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planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
author nml
date Mon, 20 Jun 2022 20:06:36 +0000
parents 9def47f3c1e4
children
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8:9def47f3c1e4 9:18aad692772a
1 <tool id="hydra" name="Hydra pipeline" version="0.5.1"> 1 <tool id="hydra" name="Hydra pipeline" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>Identifies drug resistance within an NGS dataset</description> 2 <description>Identifies drug resistance within an NGS dataset</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="0.5.1">quasitools</requirement> 4 <import>macros.xml</import>
5 </requirements> 5 </macros>
6 <expand macro="requirements"/>
6 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
7 8
8 quasitools hydra 9 quasitools hydra
9 10
10 ## Preparing file input. 11 ## Preparing file input.
179 <data format="bam" label="HyDRA: alignment bam output" name="output_bam" from_work_dir="output/align.bam" /> 180 <data format="bam" label="HyDRA: alignment bam output" name="output_bam" from_work_dir="output/align.bam" />
180 <data format="csv" label="HyDRA: coverage output" name="output_coverage" from_work_dir="output/coverage_file.csv" /> 181 <data format="csv" label="HyDRA: coverage output" name="output_coverage" from_work_dir="output/coverage_file.csv" />
181 <data format="csv" label="HyDRA: drug resistance output" name="output_dr" from_work_dir="output/dr_report.csv" /> 182 <data format="csv" label="HyDRA: drug resistance output" name="output_dr" from_work_dir="output/dr_report.csv" />
182 <data format="fastq" label="HyDRA: filtered reads output" name="output_filtered" from_work_dir="output/filtered.fastq" /> 183 <data format="fastq" label="HyDRA: filtered reads output" name="output_filtered" from_work_dir="output/filtered.fastq" />
183 <data format="vcf" label="HyDRA: variants output" name="output_hydra" from_work_dir="output/hydra.vcf" /> 184 <data format="vcf" label="HyDRA: variants output" name="output_hydra" from_work_dir="output/hydra.vcf" />
184 <data format="vcf" label="HyDRA: aa mutations output" name="output_aa_mt" from_work_dir="output/mutation_report.hmcf" /> 185 <data format="txt" label="HyDRA: aa mutations output" name="output_aa_mt" from_work_dir="output/mutation_report.aavf" />
185 <data format="txt" label="HyDRA: stats output" name="output_stats" from_work_dir="output/stats.txt" /> 186 <data format="txt" label="HyDRA: stats output" name="output_stats" from_work_dir="output/stats.txt" />
186 <data format="fasta" label="HyDRA: consensus output" name="output_consensus" from_work_dir="output/consensus.fasta" > 187 <data format="fasta" label="HyDRA: consensus output" name="output_consensus" from_work_dir="output/consensus.fasta" >
187 <filter>consensus['consensus_bool'] == "true_consensus"</filter> 188 <filter>consensus['consensus_bool'] == "true_consensus"</filter>
188 </data> 189 </data>
189 </outputs> 190 </outputs>
219 <has_text_matching expression="hxb2_pol\s958\s.\sc\sa\s100\sPASS\sDP=2503;AC=28;AF=0.0112" /> 220 <has_text_matching expression="hxb2_pol\s958\s.\sc\sa\s100\sPASS\sDP=2503;AC=28;AF=0.0112" />
220 </assert_contents> 221 </assert_contents>
221 </output> 222 </output>
222 <output name="output_aa_mt"> 223 <output name="output_aa_mt">
223 <assert_contents> 224 <assert_contents>
224 <has_text_matching expression="#CHROM\sGENE\sTYPE\sWILDTYPE\sPOS\sMUTANT\sFILTER\sMUTANT_FREQ\sCOVERAGE\sINFO"/> 225 <has_text_matching expression="#CHROM\tGENE\tPOS\tREF\tALT\tFILTER\tALT_FREQ\tCOVERAGE\tINFO"/>
225 <has_text_matching expression="hxb2_pol\sRT\smutation\sK\s101\sP\sPASS\s0.1423\s1574\sWC=aaa;MC=CCa;MCF=0.1423;CAT=NNRTI;SRVL=Yes" /> 226 <has_text_matching expression="hxb2_pol\tRT\t101\tK\tP\tPASS\t0.1423\t1574\tRC=aaa;AC=CCa;ACF=0.1423;CAT=NNRTI;SRVL=Yes" />
226 <has_text_matching expression="hxb2_pol\sRT\smutation\sH\s221\sN\sPASS\s0.0113\s2475\sWC=cat;MC=Aat;MCF=0.0113;CAT=.;SRVL=." /> 227 <has_text_matching expression="hxb2_pol\tRT\t101\tK\tT\tmf0.01\t0.0013\t1574\tRC=aaa;AC=aCa;ACF=0.0013;CAT=.;SRVL=." />
227 </assert_contents> 228 </assert_contents>
228 </output> 229 </output>
229 230
230 <output name="output_stats"> 231 <output name="output_stats">
231 <assert_contents> 232 <assert_contents>
278 * align.bam 279 * align.bam
279 * coverage_file.csv 280 * coverage_file.csv
280 * dr_report.csv 281 * dr_report.csv
281 * filtered.fastq 282 * filtered.fastq
282 * hydra.vcf 283 * hydra.vcf
283 * mutation_report.hmcf 284 * mutation_report.aavf
284 * stats.txt 285 * stats.txt
285 286
286 The description of each of these directories/files are as follows: 287 The description of each of these directories/files are as follows:
287 288
288 * __run.conf__: The configuration used when this output was produced. 289 * __run.conf__: The configuration used when this output was produced.
290 * __align.bam__: The alignment file in bam format. 291 * __align.bam__: The alignment file in bam format.
291 * __coverage_file.csv__: A file with one entry per line with the AA position and the coverage at the position. 292 * __coverage_file.csv__: A file with one entry per line with the AA position and the coverage at the position.
292 * __dr_report.csv__: A report detailing the drug resistant mutations found, above the reporting threshold (default: 1%). 293 * __dr_report.csv__: A report detailing the drug resistant mutations found, above the reporting threshold (default: 1%).
293 * __filtered.fastq__: The reads remaining after the filtering stage. 294 * __filtered.fastq__: The reads remaining after the filtering stage.
294 * __hydra.vcf__: The variants found by the pipeline. 295 * __hydra.vcf__: The variants found by the pipeline.
295 * __mutation_report.hmcf__: The AA mutations found by the pipeline. 296 * __mutation_report.aavf__: The AA mutations found by the pipeline.
296 * __stats.txt__: A log file detailing size after filtering and major stages. 297 * __stats.txt__: A log file detailing size after filtering and major stages.
297 298
298 The __dr_report.csv__ file lists all found drug resistant mutations (mutations included in the mutation database) which have frequency greater than the reporting threshold. An example of this file is given below. 299 The __dr_report.csv__ file lists all found drug resistant mutations (mutations included in the mutation database) which have frequency greater than the reporting threshold. An example of this file is given below.
299 300
300 Example: __dr_report.csv__ 301 Example: __dr_report.csv__
301 302
302 Gene,Category,Surveillance,Wildtype,Position,Mutation,Mutation Frequency,Coverage 303 Gene,Category,Surveillance,Wildtype,Position,Mutation,Mutation Frequency,Coverage
303 RT,NNRTI,Yes,K,103,N,9.03,155 304 RT,NNRTI,Yes,K,103,N,9.03,155
304 305
305 The __mutation_report.hmcf__ files is our custom VCF like file which details all of the AA mutations found by the pipeline. An example if this file is given below. 306 The __mutation_report.aavf__ file is in AAVF format (https://github.com/winhiv/aavf-spec), an amino acid variant format inspired by the VCF format. The __mutation_report.aavf__ file details all of the AA mutations found by the pipeline. An example if this file is given below.
306 307
307 Example: __mutation_report.hmcf__ 308 Example: __mutation_report.aavf__
308 309
309 ##fileformat=HMCFv1 310 ##fileformat=AAVFv1.0
310 ##fileDate=20150008 311 ##fileDate=20220615
311 ##source=HyDRA 312 ##source=quasitools:hydra
312 ##reference=/home/ericenns/hydra/var/hxb2_pol.fas 313 ##reference=hxb2_pol.fas
313 ##INFO=<ID=MC,Number=.,Description="String"> 314 ##INFO=<ID=RC,Number=1,Type=String,Description="Reference Codon">
314 ##INFO=<ID=MCF,Number=.,Description="String"> 315 ##INFO=<ID=AC,Number=.,Type=String,Description="Alternate Codon">
315 ##INFO=<ID=WC,Number=.,Description="String"> 316 ##INFO=<ID=ACF,Number=.,Type=Float,Description="Alternate Codon Frequency,for each Alternate Codon,in the same order aslisted.">
316 ##FILTER=<ID=mf0.01,Description="Mutant freq below 0.01"> 317 ##INFO=<ID=CAT,Number=.,Type=String,Description="Drug Resistance Category">
317 #GENE CATEGORY SURVEILLANCE TYPE WILDTYPE POS MUTANT FILTER MUTANT_FREQ COVERAGE INFO 318 ##INFO=<ID=SRVL,Number=.,Type=String,Description="Drug Resistance Surveillance">
318 RT NNRTI Yes mutation K 103 N PASS 0.0903 155 WC=aaa;MC=aaC;MCF=0.0903 319 ##FILTER=<ID=af0.01,Description="Set if True; alt_freq<0.01">
320 #CHROM GENE POS REF ALT FILTER ALT_FREQ COVERAGE INFO
321 hxb2_pol RT 101 K P PASS 0.1423 1574 RC=aaa;AC=CCa;ACF=0.1423;CAT=NNRTI;SRVL=Yes
319 322
320 ]]></help> 323 ]]></help>
321 <citations> 324 <expand macro="citations" />
322 <citation type="bibtex">
323 @misc{GitHubquasitoolshydra,
324 title = {quasitools hydra},
325 publisher = {phac-nml},
326 journal = {GitHub repository},
327 url = {https://github.com/phac-nml/quasitools},
328 }
329 </citation>
330 </citations>
331 </tool> 325 </tool>