Mercurial > repos > devteam > bwa
comparison bwa-mem.xml @ 5:fbf460831036 draft
planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
| author | devteam |
|---|---|
| date | Tue, 21 Jul 2015 13:51:02 -0400 |
| parents | ac30bfd3e2a8 |
| children | 09a7281d24c5 |
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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 (> 100 bp) against reference genome</description> | 3 <description>- map medium and long reads (> 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> |