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comparison aggregate_gd_indivs.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 91e835060ad2
children a631c2f6d913
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26:91e835060ad2 27:8997f2ca8c7a
1 <tool id="gd_sum_gd_snp" name="Aggregate Individuals" version="1.1.0"> 1 <tool id="gd_sum_gd_snp" name="Aggregate Individuals" version="1.1.0">
2 <description>: Append summary columns for a population</description> 2 <description>: Append summary columns for a population</description>
3 3
4 <command interpreter="python"> 4 <command interpreter="python">
5 aggregate_gd_indivs.py "$input" "$p1_input" "$output" 5 #import json
6 #import base64
7 #import zlib
8 #set $ind_names = $input.dataset.metadata.individual_names
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 aggregate_gd_indivs.py '$input' '$p1_input' '$output'
6 #if $input_type.choice == '0' 15 #if $input_type.choice == '0'
7 "gd_snp" 16 'gd_snp'
8 #else if $input_type.choice == '1' 17 #else if $input_type.choice == '1'
9 "gd_genotype" 18 'gd_genotype'
10 #end if 19 #end if
11 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns) 20 '$ind_arg'
12 #set $arg = '%s:%s' % ($individual_col, $individual)
13 "$arg"
14 #end for
15 </command> 21 </command>
16 22
17 <inputs> 23 <inputs>
18 24
19 <conditional name="input_type"> 25 <conditional name="input_type">