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comparison bwa.xml @ 25:e188dc7a68e6 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 8f4d108191d52e3b60212dfcc3f57541e5f849d0
author iuc
date Fri, 19 Aug 2022 18:51:56 +0000
parents 3fe632431b68
children
comparison
equal deleted inserted replaced
24:64f11cf59c6e 25:e188dc7a68e6
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="bwa" name="Map with BWA" version="@VERSION@.4"> 2 <tool id="bwa" name="Map with BWA" version="@VERSION@.5">
3 <description>- map short reads (&lt; 100 bp) against reference genome</description> 3 <description>- map short reads (&lt; 100 bp) against reference genome</description>
4 <xrefs>
5 <xref type="bio.tools">bwa</xref>
6 </xrefs>
4 <macros> 7 <macros>
5 <import>read_group_macros.xml</import> 8 <import>read_group_macros.xml</import>
6 <import>bwa_macros.xml</import> 9 <import>bwa_macros.xml</import>
7 <token name="@command_options@"> 10 <token name="@command_options@">
8 #if str( $analysis_type.analysis_type_selector ) == "full": 11 #if str( $analysis_type.analysis_type_selector ) == "full":
124 #if str( $input_type.adv_pe_options.adv_pe_options_selector) == "True": 127 #if str( $input_type.adv_pe_options.adv_pe_options_selector) == "True":
125 -a ${$input_type.adv_pe_options.a} 128 -a ${$input_type.adv_pe_options.a}
126 -o ${$input_type.adv_pe_options.o} 129 -o ${$input_type.adv_pe_options.o}
127 -n ${$input_type.adv_pe_options.n} 130 -n ${$input_type.adv_pe_options.n}
128 -N ${$input_type.adv_pe_options.N} 131 -N ${$input_type.adv_pe_options.N}
132 -c ${$input_type.adv_pe_options.c}
129 #end if 133 #end if
130 @read_group_options@ 134 @read_group_options@
131 #if str( $input_type.input_type_selector ) == "paired_collection": 135 #if str( $input_type.input_type_selector ) == "paired_collection":
132 '${reference_fasta_filename}' first.sai second.sai '${input_type.fastq_input1.forward}' '${input_type.fastq_input1.reverse}' 136 '${reference_fasta_filename}' first.sai second.sai '${input_type.fastq_input1.forward}' '${input_type.fastq_input1.reverse}'
133 #else: 137 #else: