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comparison bwa.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" 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 (&lt; 100 bp) against reference genome</description> 3 <description>- map short reads (&lt; 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 ) &amp;&amp; 108 ) &amp;&amp;
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>