Mercurial > repos > dereeper > plink

annotate plink.xml @ 8:f733bf4f49ca draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
author dereeper
date Mon, 16 Apr 2018 08:58:55 -0400
parents d6a7be1b5adb
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
1 <tool id="sniplay_plink" name="PLINK" version="2.0.0">
4
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
2
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
3 <!-- [REQUIRED] Tool description displayed after the tool name -->
8
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
4 <description>Filter large VCF file</description>
4
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
5
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
7 <requirements>
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
8 <requirement type="binary">perl</requirement>
7
d6a7be1b5adb Uploaded
dereeper
parents: 4
diff changeset
9 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
4
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
10 <requirement type="package" version="1.90b4">plink</requirement>
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
11 </requirements>
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
12
7
d6a7be1b5adb Uploaded
dereeper
parents: 4
diff changeset
13 <code file="find_indiv.py"/>
4
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
14
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
15 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
16 <stdio>
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
17 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
18 <exit_code range="1:" level="fatal" />
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
19 </stdio>
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
20
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
21 <!-- [REQUIRED] The command to execute -->
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
22 <command interpreter="bash">
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
23 ./plink.sh $vcf $fileout $filelog $frequency $max_freq $allow_missing $type_p $bound_start $bound_end
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
24 #if str( $samples ) == "":
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
25 'None'
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
26 #else
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
27 $samples
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
28 #end if
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
29 #if str( $chromosomes ) == "":
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
30 'None'
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
31 #else
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
32 $chromosomes
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
33 #end if
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
34 </command>
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
35 <!-- [REQUIRED] Input files and tool parameters -->
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
36 <inputs>
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
37 <param name="vcf" type="data" format="vcf" optional="false" label="VCF input" />
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
38
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
39 <param name="samples" type="select" label="Samples" multiple="true" dynamic_options="get_field_samples_options(vcf)" help="Samples to be analyzed." />
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
40 <!--<param name="samples" type="text" label="Samples" multiple="true" help="Samples to be analyzed." />-->
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
41 <!--<param name="chromosomes" type="select" label="Chromosomes" multiple="true" dynamic_options="get_field_chrs_options(input)" help="Chromosomes to be analyzed." />-->
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
42 <param name="frequency" type="float" value="0" label="Minimum MAF" help="Minimum Minor Allele Frequency (MAF)" />
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
43 <param name="max_freq" type="float" value="0.5" label="Maximum MAF" help="Maximum Minor Allele Frequency (MAF)" />
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
44 <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." />
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
45 <param name="type_p" type="select" label="Polymorphisms" help="Type of polymorphisms to keep." >
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
46 <option value="ALL" selected="true">All</option>
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
47 <option value="SNP">SNPs only</option>
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
48 </param>
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
49 <param name="chromosomes" type="text" label="Chromosomes" multiple="true" help="Chromosomes to be analyzed. (Comma-separated list of reference sequences, ex: Chr1,Chr2)" />
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
50 <param name="bound_start" type="integer" value="1" label="Lower bound" help="Lower bound for a range of sites to be processed." />
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
51 <param name="bound_end" type="integer" value="100000000" label="Upper bound" help="Upper bound for a range of sites to be processed." />
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
52 </inputs>
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
53
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
54 <!-- [REQUIRED] Output files -->
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
55 <outputs>
8
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
56 <data name="fileout" format="vcf" label="PLINK filtered VCF"/>
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
57 <data name="filelog" format="txt" label="PLINK logfile" />
4
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
58 </outputs>
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
59
7
d6a7be1b5adb Uploaded
dereeper
parents: 4
diff changeset
60 <tests>
d6a7be1b5adb Uploaded
dereeper
parents: 4
diff changeset
61 <test>
8
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
62 <param name="vcf" value="plink_input.vcf"/>
7
d6a7be1b5adb Uploaded
dereeper
parents: 4
diff changeset
63 <param name="samples" value="AZUCENA,BULUPANDAK,GIZA171,IAC165,KHAODAM,M202,MOROBEREKAN,NIPPONBARE.D,62667,63-104,ARAGUAIA,ARIAS,ARROZCEBADA,BABER,BAGANANASALAO,BAKUNGH,BENGALYVAKARINA,BICOBRANCO,BINULAWAN,CAIAPO,CANAROXA,CANELADEFERRO,CHALOYOE,CHAPHUMA,CICIHBETON,CIRAD358,CIRAD392,CIRAD394,CIRAD403,CIRAD409,CIRAD488,CNA-7.BO.1.1.33-13-6-1,COLOMBIA1,CT13582-15-5-M,CUBA65,CUIABANA,CURINCA,DAM,DANGREY,DAVAO,DAWASANRED,DINORADO,DOURADOAGULHA,DOURADOPRECOCE,ESPERANZA,FOHISOMOTRA,GANIGI,GEMJYAJYANAM,GOGO,GOGOLEMPUK,GOGOLEMPAK,GOMPA2,GRAZI,GUARANI,GUNDILKUNING,HAWMOM,HD1-4,IAC25,IAC47,IDSA77,IGUAPECATETO,INDANE,IR60080-46A,IR63380-16,IR63372-08,IR65907-188-1-B,IR66421-096-2-1-1,IR68704-145-1-1-B,IR71525-19-1-1,IRAT104,IRAT109,IRAT112,IRAT13,IRAT144,IRAT170,IRAT177,IRAT2,IRAT212,IRAT216,IRAT234,IRAT257,IRAT335,IRAT362,IRAT364,IRAT366,IRAT380,JAOHAW,JIMBRUKJOLOWORO,JUMALI,JUMULA2,KAKANI2,KANIRANGA,KARASUKARASURANKASU,KEDAYAN,KENDINGA5H,KETANKONIR,KETANLUMBU,KETANMENAH,KHAOKAPXANG,KINANDANGPATONG,KOMOJAMANITRA,KU115,KUROKA,LAMBAYQUE1,LUDAN,MAHAE,MAINTIMOLOTSY1226,MALAGKITPIRURUTONG,MANANELATRA520,MANDRIRAVINA3512,MARAVILHA,MITSANGANAHIJERY,MOLOK,NABESHI,NEPHOAVANG,NHTA10,NHTA5,NPE253,NPE826,ORYZICASABANA6,OS4,OS6,P5589-1-1-3-P,PACHOLINHA,PADIBOENAR,PADIKASALLE,PALAWAN,PATEBLANCMAN1,PCT11.0.0.2.BO.1.55-1-3-1,PCT4.SA.4.1.1076-2-4-1-5,PEHPINUO,POENOETHITAM,PULULAPA,RATHAL,REKETMAUN,RT1031-69,SENG,SPEAKER,TANDUI,TREMBESE,TRESMESES,TSIPALA89,VARYLAVA90,VARYLAVADEBETAFO,VARYMADINIKA3566,VARYMALADY,VARYSOMOTRASIHANAKA,WAB56-125,WAB56-50,WAB706-3-4-K4-KB-1,YANCAOUSSA,YANGKUMRED,YUNLU7,IR47686-09-01-B-1,IR53236-275-1,IR65261-19-1-B,IR65907-206-4-B,IR66421-105-1-1,IR71524-44-1-1,VIETNAM1,VIETNAM3,IR47684-05-1-B,PRIMAVERA,CHUAN3,CHUAN4,EARLYMUTANTIAC165"/>
d6a7be1b5adb Uploaded
dereeper
parents: 4
diff changeset
64 <param name="frequency" value="0"/>
d6a7be1b5adb Uploaded
dereeper
parents: 4
diff changeset
65 <param name="max_freq" value="0.5"/>
d6a7be1b5adb Uploaded
dereeper
parents: 4
diff changeset
66 <param name="allow_missing" value="1"/>
d6a7be1b5adb Uploaded
dereeper
parents: 4
diff changeset
67 <param name="type_p" value="ALL"/>
d6a7be1b5adb Uploaded
dereeper
parents: 4
diff changeset
68 <param name="chromosomes" value=""/>
d6a7be1b5adb Uploaded
dereeper
parents: 4
diff changeset
69 <param name="bound_start" value="1"/>
d6a7be1b5adb Uploaded
dereeper
parents: 4
diff changeset
70 <param name="bound_end" value="100000000"/>
8
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
71 <output name="fileout" file="plink_output.vcf" compare="diff" lines_diff="2"/>
7
d6a7be1b5adb Uploaded
dereeper
parents: 4
diff changeset
72 </test>
d6a7be1b5adb Uploaded
dereeper
parents: 4
diff changeset
73 </tests>
4
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
74
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
75 <!-- [OPTIONAL] Help displayed in Galaxy -->
8
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
76 <help><![CDATA[
4
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
77
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
78 .. class:: infomark
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
79
8
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
80 **Authors** Shaun Purcell : https://www.cog-genomics.org/plink2
4
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
81
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
82 | **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
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
83
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
84 .. class:: infomark
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
85
8
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
86 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
4
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
87
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
88 .. class:: infomark
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
89
8
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
90 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
91
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
92 ---------------------------------------------------
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
93
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
94 =====
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
95 PLINK
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
96 =====
4
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
97
8
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
98 -----------
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
99 Description
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
100 -----------
4
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
101
8
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
102 | Genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
103 | For further informations, please visit the plink website_.
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
104
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
105 .. _website: https://www.cog-genomics.org/plink2
4
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
106
8
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
107 ------------
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
108 Dependencies
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
109 ------------
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
110
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
111 PLINK
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
112 plink_ 1.90b4, Conda version
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
113 Bioperl
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
114 perl-bioperl_ 1.6.924, Conda version
4
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
115
8
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
116 .. _plink: https://anaconda.org/bioconda/plink
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
117 .. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
118
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
119 ]]></help>
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
120 <citations>
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
121 <citation type="doi">10.1086/519795</citation>
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
122 <citation type="doi">10.1186/s13742-015-0047-8</citation>
f733bf4f49ca planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
dereeper
parents: 7
diff changeset
123 </citations>
4
6d1122b57344 Uploaded
dereeper
parents:
diff changeset
124 </tool>