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comparison bwa-mem.xml @ 5:fbf460831036 draft

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planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
author devteam
date Tue, 21 Jul 2015 13:51:02 -0400
parents ac30bfd3e2a8
children 09a7281d24c5
comparison
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4:ac30bfd3e2a8 5:fbf460831036
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="bwa_mem" name="Map with BWA-MEM" version="0.2.2"> 2 <tool id="bwa_mem" name="Map with BWA-MEM" version="0.3">
3 <description>- map medium and long reads (&gt; 100 bp) against reference genome</description> 3 <description>- map medium and long reads (&gt; 100 bp) against reference genome</description>
4 <macros> 4 <macros>
5 <import>read_group_macros.xml</import>
5 <import>bwa_macros.xml</import> 6 <import>bwa_macros.xml</import>
6 </macros> 7 </macros>
7 <requirements> 8 <requirements>
8 <requirement type="package" version="0.7.10.039ea20639">bwa</requirement> 9 <requirement type="package" version="0.7.10.039ea20639">bwa</requirement>
9 <requirement type="package" version="1.1">samtools</requirement> 10 <requirement type="package" version="1.1">samtools</requirement>
101 ${analysis_type.io_options.M} 102 ${analysis_type.io_options.M}
102 #end if 103 #end if
103 104
104 #end if 105 #end if
105 106
106 #if str( $rg.rg_selector ) == "set": 107 ## Handle read group options...
108 @define_read_group_helpers@
109 #if str( $fastq_input.fastq_input_selector ) == "paired":
110 #set $rg_auto_name = $read_group_name_default($fastq_input.fastq_input1, $fastq_input.fastq_input2)
111 #else:
112 #set $rg_auto_name = $read_group_name_default($fastq_input.fastq_input1)
113 #end if
114 @set_use_rg_var@
115 @set_read_group_vars@
116 #if $use_rg
107 @set_rg_string@ 117 @set_rg_string@
108 -R '$rg_string' 118 -R '$rg_string'
109 #end if 119 #end if
110 120
111 #if str( $fastq_input.fastq_input_selector ) == "paired": 121 #if str( $fastq_input.fastq_input_selector ) == "paired":
187 </sanitizer> 197 </sanitizer>
188 </param> 198 </param>
189 </when> 199 </when>
190 </conditional> 200 </conditional>
191 201
192 <expand macro="readgroup_params" /> 202 <expand macro="read_group_conditional" />
193 203
194 <conditional name="analysis_type"> 204 <conditional name="analysis_type">
195 <param name="analysis_type_selector" type="select" label="Select analysis mode"> 205 <param name="analysis_type_selector" type="select" label="Select analysis mode">
196 <option value="illumina">1.Simple Illumina mode</option> 206 <option value="illumina">1.Simple Illumina mode</option>
197 <option value="pacbio">2.PacBio mode (-x pacbio)</option> 207 <option value="pacbio">2.PacBio mode (-x pacbio)</option>