Mercurial > repos > iuc > bcftools_mpileup

comparison bcftools_mpileup.xml @ 20:4f3623db0d08 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 5b9441b69b3c176ab7b89609495f66cb29d1091a
author iuc
date Sun, 11 Aug 2024 21:26:49 +0000
parents d8a653c52f61
children 2f6e26a65721
comparison
equal deleted inserted replaced
19:98ed897722c3 20:4f3623db0d08
1 <?xml version='1.0' encoding='utf-8'?> 1 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy4" profile="@PROFILE@">
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
3 <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description> 2 <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description>
4 <macros> 3 <macros>
5 <token name="@EXECUTABLE@">mpileup</token> 4 <token name="@EXECUTABLE@">mpileup</token>
6 <import>macros.xml</import> 5 <import>macros.xml</import>
7 <xml name="bam_flag_options"> 6 <xml name="bam_flag_options">
91 -m "${section.perform_indel_calling.minimum_gapped_reads_for_indel_candidates}" 90 -m "${section.perform_indel_calling.minimum_gapped_reads_for_indel_candidates}"
92 --open-prob "${section.perform_indel_calling.open_seq_error_probability}" 91 --open-prob "${section.perform_indel_calling.open_seq_error_probability}"
93 -F "${section.perform_indel_calling.minimum_gapped_read_fraction}" 92 -F "${section.perform_indel_calling.minimum_gapped_read_fraction}"
94 ${section.perform_indel_calling.gapped_read_per_sample} 93 ${section.perform_indel_calling.gapped_read_per_sample}
95 #if len( $section.perform_indel_calling.platform_list_repeat ): 94 #if len( $section.perform_indel_calling.platform_list_repeat ):
96 -P "${ ",".join( [ str( platform.platform_entry ) for platform in $section.perform_indel_calling.platform_list_repeat ] ) }" 95 -P "${ ",".join( [ str( platform['platform_entry'] ) for platform in $section.perform_indel_calling.platform_list_repeat ] ) }"
97 #end if 96 #end if
98 #end if 97 #end if
99 98
100 #if $section.ambig_reads 99 #if $section.ambig_reads
101 --ambig-reads $section.ambig_reads 100 --ambig-reads $section.ambig_reads