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comparison dpmix.xml @ 24:248b06e86022

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Added gd_genotype datatype. Modified tools to support new datatype.
author Richard Burhans <burhans@bx.psu.edu>
date Tue, 28 May 2013 16:24:19 -0400
parents d6b961721037
children cba0d7a63b82
comparison
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23:66a183c44dd5 24:248b06e86022
1 <tool id="gd_dpmix" name="Admixture" version="1.0.0"> 1 <tool id="gd_dpmix" name="Admixture" version="1.1.0">
2 <description>: Map genomic intervals resembling specified ancestral populations</description> 2 <description>: Map genomic intervals resembling specified ancestral populations</description>
3 3
4 <command interpreter="python"> 4 <command interpreter="python">
5 dpmix.py "$input" "$data_source" "$switch_penalty" "$ap1_input" "$ap2_input" "$p_input" "$output" "$output2" "$output2.files_path" "$input.dataset.metadata.dbkey" "$input.dataset.metadata.ref" "$GALAXY_DATA_INDEX_DIR" "gd.heterochromatic.loc" 5 dpmix.py "$input"
6 #if $input_type.choice == '0'
7 "gd_snp" "$input_type.data_source"
8 #else if $input_type.choice == '1'
9 "gd_genotype" "1"
10 #end if
11 "$switch_penalty" "$ap1_input" "$ap2_input" "$p_input" "$output" "$output2" "$output2.files_path" "$input.dataset.metadata.dbkey" "$input.dataset.metadata.ref" "$GALAXY_DATA_INDEX_DIR" "gd.heterochromatic.loc"
6 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns) 12 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
7 #set $arg = '%s:%s' % ($individual_col, $individual) 13 #set $arg = '%s:%s' % ($individual_col, $individual)
8 "$arg" 14 "$arg"
9 #end for 15 #end for
10 </command> 16 </command>
11 17
12 <inputs> 18 <inputs>
13 <param name="input" type="data" format="gd_snp" label="SNP dataset"> 19 <conditional name="input_type">
14 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" /> 20 <param name="choice" type="select" format="integer" label="Input format">
15 </param> 21 <option value="0" selected="true">gd_snp</option>
22 <option value="1">gd_genotype</option>
23 </param>
24 <when value="0">
25 <param name="input" type="data" format="gd_snp" label="SNP dataset">
26 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" />
27 </param>
28
29 <param name="data_source" type="select" format="integer" label="Similarity metric">
30 <option value="0">sequence coverage</option>
31 <option value="1" selected="true">estimated genotype</option>
32 </param>
33 </when>
34 <when value="1">
35 <param name="input" type="data" format="gd_genotype" label="Genotype dataset">
36 <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" />
37 </param>
38 </when>
39 </conditional>
40
16 <param name="ap1_input" type="data" format="gd_indivs" label="Ancestral population 1 individuals" /> 41 <param name="ap1_input" type="data" format="gd_indivs" label="Ancestral population 1 individuals" />
17 <param name="ap2_input" type="data" format="gd_indivs" label="Ancestral population 2 individuals" /> 42 <param name="ap2_input" type="data" format="gd_indivs" label="Ancestral population 2 individuals" />
18 <param name="p_input" type="data" format="gd_indivs" label="Potentially admixed individuals" /> 43 <param name="p_input" type="data" format="gd_indivs" label="Potentially admixed individuals" />
19
20 <param name="data_source" type="select" format="integer" label="Similarity metric">
21 <option value="0" selected="true">sequence coverage</option>
22 <option value="1">estimated genotype</option>
23 </param>
24 44
25 <param name="switch_penalty" type="integer" min="0" value="10" label="Genotype switch penalty" help="Note: typically between 10 and 100."/> 45 <param name="switch_penalty" type="integer" min="0" value="10" label="Genotype switch penalty" help="Note: typically between 10 and 100."/>
26 </inputs> 46 </inputs>
27 47
28 <outputs> 48 <outputs>
50 70
51 <help> 71 <help>
52 72
53 **Dataset formats** 73 **Dataset formats**
54 74
55 The input datasets are in gd_snp_ and gd_indivs_ formats. It is important for 75 The input datasets are in gd_snp_, gd_genotype_, and gd_indivs_ formats. It is important for
56 the Individuals datasets to have unique names and for there to be no overlap 76 the Individuals datasets to have unique names and for there to be no overlap
57 between the two populations. Rename these datasets if 77 between the two populations. Rename these datasets if
58 needed to make them unique. 78 needed to make them unique.
59 There are two output datasets, one tabular_ and one composite. (`Dataset missing?`_) 79 There are two output datasets, one tabular_ and one composite. (`Dataset missing?`_)
60 80
61 .. _gd_snp: ./static/formatHelp.html#gd_snp 81 .. _gd_snp: ./static/formatHelp.html#gd_snp
82 .. _gd_genotype: ./static/formatHelp.html#gd_genotype
62 .. _gd_indivs: ./static/formatHelp.html#gd_indivs 83 .. _gd_indivs: ./static/formatHelp.html#gd_indivs
63 .. _tabular: ./static/formatHelp.html#tab 84 .. _tabular: ./static/formatHelp.html#tab
64 .. _Dataset missing?: ./static/formatHelp.html 85 .. _Dataset missing?: ./static/formatHelp.html
65 86
66 ----- 87 -----