Mercurial > repos > devteam > bwa

comparison bwa-mem.xml @ 11:546ada4a9f43 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 610045611b00099e0a24183c8cf33aebfa9635cf
author devteam
date Tue, 19 Jan 2016 11:20:59 -0500
parents 6069ffa8b240
children bd3a1e0de84c
comparison
equal deleted inserted replaced
10:6069ffa8b240 11:546ada4a9f43
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="bwa_mem" name="Map with BWA-MEM" version="0.7.12"> 2 <tool id="bwa_mem" name="Map with BWA-MEM" version="@VERSION@.1">
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>read_group_macros.xml</import>
6 <import>bwa_macros.xml</import> 6 <import>bwa_macros.xml</import>
7 </macros> 7 </macros>
8 <expand macro="requirements" /> 8 <expand macro="requirements" />
9 <expand macro="stdio" /> 9 <expand macro="stdio" />
10 <command> 10 <command>
11 <![CDATA[ 11 <![CDATA[
12 #set $reference_fasta_filename = "localref.fa" 12 @set_reference_fasta_filename@
13
14 #if str( $reference_source.reference_source_selector ) == "history":
15 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
16
17 ## The following shell commands decide which of the BWA indexing algorithms (IS or BWTSW) will be run
18 ## depending on the size of the input FASTA dataset
19 ( size=`stat -c %s "${reference_source.ref_file}" 2>/dev/null`; ## Linux
20 if [ $? -ne 0 ]; then
21 size=\$(stat -f %z "${reference_source.ref_file}"); ## OSX
22 fi &&
23 if [ "\$size" -lt 2000000000 ]; then
24 echo "Reference genome size is \$size bytes, generating BWA index with is algorithm";
25 bwa index -a is "${reference_fasta_filename}";
26 else
27 echo "Reference genome size is \$size bytes, generating BWA index with bwtsw algorithm";
28 bwa index -a bwtsw "${reference_fasta_filename}";
29 fi
30 ) &&
31 #else:
32 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
33 #end if
34 13
35 ## Begin BWA-MEM command line 14 ## Begin BWA-MEM command line
36 15
37 bwa mem 16 bwa mem
38 -t "\${GALAXY_SLOTS:-1}" 17 -t "\${GALAXY_SLOTS:-1}"
122 samtools sort -f temporary_bam_file.bam ${bam_output} 101 samtools sort -f temporary_bam_file.bam ${bam_output}
123 ]]> 102 ]]>
124 </command> 103 </command>
125 104
126 <inputs> 105 <inputs>
127 106 <expand macro="reference_source_conditional" />
128 <conditional name="reference_source">
129 <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
130 <option value="cached">Use a built-in genome index</option>
131 <option value="history">Use a genome from history and build index</option>
132 </param>
133 <when value="cached">
134 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
135 <options from_data_table="bwa_mem_indexes">
136 <filter type="sort_by" column="2" />
137 <validator type="no_options" message="No indexes are available" />
138 </options>
139 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
140 </param>
141 </when>
142 <when value="history">
143 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference" />
144 </when>
145 </conditional>
146 <conditional name="fastq_input"> 107 <conditional name="fastq_input">
147 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data"> 108 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
148 <option value="paired">Paired</option> 109 <option value="paired">Paired</option>
149 <option value="single">Single</option> 110 <option value="single">Single</option>
150 <option value="paired_collection">Paired Collection</option> 111 <option value="paired_collection">Paired Collection</option>
288 <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="2" /> 249 <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="2" />
289 </test> 250 </test>
290 <test> 251 <test>
291 <param name="reference_source_selector" value="history" /> 252 <param name="reference_source_selector" value="history" />
292 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> 253 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
254 <param name="index_a" value="is"/>
293 <param name="fastq_input_selector" value="paired"/> 255 <param name="fastq_input_selector" value="paired"/>
294 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> 256 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
295 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> 257 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
296 <param name="rg_selector" value="set"/> 258 <param name="rg_selector" value="set"/>
297 <param name="ID" value="rg1"/> 259 <param name="ID" value="rg1"/>