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planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
author dereeper
date Mon, 16 Apr 2018 08:58:55 -0400
parents d6a7be1b5adb
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7:d6a7be1b5adb 8:f733bf4f49ca
1 <tool id="sniplay_plink" name="plink" version="1.0"> 1 <tool id="sniplay_plink" name="PLINK" version="2.0.0">
2 2
3 <!-- [REQUIRED] Tool description displayed after the tool name --> 3 <!-- [REQUIRED] Tool description displayed after the tool name -->
4 <description> - Filter large VCF file</description> 4 <description>Filter large VCF file</description>
5 5
6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> 6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
7 <requirements> 7 <requirements>
8 <requirement type="binary">perl</requirement> 8 <requirement type="binary">perl</requirement>
9 <requirement type="package" version="1.6.924">perl-bioperl</requirement> 9 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
51 <param name="bound_end" type="integer" value="100000000" label="Upper bound" help="Upper bound for a range of sites to be processed." /> 51 <param name="bound_end" type="integer" value="100000000" label="Upper bound" help="Upper bound for a range of sites to be processed." />
52 </inputs> 52 </inputs>
53 53
54 <!-- [REQUIRED] Output files --> 54 <!-- [REQUIRED] Output files -->
55 <outputs> 55 <outputs>
56 <data name="fileout" format="vcf" label="Plink filtered VCF"/> 56 <data name="fileout" format="vcf" label="PLINK filtered VCF"/>
57 <data name="filelog" format="txt" label="Plink logfile" /> 57 <data name="filelog" format="txt" label="PLINK logfile" />
58 </outputs> 58 </outputs>
59 59
60 <tests> 60 <tests>
61 <test> 61 <test>
62 <param name="vcf" value="input.vcf"/> 62 <param name="vcf" value="plink_input.vcf"/>
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"/> 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"/>
64 <param name="frequency" value="0"/> 64 <param name="frequency" value="0"/>
65 <param name="max_freq" value="0.5"/> 65 <param name="max_freq" value="0.5"/>
66 <param name="allow_missing" value="1"/> 66 <param name="allow_missing" value="1"/>
67 <param name="type_p" value="ALL"/> 67 <param name="type_p" value="ALL"/>
68 <param name="chromosomes" value=""/> 68 <param name="chromosomes" value=""/>
69 <param name="bound_start" value="1"/> 69 <param name="bound_start" value="1"/>
70 <param name="bound_end" value="100000000"/> 70 <param name="bound_end" value="100000000"/>
71 <output name="fileout" file="output.vcf" compare="diff" lines_diff="2"/> 71 <output name="fileout" file="plink_output.vcf" compare="diff" lines_diff="2"/>
72 </test> 72 </test>
73 </tests> 73 </tests>
74 74
75 <!-- [OPTIONAL] Help displayed in Galaxy --> 75 <!-- [OPTIONAL] Help displayed in Galaxy -->
76 <help> 76 <help><![CDATA[
77 77
78 .. class:: infomark 78 .. class:: infomark
79 79
80 **Authors** Shaun Purcell : plink_ 80 **Authors** Shaun Purcell : https://www.cog-genomics.org/plink2
81
82 .. _plink: https://www.cog-genomics.org/plink2
83 81
84 | **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 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
85 83
86 .. class:: infomark 84 .. class:: infomark
87 85
88 **Galaxy integration** Dereeper Alexis (IRD), Andres Gwendoline (Institut Français de Bioinformatique). 86 **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)
89 87
90 .. class:: infomark 88 .. class:: infomark
91 89
92 **Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr 90 **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr
93 91
92 ---------------------------------------------------
94 93
94 =====
95 PLINK
96 =====
95 97
96 </help> 98 -----------
99 Description
100 -----------
97 101
102 | Genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
103 | For further informations, please visit the plink website_.
104
105 .. _website: https://www.cog-genomics.org/plink2
106
107 ------------
108 Dependencies
109 ------------
110
111 PLINK
112 plink_ 1.90b4, Conda version
113 Bioperl
114 perl-bioperl_ 1.6.924, Conda version
115
116 .. _plink: https://anaconda.org/bioconda/plink
117 .. _perl-bioperl: https://anaconda.org/bioconda/perl-bioperl
118
119 ]]></help>
120 <citations>
121 <citation type="doi">10.1086/519795</citation>
122 <citation type="doi">10.1186/s13742-015-0047-8</citation>
123 </citations>
98 </tool> 124 </tool>