Mercurial > repos > miller-lab > genome_diversity

comparison diversity_pi.xml @ 27:8997f2ca8c7a

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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_diversity_pi" name="Diversity" version="1.0.0"> 1 <tool id="gd_diversity_pi" name="Diversity" version="1.0.0">
2 <description>&amp;pi;</description> 2 <description>&amp;pi;</description>
3 3
4 <command interpreter="python"> 4 <command interpreter="python">
5 diversity_pi.py "$input" "$coverage_input" "$indiv_input" "$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 diversity_pi.py '$input' '$coverage_input' '$indiv_input' '$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="coverage_input" type="data" format="interval" label="Coverage dataset" /> 19 <param name="coverage_input" type="data" format="interval" label="Coverage dataset" />