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comparison bwa.xml @ 4:774491f4a074 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 33c17fa6a2d8c15972d93031b2ca4182cdf31439
author devteam
date Thu, 01 Jun 2017 11:38:11 -0400
parents 0bde88ff668c
children cbc665adcde4
comparison
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3:0bde88ff668c 4:774491f4a074
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="bwa" name="Map with BWA" version="@VERSION@.1"> 2 <tool id="bwa" name="Map with BWA" version="@VERSION@.2">
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>read_group_macros.xml</import>
6 <import>bwa_macros.xml</import> 6 <import>bwa_macros.xml</import>
7 <token name="@command_options@"> 7 <token name="@command_options@">
231 <option value="single">Single fastq</option> 231 <option value="single">Single fastq</option>
232 <option value="paired_bam">Paired BAM</option> 232 <option value="paired_bam">Paired BAM</option>
233 <option value="single_bam">Single BAM</option> 233 <option value="single_bam">Single BAM</option>
234 </param> 234 </param>
235 <when value="paired"> 235 <when value="paired">
236 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify dataset with forward reads"/> 236 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
237 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/> 237 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
238 <conditional name="adv_pe_options"> 238 <conditional name="adv_pe_options">
239 239
240 <expand macro="advanced_pe_options" /> 240 <expand macro="advanced_pe_options" />
241 241
242 </conditional> 242 </conditional>
250 250
251 </conditional> 251 </conditional>
252 </when> 252 </when>
253 253
254 <when value="single"> 254 <when value="single">
255 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with single reads"/> 255 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
256 <conditional name="adv_se_options"> 256 <conditional name="adv_se_options">
257 257
258 <expand macro="advanced_se_options" /> 258 <expand macro="advanced_se_options" />
259 259
260 </conditional> 260 </conditional>
317 <expand macro="dbKeyActionsBwa" /> 317 <expand macro="dbKeyActionsBwa" />
318 </data> 318 </data>
319 </outputs> 319 </outputs>
320 320
321 <tests> 321 <tests>
322 <test>
323 <param name="reference_source_selector" value="history" />
324 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
325 <param name="input_type_selector" value="single"/>
326 <param name="fastq_input1" ftype="fasta" value="bwa-mem-fasta1.fa"/>
327 <param name="analysis_type_selector" value="illumina"/>
328 <output name="bam_output" ftype="bam" file="bwa-aln-test1-fasta.bam" lines_diff="2" />
329 </test>
322 <test> 330 <test>
323 <param name="reference_source_selector" value="history" /> 331 <param name="reference_source_selector" value="history" />
324 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> 332 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
325 <param name="input_type_selector" value="paired"/> 333 <param name="input_type_selector" value="paired"/>
326 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> 334 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>