Mercurial > repos > devteam > bwa
comparison bwa.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" name="Map with BWA" version="0.2.3"> | 2 <tool id="bwa" name="Map with BWA" version="0.3.0"> |
| 3 <description>- map short reads (< 100 bp) against reference genome</description> | 3 <description>- map short 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 <token name="@command_options@"> | 7 <token name="@command_options@"> |
| 7 #if str( $analysis_type.analysis_type_selector ) == "full": | 8 #if str( $analysis_type.analysis_type_selector ) == "full": |
| 8 -n ${analysis_type.n} | 9 -n ${analysis_type.n} |
| 9 -o ${analysis_type.o} | 10 -o ${analysis_type.o} |
| 27 -L ${analysis_type.L} | 28 -L ${analysis_type.L} |
| 28 #end if | 29 #end if |
| 29 #end if | 30 #end if |
| 30 </token> | 31 </token> |
| 31 <token name="@read_group_options@"> | 32 <token name="@read_group_options@"> |
| 32 #if str( $rg.rg_selector ) == "set": | 33 #if $use_rg: |
| 33 @set_rg_string@ | 34 @set_rg_string@ |
| 34 -r '$rg_string' | 35 -r '$rg_string' |
| 35 #end if | 36 #end if |
| 36 </token> | 37 </token> |
| 37 | 38 |
| 107 ) && | 108 ) && |
| 108 #else: | 109 #else: |
| 109 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) | 110 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) |
| 110 #end if | 111 #end if |
| 111 | 112 |
| 113 ## setup vars for rg handling... | |
| 114 @define_read_group_helpers@ | |
| 115 #if str( $input_type.input_type_selector ) == "paired": | |
| 116 #set $rg_auto_name = $read_group_name_default($input_type.fastq_input1, $input_type.fastq_input2) | |
| 117 #elif str( $input_type.input_type_selector ) in ["single_bam", "paired_bam"]: | |
| 118 #set $rg_auto_name = $read_group_name_default($input_type.bam_input) | |
| 119 #else | |
| 120 #set $rg_auto_name = $read_group_name_default($input_type.fastq_input1) | |
| 121 #end if | |
| 122 @set_use_rg_var@ | |
| 123 @set_read_group_vars@ | |
| 124 | |
| 112 ## Begin bwa command line | 125 ## Begin bwa command line |
| 113 | 126 |
| 114 ####### Fastq paired | 127 ####### Fastq paired |
| 115 | 128 |
| 116 #if str( $input_type.input_type_selector ) == "paired" or str( $input_type.input_type_selector ) == "paired_collection": | 129 #if str( $input_type.input_type_selector ) == "paired" or str( $input_type.input_type_selector ) == "paired_collection": |
| 325 </conditional> | 338 </conditional> |
| 326 </when> | 339 </when> |
| 327 | 340 |
| 328 </conditional> | 341 </conditional> |
| 329 | 342 |
| 330 <expand macro="readgroup_params" /> | 343 <expand macro="read_group_conditional" /> |
| 331 | 344 |
| 332 <conditional name="analysis_type"> | 345 <conditional name="analysis_type"> |
| 333 <param name="analysis_type_selector" type="select" label="Select analysis mode"> | 346 <param name="analysis_type_selector" type="select" label="Select analysis mode"> |
| 334 <option value="illumina">1.Simple Illumina mode</option> | 347 <option value="illumina">1.Simple Illumina mode</option> |
| 335 <option value="full">2.Full list of options</option> | 348 <option value="full">2.Full list of options</option> |