Mercurial > repos > devteam > bwa
comparison bwa.xml @ 25:e188dc7a68e6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 8f4d108191d52e3b60212dfcc3f57541e5f849d0
author | iuc |
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date | Fri, 19 Aug 2022 18:51:56 +0000 |
parents | 3fe632431b68 |
children | 2477830927ec |
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24:64f11cf59c6e | 25:e188dc7a68e6 |
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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 (< 100 bp) against reference genome</description> | 3 <description>- map short reads (< 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: |