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comparison nucleotide_diversity_pi.xml @ 27:8997f2ca8c7a

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Update to Miller Lab devshed revision bae0d3306d3b
author Richard Burhans <burhans@bx.psu.edu>
date Mon, 15 Jul 2013 10:47:35 -0400
parents 95a05c1ef5d5
children a631c2f6d913
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26:91e835060ad2 27:8997f2ca8c7a
1 <tool id="gd_nucleotide_diversity_pi" name="Nucleotide Diversity" version="1.0.0"> 1 <tool id="gd_nucleotide_diversity_pi" name="Nucleotide Diversity" version="1.0.0">
2 <description>: &amp;pi; and &amp;theta;</description> 2 <description>: &amp;pi; and &amp;theta;</description>
3 3
4 <command interpreter="python"> 4 <command interpreter="python">
5 nucleotide_diversity_pi.py "$saps" "$snps" "$intervals" "$indivs" "$output" 5 #import json
6 #for $individual_name, $individual_col in zip($snps.dataset.metadata.individual_names, $snps.dataset.metadata.individual_columns) 6 #import base64
7 #set $arg = '%s:%s' % ($individual_col, $individual_name) 7 #import zlib
8 "$arg" 8 #set $ind_names = $snps.dataset.metadata.individual_names
9 #end for 9 #set $ind_colms = $snps.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 nucleotide_diversity_pi.py '$saps' '$snps' '$intervals' '$indivs' '$output' '$ind_arg'
10 </command> 15 </command>
11 16
12 <inputs> 17 <inputs>
13 <param name="saps" type="data" format="gd_sap" label="SAP Dataset" /> 18 <param name="saps" type="data" format="gd_sap" label="SAP Dataset" />
14 <param name="snps" type="data" format="gd_snp" label="SNP Dataset" /> 19 <param name="snps" type="data" format="gd_snp" label="SNP Dataset" />