Mercurial > repos > miller-lab > genome_diversity
comparison draw_variants.xml @ 27:8997f2ca8c7a
Update to Miller Lab devshed revision bae0d3306d3b
author | Richard Burhans <burhans@bx.psu.edu> |
---|---|
date | Mon, 15 Jul 2013 10:47:35 -0400 |
parents | 248b06e86022 |
children | a631c2f6d913 |
comparison
equal
deleted
inserted
replaced
26:91e835060ad2 | 27:8997f2ca8c7a |
---|---|
1 <tool id="gd_draw_variants" name="Draw" version="1.0.0"> | 1 <tool id="gd_draw_variants" name="Draw" version="1.0.0"> |
2 <description>variants</description> | 2 <description>variants</description> |
3 | 3 |
4 <command interpreter="python"> | 4 <command interpreter="python"> |
5 draw_variants.py "$input" "$indel_input" "$coverage_input" "$annotation_input" "$indiv_input" "$ref_name" "$min_coverage" "$output" | 5 #import json |
6 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns) | 6 #import base64 |
7 #set $arg = '%s:%s' % ($individual_col, $individual) | 7 #import zlib |
8 "$arg" | 8 #set $ind_names = $input.dataset.metadata.individual_names |
9 #end for | 9 #set $ind_colms = $input.dataset.metadata.individual_columns |
10 #set $ind_dict = dict(zip($ind_names, $ind_colms)) | |
11 #set $ind_json = json.dumps($ind_dict, separators=(',',':')) | |
12 #set $ind_comp = zlib.compress($ind_json, 9) | |
13 #set $ind_arg = base64.b64encode($ind_comp) | |
14 draw_variants.py '$input' '$indel_input' '$coverage_input' '$annotation_input' '$indiv_input' '$ref_name' '$min_coverage' '$output' '$ind_arg' | |
10 </command> | 15 </command> |
11 | 16 |
12 <inputs> | 17 <inputs> |
13 <param name="input" type="data" format="gd_snp" label="SNP dataset" /> | 18 <param name="input" type="data" format="gd_snp" label="SNP dataset" /> |
14 <param name="indel_input" type="data" format="gd_snp" label="Indel dataset" /> | 19 <param name="indel_input" type="data" format="gd_snp" label="Indel dataset" /> |