diversity/test_in/sample.wsf" ftype="wsf" /> + <param name="individuals" value="PB1,PB2" /> + <output name="output" file="genome_diversity/test_in/a.ind" /> + </test> + </tests> + + <help> +**What it does** + +The user selects a SNP table and a set of individuals from the table. +The command saves that list of individuals for use by other Galaxy tools. + </help> +</tool>