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comparison average_fst.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 248b06e86022
children a631c2f6d913
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26:91e835060ad2 27:8997f2ca8c7a
1 <tool id="gd_average_fst" name="Overall FST" version="1.3.0"> 1 <tool id="gd_average_fst" name="Overall FST" version="1.3.0">
2 <description>: Estimate the relative fixation index between two populations</description> 2 <description>: Estimate the relative fixation index between two populations</description>
3 3
4 <command interpreter="python"> 4 <command interpreter="python">
5 average_fst.py "$input" "$p1_input" "$p2_input" 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 average_fst.py '$input' '$p1_input' '$p2_input'
6 #if $input_type.choice == '0' 15 #if $input_type.choice == '0'
7 "gd_snp" "$input_type.data_source.choice" 16 'gd_snp' '$input_type.data_source.choice'
8 #if $input_type.data_source.choice == '0' 17 #if $input_type.data_source.choice == '0'
9 "$input_type.data_source.min_value" 18 '$input_type.data_source.min_value'
10 #else if $input_type.data_source.choice == '1' 19 #else if $input_type.data_source.choice == '1'
11 "1" 20 '1'
12 #end if 21 #end if
13 #else if $input_type.choice == '1' 22 #else if $input_type.choice == '1'
14 "gd_genotype" "1" "1" 23 'gd_genotype' '1' '1'
15 #end if 24 #end if
16 "$discard_fixed" "$output" 25 '$discard_fixed' '$output'
17 #if $use_randomization.choice == '0' 26 #if $use_randomization.choice == '0'
18 "0" "/dev/null" 27 '0' '/dev/null'
19 #else if $use_randomization.choice == '1' 28 #else if $use_randomization.choice == '1'
20 "$use_randomization.shuffles" "$use_randomization.p0_input" 29 '$use_randomization.shuffles' '$use_randomization.p0_input'
21 #end if 30 #end if
22 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns) 31 '$ind_arg'
23 #set $arg = '%s:%s' % ($individual_col, $individual)
24 "$arg"
25 #end for
26 </command> 32 </command>
27 33
28 <inputs> 34 <inputs>
29 <conditional name="input_type"> 35 <conditional name="input_type">
30 <param name="choice" type="select" format="integer" label="Input format"> 36 <param name="choice" type="select" format="integer" label="Input format">