Mercurial > repos > dereeper > plink

comparison plink.xml @ 0:fe39a4677281 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author dereeper
date Fri, 05 Aug 2016 09:46:55 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:fe39a4677281
1 <tool id="sniplay_plink" name="plink" version="1.0">
2
3 <!-- [REQUIRED] Tool description displayed after the tool name -->
4 <description> - Filter large VCF file</description>
5
6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
7 <requirements>
8 <requirement type="binary">perl</requirement>
9 <requirement type="package" version="1.90">plink</requirement>
10 </requirements>
11
12
13 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
14 <stdio>
15 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
16 <exit_code range="1:" level="fatal" />
17 </stdio>
18
19 <!-- [REQUIRED] The command to execute -->
20 <command interpreter="bash">
21 ./plink.sh $vcf $fileout $filelog $frequency $max_freq $allow_missing $type_p $bound_start $bound_end
22 #if str( $samples ) == "":
23 'None'
24 #else
25 $samples
26 #end if
27 #if str( $chromosomes ) == "":
28 'None'
29 #else
30 $chromosomes
31 #end if
32 </command>
33 <code file="find_indiv.py"/>
34 <!-- [REQUIRED] Input files and tool parameters -->
35 <inputs>
36 <param name="vcf" type="data" format="vcf" optional="false" label="VCF input" />
37
38 <param name="samples" type="select" label="Samples" multiple="true" dynamic_options="get_field_samples_options(vcf)" help="Samples to be analyzed." />
39 <!--<param name="samples" type="text" label="Samples" multiple="true" help="Samples to be analyzed." />-->
40 <!--<param name="chromosomes" type="select" label="Chromosomes" multiple="true" dynamic_options="get_field_chrs_options(input)" help="Chromosomes to be analyzed." />-->
41 <param name="frequency" type="float" value="0" label="Minimum MAF" help="Minimum Minor Allele Frequency (MAF)" />
42 <param name="max_freq" type="float" value="0.5" label="Maximum MAF" help="Maximum Minor Allele Frequency (MAF)" />
43 <param name="allow_missing" type="float" value="1" min="0" max="1" label="Missing data proportion" help="Allowed missing data proportion per site. Must be comprised between 0 and 1." />
44 <param name="type_p" type="select" label="Polymorphisms" help="Type of polymorphisms to keep." >
45 <option value="ALL" selected="true">All</option>
46 <option value="SNP">SNPs only</option>
47 </param>
48 <param name="chromosomes" type="text" label="Chromosomes" multiple="true" help="Chromosomes to be analyzed. (Comma-separated list of reference sequences, ex: Chr1,Chr2)" />
49 <param name="bound_start" type="integer" value="1" label="Lower bound" help="Lower bound for a range of sites to be processed." />
50 <param name="bound_end" type="integer" value="100000000" label="Upper bound" help="Upper bound for a range of sites to be processed." />
51 </inputs>
52
53 <!-- [REQUIRED] Output files -->
54 <outputs>
55 <data name="fileout" format="vcf" label="Plink filtered VCF"/>
56 <data name="filelog" format="txt" label="Plink logfile" />
57 </outputs>
58
59
60 <!-- [OPTIONAL] Help displayed in Galaxy -->
61 <help>
62
63 .. class:: infomark
64
65 **Authors** Shaun Purcell : plink_
66
67 .. _plink: https://www.cog-genomics.org/plink2
68
69 | **Please cite** "PLINK: a toolset for whole-genome association and population-based linkage analysis.", Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC, **American Journal of Human Genetics**, 2007
70
71 .. class:: infomark
72
73 **Galaxy integration** Dereeper Alexis (IRD), Andres Gwendoline (Institut Français de Bioinformatique).
74
75 .. class:: infomark
76
77 **Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr
78
79
80
81 </help>
82
83 </tool>