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comparison bbmap.xml @ 7:3fa2af3231df draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
author iuc
date Mon, 06 Feb 2023 18:04:53 +0000
parents c7a39190a385
children 83d0df824438
comparison
equal deleted inserted replaced
6:c7a39190a385 7:3fa2af3231df
1 <tool id="bbtools_bbmap" name="BBTools: BBMap" version="@WRAPPER_VERSION@+galaxy4" profile="@PROFILE@"> 1 <tool id="bbtools_bbmap" name="BBTools: BBMap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>short-read aligner</description> 2 <description>short-read aligner</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="edam_ontology"/>
6 <expand macro="requirements"/> 7 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
8 #import os 9 #import os
9 #import re 10 #import re
10 11
267 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/> 268 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/>
268 <param name="output_sort" value="coordinate"/> 269 <param name="output_sort" value="coordinate"/>
269 <output name="output_all_reads" ftype="bam"> 270 <output name="output_all_reads" ftype="bam">
270 <metadata name="dbkey" value="89"/> 271 <metadata name="dbkey" value="89"/>
271 <assert_contents> 272 <assert_contents>
272 <has_size value="9639" delta="300"/> 273 <has_size value="9310" delta="300"/>
273 </assert_contents> 274 </assert_contents>
274 </output> 275 </output>
275 <output name="output_unmapped_reads" ftype="bam"> 276 <output name="output_unmapped_reads" ftype="bam">
276 <metadata name="dbkey" value="89"/> 277 <metadata name="dbkey" value="89"/>
277 <assert_contents> 278 <assert_contents>
278 <has_size value="9639" delta="300"/> 279 <has_size value="9310" delta="300"/>
279 </assert_contents> 280 </assert_contents>
280 </output> 281 </output>
281 <output name="output_mapped_reads" ftype="bam"> 282 <output name="output_mapped_reads" ftype="bam">
282 <metadata name="dbkey" value="89"/> 283 <metadata name="dbkey" value="89"/>
283 <assert_contents> 284 <assert_contents>
292 <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/> 293 <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/>
293 <param name="output_sort" value="name"/> 294 <param name="output_sort" value="name"/>
294 <output name="output_all_reads" ftype="qname_sorted.bam"> 295 <output name="output_all_reads" ftype="qname_sorted.bam">
295 <metadata name="dbkey" value="89"/> 296 <metadata name="dbkey" value="89"/>
296 <assert_contents> 297 <assert_contents>
297 <has_size value="17540" delta="600"/> 298 <has_size value="16893" delta="600"/>
298 </assert_contents> 299 </assert_contents>
299 </output> 300 </output>
300 <output name="output_unmapped_reads" ftype="qname_sorted.bam"> 301 <output name="output_unmapped_reads" ftype="qname_sorted.bam">
301 <metadata name="dbkey" value="89"/> 302 <metadata name="dbkey" value="89"/>
302 <assert_contents> 303 <assert_contents>
303 <has_size value="17540" delta="600"/> 304 <has_size value="16893" delta="600"/>
304 </assert_contents> 305 </assert_contents>
305 </output> 306 </output>
306 <output name="output_mapped_reads" ftype="qname_sorted.bam"> 307 <output name="output_mapped_reads" ftype="qname_sorted.bam">
307 <metadata name="dbkey" value="89"/> 308 <metadata name="dbkey" value="89"/>
308 <assert_contents> 309 <assert_contents>
323 <param name="reference" value="NC_002945v4.fasta" dbkey="89" ftype="fasta"/> 324 <param name="reference" value="NC_002945v4.fasta" dbkey="89" ftype="fasta"/>
324 <param name="output_sort" value="unsorted"/> 325 <param name="output_sort" value="unsorted"/>
325 <output name="output_all_reads" ftype="qname_input_sorted.bam"> 326 <output name="output_all_reads" ftype="qname_input_sorted.bam">
326 <metadata name="dbkey" value="89"/> 327 <metadata name="dbkey" value="89"/>
327 <assert_contents> 328 <assert_contents>
328 <has_size value="17602" delta="600"/> 329 <has_size value="16928" delta="600"/>
329 </assert_contents> 330 </assert_contents>
330 </output> 331 </output>
331 <output name="output_unmapped_reads" ftype="qname_input_sorted.bam"> 332 <output name="output_unmapped_reads" ftype="qname_input_sorted.bam">
332 <metadata name="dbkey" value="89"/> 333 <metadata name="dbkey" value="89"/>
333 <assert_contents> 334 <assert_contents>
334 <has_size value="17602" delta="600"/> 335 <has_size value="16928" delta="600"/>
335 </assert_contents> 336 </assert_contents>
336 </output> 337 </output>
337 <output name="output_mapped_reads" ftype="qname_input_sorted.bam"> 338 <output name="output_mapped_reads" ftype="qname_input_sorted.bam">
338 <metadata name="dbkey" value="89"/> 339 <metadata name="dbkey" value="89"/>
339 <assert_contents> 340 <assert_contents>