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comparison bwa.xml @ 3:0bde88ff668c draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 3442b18860bc4398d917e3a35943351a9cf031ea
author devteam
date Mon, 30 Jan 2017 08:49:11 -0500
parents b4dfb5470bf3
children 774491f4a074
comparison
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2:b4dfb5470bf3 3:0bde88ff668c
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" label="Select first set of reads" help="Specify dataset with forward reads"/> 236 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify dataset with forward reads"/>
237 <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/> 237 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz" 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>
243 </when> 243 </when>
244 244
245 <when value="paired_collection"> 245 <when value="paired_collection">
246 <param name="fastq_input1" format="fastqsanger" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> 246 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
247 <conditional name="adv_pe_options"> 247 <conditional name="adv_pe_options">
248 248
249 <expand macro="advanced_pe_options" /> 249 <expand macro="advanced_pe_options" />
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" label="Select fastq dataset" help="Specify dataset with single reads"/> 255 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" 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>
322 <test> 322 <test>
323 <param name="reference_source_selector" value="history" /> 323 <param name="reference_source_selector" value="history" />
324 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> 324 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
325 <param name="input_type_selector" value="paired"/> 325 <param name="input_type_selector" value="paired"/>
326 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> 326 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
327 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
328 <param name="analysis_type_selector" value="illumina"/>
329 <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="2" />
330 </test>
331 <test>
332 <param name="reference_source_selector" value="history" />
333 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
334 <param name="input_type_selector" value="paired"/>
335 <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
327 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> 336 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
328 <param name="analysis_type_selector" value="illumina"/> 337 <param name="analysis_type_selector" value="illumina"/>
329 <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="2" /> 338 <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="2" />
330 </test> 339 </test>
331 <test> 340 <test>