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comparison dpmix.xml @ 31:a631c2f6d913

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Update to Miller Lab devshed revision 3c4110ffacc3
author Richard Burhans <burhans@bx.psu.edu>
date Fri, 20 Sep 2013 13:25:27 -0400
parents 4188853b940b
children
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30:4188853b940b 31:a631c2f6d913
1 <tool id="gd_dpmix" name="Admixture" version="1.1.0"> 1 <tool id="gd_dpmix" name="Admixture" version="1.2.0">
2 <description>: Map genomic intervals resembling specified source populations</description> 2 <description>: Map genomic intervals resembling specified source populations</description>
3 3
4 <command interpreter="python"> 4 <command interpreter="python">
5 #import json 5 #import json
6 #import base64 6 #import base64
29 #else if $user_het.choice == '1' 29 #else if $user_het.choice == '1'
30 #set $het_arg = $user_het.het_file 30 #set $het_arg = $user_het.het_file
31 #else if $user_het.choice == '2' 31 #else if $user_het.choice == '2'
32 #set $het_arg = 'use_none' 32 #set $het_arg = 'use_none'
33 #end if 33 #end if
34 '$switch_penalty' '$ap1_input' '$ap1_input.name' '$ap2_input' '$ap2_input.name' '$ap3_arg' '$ap3_name_arg' '$p_input' '$output' '$output2' '$output2.files_path' '$input.dataset.metadata.dbkey' '$input.dataset.metadata.ref' '$GALAXY_DATA_INDEX_DIR' 'gd.heterochromatic.loc' '$ind_arg' '$het_arg' '1' 34 '$switch_penalty'
35 #if $use_reference.choice == '0'
36 '$ap1_input' '$ap1_input.name'
37 #else if $use_reference.choice == '1'
38 '/dev/null' 'reference'
39 #end if
40 '$ap2_input' '$ap2_input.name' '$ap3_arg' '$ap3_name_arg' '$p_input' '$output' '$output2' '$output2.files_path' '$input.dataset.metadata.dbkey' '$input.dataset.metadata.ref' '$GALAXY_DATA_INDEX_DIR' 'gd.heterochromatic.loc' '$ind_arg' '$het_arg' '$add_logs'
35 </command> 41 </command>
36 42
37 <inputs> 43 <inputs>
38 <conditional name="input_type"> 44 <conditional name="input_type">
39 <param name="choice" type="select" format="integer" label="Input format"> 45 <param name="choice" type="select" format="integer" label="Input format">
55 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" /> 61 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" />
56 </param> 62 </param>
57 </when> 63 </when>
58 </conditional> 64 </conditional>
59 65
60 <param name="ap1_input" type="data" format="gd_indivs" label="Source population 1 individuals" /> 66 <conditional name="use_reference">
67 <param name="choice" type="select" format="integer" label="History item or Reference sequence">
68 <option value="0" selected="true">History item</option>
69 <option value="1">Reference sequence</option>
70 </param>
71 <when value="0">
72 <param name="ap1_input" type="data" format="gd_indivs" label="Source population 1 individuals" />
73 </when>
74 <when value="1" />
75 </conditional>
76
61 <param name="ap2_input" type="data" format="gd_indivs" label="Source population 2 individuals" /> 77 <param name="ap2_input" type="data" format="gd_indivs" label="Source population 2 individuals" />
62 78
63 <conditional name="third_pop"> 79 <conditional name="third_pop">
64 <param name="choice" type="select" format="integer" label="Include third source population"> 80 <param name="choice" type="select" format="integer" label="Include third source population">
65 <option value="0" selected="true">no</option> 81 <option value="0" selected="true">no</option>
85 <when value="1"> 101 <when value="1">
86 <param name="het_file" type="data" format="txt" label="Heterochromatin dataset" /> 102 <param name="het_file" type="data" format="txt" label="Heterochromatin dataset" />
87 </when> 103 </when>
88 </conditional> 104 </conditional>
89 105
90 <!--
91 <param name="add_logs" type="select" format="integer" label="Probabilities"> 106 <param name="add_logs" type="select" format="integer" label="Probabilities">
92 <option value="1" selected="true">add logs of probabilities</option> 107 <option value="1" selected="true">add logs of probabilities</option>
93 <option value="0">add probabilities</option> 108 <option value="0">add probabilities</option>
94 </param> 109 </param>
95 -->
96 110
97 </inputs> 111 </inputs>
98 112
99 <outputs> 113 <outputs>
100 <data name="output" format="tabular" /> 114 <data name="output" format="tabular" />
101 <data name="output2" format="html" /> 115 <data name="output2" format="html" />
102 </outputs> 116 </outputs>
117
118 <requirements>
119 <requirement type="package" version="0.1">gd_c_tools</requirement>
120 <requirement type="package" version="1.2.1">matplotlib</requirement>
121 </requirements>
103 122
104 <tests> 123 <tests>
105 <test> 124 <test>
106 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" /> 125 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />
107 <param name="ap1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" /> 126 <param name="ap1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" />