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comparison coverage_distributions.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 f04f40a36cc8
children a631c2f6d913
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26:91e835060ad2 27:8997f2ca8c7a
1 <tool id="gd_coverage_distributions" name="Coverage Distributions" version="1.0.0"> 1 <tool id="gd_coverage_distributions" name="Coverage Distributions" version="1.0.0">
2 <description>: Examine sequence coverage for SNPs</description> 2 <description>: Examine sequence coverage for SNPs</description>
3 3
4 <command interpreter="python"> 4 <command interpreter="python">
5 coverage_distributions.py "$input" "0" "$output" "$output.files_path" 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 coverage_distributions.py '$input' '0' '$output' '$output.files_path' '$ind_arg'
6 #if $individuals.choice == '0' 15 #if $individuals.choice == '0'
7 "all_individuals" 16 'all_individuals'
8 #else if $individuals.choice == '1' 17 #else if $individuals.choice == '1'
9 #set $arg = 'individuals:%s' % str($individuals.p1_input) 18 #set $arg = 'individuals:%s' % str($individuals.p1_input)
10 "$arg" 19 '$arg'
11 #else if $individuals.choice == '2' 20 #else if $individuals.choice == '2'
12 #for $population in $individuals.populations 21 #for $population in $individuals.populations
13 #set $arg = 'population:%s:%s' % (str($population.p_input), str($population.p_input.name)) 22 #set $arg = 'population:%s:%s' % (str($population.p_input), str($population.p_input.name))
14 "$arg" 23 '$arg'
15 #end for 24 #end for
16 #end if 25 #end if
17 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
18 #set $individual_arg = 'individual:%s:%s' % ($individual_col, $individual)
19 "$individual_arg"
20 #end for
21 </command> 26 </command>
22 27
23 <inputs> 28 <inputs>
24 <param name="input" type="data" format="gd_snp" label="SNP dataset" /> 29 <param name="input" type="data" format="gd_snp" label="SNP dataset" />
25 30