Mercurial > repos > miller-lab > genome_diversity
annotate select_individuals.xml @ 10:9b92372de9f6
rename snp to gsSnp, sap to gdSap
| author | Richard Burhans <burhans@bx.psu.edu> |
|---|---|
| date | Tue, 04 Sep 2012 12:49:53 -0400 |
| parents | e29f4d801bb0 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="gd_select_individuals" name="Select" version="1.0.0"> |
| 2 <description>individuals from a SNP table</description> | |
| 3 | |
| 4 <command interpreter="bash"> | |
| 5 echo.bash "$input" "$output" | |
| 6 #for $individual in str($individuals).split(',') | |
| 7 #set $individual_idx = $input.dataset.metadata.individual_names.index($individual) | |
| 8 #set $individual_col = str( $input.dataset.metadata.individual_columns[$individual_idx] ) | |
| 9 #set $arg = '\t'.join([$individual_col, $individual, '']) | |
| 10 "$arg" | |
| 11 #end for | |
| 12 </command> | |
| 13 | |
| 14 <inputs> | |
|
10
9b92372de9f6
rename snp to gsSnp, sap to gdSap
Richard Burhans <burhans@bx.psu.edu>
parents:
7
diff
changeset
|
15 <param name="input" type="data" format="gdSnp"/> |
| 0 | 16 <param name="individuals" type="select" display="checkboxes" multiple="true" label="Individuals to include"> |
| 17 <options> | |
| 18 <filter type="data_meta" ref="input" key="individual_names" /> | |
| 19 </options> | |
| 20 <validator type="no_options" message="You must select at least one individual"/> | |
| 21 </param> | |
| 22 </inputs> | |
| 23 | |
| 24 <outputs> | |
| 25 <data name="output" format="ind" label="Individuals from ${input.hid}" /> | |
| 26 </outputs> | |
| 27 | |
| 28 <tests> | |
| 29 <test> | |
|
10
9b92372de9f6
rename snp to gsSnp, sap to gdSap
Richard Burhans <burhans@bx.psu.edu>
parents:
7
diff
changeset
|
30 <param name="input" value="test_in/sample.gdSnp" ftype="gdSnp" /> |
| 0 | 31 <param name="individuals" value="PB1,PB2" /> |
| 32 <output name="output" file="test_in/a.ind" /> | |
| 33 </test> | |
| 34 </tests> | |
| 35 | |
| 36 <help> | |
| 37 **What it does** | |
| 38 | |
| 39 The user selects a SNP table and a set of individuals from the table. | |
| 40 The command saves that list of individuals for use by other Galaxy tools. | |
| 41 </help> | |
| 42 </tool> |