Mercurial > repos > iuc > gatk4_mutect2

comparison gatk4_Mutect2.xml @ 2:3be27a9a7313 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 093a027ca9e7d34e7d12cd14ca0d0dacadfcb78b"
author iuc
date Fri, 10 Apr 2020 14:10:55 -0400
parents fd2d6e035c3f
children 287c4af133e6
comparison
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1:fd2d6e035c3f 2:3be27a9a7313
1 <tool id="gatk4_mutect2" name="GATK4 Mutect2" version="@WRAPPER_VERSION@1" profile="18.05"> 1 <tool id="gatk4_mutect2" name="GATK4 Mutect2" version="@WRAPPER_VERSION@2" profile="18.05">
2 <description>- Call somatic SNVs and indels via local assembly of haplotypes</description> 2 <description>- Call somatic SNVs and indels via local assembly of haplotypes</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
36 #if str($outputs.debug_bam) == 'yes' 36 #if str($outputs.debug_bam) == 'yes'
37 ln -s '$bam_output' debug.bam && 37 ln -s '$bam_output' debug.bam &&
38 #end if 38 #end if
39 #end if 39 #end if
40 40
41 @CMD_BEGIN@ GetSampleName --input="input.bam" --output="samplename.txt" && 41 gatk GetSampleName --input="input.bam" --output="samplename.txt" &&
42 sample=`cat samplename.txt` && 42 sample=`cat samplename.txt | sed 's/"//g'` &&
43 43
44 #if str($optional.optional_parameters) == 'yes' 44 #if str($optional.optional_parameters) == 'yes'
45 #if $optional.panel_of_normals 45 #if $optional.panel_of_normals
46 #set datatype = $optional.panel_of_normals.datatype 46 #set datatype = $optional.panel_of_normals.datatype
47 #if $optional.panel_of_normals.is_of_type("vcf_bgzip") 47 #if $optional.panel_of_normals.is_of_type("vcf_bgzip")
74 #end if 74 #end if
75 #end if 75 #end if
76 76
77 #end if 77 #end if
78 78
79 @CMD_BEGIN@ Mutect2 --QUIET $ref_flag --tumor-sample \$sample 79 gatk Mutect2 --QUIET $ref_flag --tumor-sample "\$sample"
80 80
81 #include source=$gatk_bam_input# 81 #include source=$gatk_bam_input#
82 82
83 ## OPTIONAL PARAMETERS ## 83 ## OPTIONAL PARAMETERS ##
84 84