Mercurial > repos > iuc > bbtools_bbmap
comparison bbmap.xml @ 7:9ed6579f52f3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
| author | iuc |
|---|---|
| date | Mon, 06 Feb 2023 18:06:17 +0000 |
| parents | 858a65b52cf9 |
| children | 7f19559b8b55 |
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| 6:858a65b52cf9 | 7:9ed6579f52f3 |
|---|---|
| 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> |