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comparison plink.xml @ 7:d6a7be1b5adb draft

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author dereeper
date Wed, 07 Feb 2018 00:16:59 -0500
parents 6d1122b57344
children f733bf4f49ca
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6:da372a164001 7:d6a7be1b5adb
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="1.90b4">plink</requirement> 10 <requirement type="package" version="1.90b4">plink</requirement>
10 </requirements> 11 </requirements>
11 12
13 <code file="find_indiv.py"/>
12 14
13 <!-- [STRONGLY RECOMMANDED] Exit code rules --> 15 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
14 <stdio> 16 <stdio>
15 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> 17 <!-- [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" /> 18 <exit_code range="1:" level="fatal" />
28 'None' 30 'None'
29 #else 31 #else
30 $chromosomes 32 $chromosomes
31 #end if 33 #end if
32 </command> 34 </command>
33 <code file="find_indiv.py"/>
34 <!-- [REQUIRED] Input files and tool parameters --> 35 <!-- [REQUIRED] Input files and tool parameters -->
35 <inputs> 36 <inputs>
36 <param name="vcf" type="data" format="vcf" optional="false" label="VCF input" /> 37 <param name="vcf" type="data" format="vcf" optional="false" label="VCF input" />
37 38
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="select" label="Samples" multiple="true" dynamic_options="get_field_samples_options(vcf)" help="Samples to be analyzed." />
54 <outputs> 55 <outputs>
55 <data name="fileout" format="vcf" label="Plink filtered VCF"/> 56 <data name="fileout" format="vcf" label="Plink filtered VCF"/>
56 <data name="filelog" format="txt" label="Plink logfile" /> 57 <data name="filelog" format="txt" label="Plink logfile" />
57 </outputs> 58 </outputs>
58 59
60 <tests>
61 <test>
62 <param name="vcf" value="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"/>
64 <param name="frequency" value="0"/>
65 <param name="max_freq" value="0.5"/>
66 <param name="allow_missing" value="1"/>
67 <param name="type_p" value="ALL"/>
68 <param name="chromosomes" value=""/>
69 <param name="bound_start" value="1"/>
70 <param name="bound_end" value="100000000"/>
71 <output name="fileout" file="output.vcf" compare="diff" lines_diff="2"/>
72 </test>
73 </tests>
59 74
60 <!-- [OPTIONAL] Help displayed in Galaxy --> 75 <!-- [OPTIONAL] Help displayed in Galaxy -->
61 <help> 76 <help>
62 77
63 .. class:: infomark 78 .. class:: infomark