Mercurial > repos > sanbi-uwc > shapeit_phase

comparison shapeit_phase.xml @ 21:394bd82a4c40 draft default tip

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planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 98e23aec0945a9922ab30e6ca15ab08800a2abb7-dirty
author sanbi-uwc
date Tue, 18 Sep 2018 13:38:48 -0400
parents a5ef4f2c8124
children
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20:a5ef4f2c8124 21:394bd82a4c40
1 <tool id="shapeit_phase" name="shapeit_phase" version="0.19.0"> 1 <tool id="shapeit_phase" name="shapeit_phase" version="0.20.0">
2 <description>genomic data with or without reference panel</description> 2 <description>genomic data with or without reference panel</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.r837">shapeit</requirement> 4 <requirement type="package" version="2.r837">shapeit</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
58 echo Processing NAME '${dat.name}' && 58 echo Processing NAME '${dat.name}' &&
59 #end for 59 #end for
60 #end if 60 #end if
61 61
62 shapeit 62 shapeit
63 --thread \${GALAXY_SLOTS:-1}
64 63
65 #if $check_mode != "": 64 #if $check_mode != "":
66 -check 65 -check
67 #end if 66 #end if
67
68 --thread \${GALAXY_SLOTS:-1}
68 69
69 #if $input_files.input_type_select == "vcf": 70 #if $input_files.input_type_select == "vcf":
70 --input-vcf ${input_files.vcf_file} 71 --input-vcf ${input_files.vcf_file}
71 #else if $input_files.input_type_select == "plink_ped_map": 72 #else if $input_files.input_type_select == "plink_ped_map":
72 --input-ped ${input_files.plink_ped} ${input_files.plink_map} 73 --input-ped ${input_files.plink_ped} ${input_files.plink_map}