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author gdroc
date Mon, 05 Sep 2016 07:09:43 -0400
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1 <tool id="rave" name="RAVE" version="1.0">
2 <description>- Rapid Allelic Variant Extractor</description>
3 <!-- Required for the tool to work -->
4 <!-- Wrapper compatible with Plink v1.90b3k -->
5 <requirements>
6 <requirement type="binary">perl</requirement>
7 <requirement type="package" version="1.90">plink</requirement>
8 </requirements>
9 <stdio>
10 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
11 <exit_code range="1:" level="fatal" />
12 </stdio>
13 <command interpreter="perl">./rave.pl
14 --tool_directory $__tool_directory__
15 --bfile ${plinkdb.fields.path}
16 #if $filter_var.subpopulation == 'yes':
17 --keep ${filter_var.population_select.fields.path}
18 #end if
19 #if $filter_individuals.individual == 'file':
20 --keep ${filter_individuals.variety_file}
21 #else if $filter_individuals.individual == 'list':
22 --variety_list "${filter_individuals.variety_list}"
23 #end if
24 #if $filter_loc.location == 'file':
25 --extract range ${filter_loc.location_file}
26 #else if $filter_loc.location == 'list':
27 --location_list "${filter_loc.location_list}"
28 #end if
29 #if $filter_locus.locus == 'file':
30 --extract range ${filter_locus.locus_file}
31 #else if $filter_locus.locus == 'list':
32 --locus_list "${filter_locus.locus_list}"
33 #end if
34 --maf $maf
35 --output_format $output_format
36 --out $plink_output
37 </command>
38 <inputs>
39 <param name="plinkdb" type="select" label="Select plink DB" help="If your dataset of interest is not listed, contact us">
40 <options from_data_table="plink">
41 <filter type="sort_by" column="1"/>
42 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
43 </options>
44 </param>
45 <param name="maf" type="float" value="0.01" label="Minor allele frequencies" help="--maf filters out all variants with minor allele frequency below the provided threshold (default 0.01)" />
46 <conditional name="filter_var">
47 <param name="subpopulation" type="select" label="Filter SNP based on subpopulation">
48 <option value="no">No</option>
49 <option value="yes">Yes</option>
50 </param>
51 <when value="no"/>
52 <when value="yes">
53 <param name="population_select" type="select" display="radio" label="Subpopulation">
54 <options from_data_table="subpopulation">
55 <filter type="sort_by" column="1"/>
56 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
57 </options>
58 </param>
59 </when>
60 </conditional>
61 <conditional name="filter_individuals">
62 <param name="individual" type="select" label="Filter SNP based on individual (This parameter can be empty)">
63 <option value="file">Upload a file from your history</option>
64 <option value="list">Cut &amp; Paste your list</option>
65 </param>
66 <when value="file">
67 <param name="variety_file" format="txt" type="data" optional="true" label="Variety list from file" help="One range per line, whitespace-separated (i.e : B001 B001)"/>
68 </when>
69 <when value="list">
70 <param name="variety_list" type="text" area="True" size="5x15" label="Variety list from area" help="One range per line, whitespace-separated (i.e : B001 B001)"/>
71 </when>
72 </conditional>
73
74 <conditional name="filter_loc">
75 <param name="location" type="select" label="Filter SNP based on genomic location (This parameter can be empty)">
76 <option value="file">Upload a file from your history</option>
77 <option value="list">Cut &amp; Paste your list</option>
78 </param>
79 <when value="file">
80 <param name="location_file" format="txt" type="data" optional="true" label="Range list from file" help="One range per line, whitespace-separated (i.e : 1 100000 120000 chr1)"/>
81 </when>
82 <when value="list">
83 <param name="location_list" type="text" area="True" size="5x15" label="Range list from area" help="One range per line, whitespace-separated (i.e : 1 100000 120000 chr1)"/>
84 </when>
85 </conditional>
86 <conditional name="filter_locus">
87 <param name="locus" type="select" label="Filter SNP based on specific locus (This parameter can be empty)">
88 <option value="file">Upload a file from your history</option>
89 <option value="list">Cut &amp; Paste your list</option>
90 </param>
91 <when value="file">
92 <param name="locus_file" format="txt" type="data" optional="true" label="Locus file (MSU locus name)" help="One locus per line (i.e : LOC_Os01g13620)"/>
93 </when>
94 <when value="list">
95 <param name="locus_list" type="text" area="True" size="5x15" label="Locus list from area (MSU locus name)" help="One range per line (i.e : LOC_Os01g13620)"/>
96 </when>
97 </conditional>
98 <param name="output_format" type="select" label="Select output format" help="--recode creates a new text fileset, after applying sample/variant filters and other operations.">
99 <option value="vcf">VCF</option>
100 <option value="bgz">VCF bgzip</option>
101 <option value="structure">Structure</option>
102 <option value="beagle">Beagle</option>
103 <option value="fastphase">fastPHASE</option>
104 </param>
105 </inputs>
106 <outputs>
107 <data format="vcf" name="plink_output" label="${output_format} output" />
108 <change_format>
109 <when input="output_format" value="structure" format="txt" />
110 <when input="output_format" value="beagle" format="bgzip" />
111 <when input="output_format" value="fastphase" format="bgzip" />
112 <when input="output_format" value="bgz" format="bgzip" />
113 </change_format>
114 <!--output.recode.strct_in-->
115 </outputs>
116 <help>
117
118 ==========
119 Overview
120 ==========
121
122 **PLINK Overview**
123
124 PLINK2
125 Majority of information in this page is derived from an excellent PLINK_ manual written by Shaun Purcell, Christopher Chang.
126
127 .. _PLINK: https://www.cog-genomics.org/plink2
128
129 **Input formats**
130
131 Plink binary file (bed/bim/fam)
132
133 Example : Plink binary for High Density Rice Array (HDRA, 700k SNPs, McCouch SR et al. Nat Commun 7, 10532)
134
135 See Plink genotype data bundle available at https://ricediversity.org/data/
136
137 -----
138
139 .. class:: infomark
140
141 **Galaxy integration** Droc Gaetan (CIRAD), Ruiz Manuel (CIRAD).
142
143 .. class:: infomark
144
145 **Support** For any questions about Galaxy integration, please send an e-mail to southgreen@cirad.fr
146
147 .. class:: infomark
148
149 **Program encapsulated in Galaxy by South Green**
150
151 </help>
152 <citations>
153 <citation type="doi">10.1186/s13742-015-0047-8</citation>
154 <citation type="doi">10.1086/519795</citation>
155 </citations>
156 </tool>
157