Mercurial > repos > miller-lab > genome_diversity
comparison modify_snp_table.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 |
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| 9:22fe0154fa54 | 10:9b92372de9f6 |
|---|---|
| 13 "$arg" | 13 "$arg" |
| 14 #end for | 14 #end for |
| 15 </command> | 15 </command> |
| 16 | 16 |
| 17 <inputs> | 17 <inputs> |
| 18 <param name="input" type="data" format="snp" label="SNP table" /> | 18 <param name="input" type="data" format="gdSnp" label="SNP table" /> |
| 19 <param name="p1_input" type="data" format="ind" label="Population individuals" /> | 19 <param name="p1_input" type="data" format="ind" label="Population individuals" /> |
| 20 <conditional name="limit_coverage"> | 20 <conditional name="limit_coverage"> |
| 21 <param name="choice" type="select" format="integer" label="Option"> | 21 <param name="choice" type="select" format="integer" label="Option"> |
| 22 <option value="0" selected="true">add columns to the SNP table</option> | 22 <option value="0" selected="true">add columns to the SNP table</option> |
| 23 <option value="1">discard some SNPs</option> | 23 <option value="1">discard some SNPs</option> |
| 31 </when> | 31 </when> |
| 32 </conditional> | 32 </conditional> |
| 33 </inputs> | 33 </inputs> |
| 34 | 34 |
| 35 <outputs> | 35 <outputs> |
| 36 <data name="output" format="snp" metadata_source="input" /> | 36 <data name="output" format="gdSnp" metadata_source="input" /> |
| 37 </outputs> | 37 </outputs> |
| 38 | 38 |
| 39 <tests> | 39 <tests> |
| 40 <test> | 40 <test> |
| 41 <param name="input" value="test_in/sample.snp" ftype="snp" /> | 41 <param name="input" value="test_in/sample.gdSnp" ftype="gdSnp" /> |
| 42 <param name="p1_input" value="test_in/a.ind" ftype="ind" /> | 42 <param name="p1_input" value="test_in/a.ind" ftype="ind" /> |
| 43 <param name="choice" value="1" /> | 43 <param name="choice" value="1" /> |
| 44 <param name="lo_coverage" value="0" /> | 44 <param name="lo_coverage" value="0" /> |
| 45 <param name="hi_coverage" value="1000" /> | 45 <param name="hi_coverage" value="1000" /> |
| 46 <param name="low_ind_cov" value="3" /> | 46 <param name="low_ind_cov" value="3" /> |
| 47 <param name="lo_quality" value="30" /> | 47 <param name="lo_quality" value="30" /> |
| 48 <output name="output" file="test_out/modify_snp_table/modify.snp" /> | 48 <output name="output" file="test_out/modify_snp_table/modify.gdSnp" /> |
| 49 </test> | 49 </test> |
| 50 </tests> | 50 </tests> |
| 51 | 51 |
| 52 <help> | 52 <help> |
| 53 **What it does** | 53 **What it does** |