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diff hydra.xml @ 0:1f1214983a1c draft default tip
planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e
| author | nml |
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| date | Mon, 20 Jun 2022 20:05:57 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hydra.xml Mon Jun 20 20:05:57 2022 +0000 @@ -0,0 +1,325 @@ +<tool id="hydra" name="Hydra pipeline" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> + <description>Identifies drug resistance within an NGS dataset</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + + quasitools hydra + + ## Preparing file input. + #if $data_type.type == "paired": + + '$data_type.fastq_input1' + '$data_type.fastq_input2' + + #elif $data_type.type == "collection": + + '$data_type.fastq_input1.forward' + '$data_type.fastq_input1.reverse' + + #elif $data_type.type == "single": + + '$data_type.fastq_input1' + + #end if + + #if $mutation_db: + -m '$mutation_db' + #end if + + #if $reporting_threshold: + -rt '$reporting_threshold' + #end if + + #if $consensus_pct: + -cp '$consensus_pct' + #end if + + #if $length_cutoff: + -lc '$length_cutoff' + #end if + + #if $score_cutoff: + -sc '$score_cutoff' + #end if + + #if $error_rate: + -e '$error_rate' + #end if + + #if $min_read_qual: + -rq '$min_read_qual' + #end if + + #if $min_variant_qual: + -vq '$min_variant_qual' + #end if + + #if $min_depth: + -md '$min_depth' + #end if + + #if $min_ac: + -ma '$min_ac' + #end if + + #if $min_freq: + -mf '$min_freq' + #end if + + #if $consensus.consensus_bool == "true_consensus": + --generate_consensus + + #if $consensus.fasta_id.type == "default": + --id + #if $data_type.type == "paired": + '${fastq_input1.element_identifier}'_'${fastq_input2.element_identifier}' + #elif $data_type.type == "single": + '${fastq_input1.element_identifier}' + #end if + #elif $consensus.fasta_id.type == "custom": + --id '$consensus.fasta_id.custom_id' + #end if + #end if + + #if $low_quality.qual_selector == "filter_ns": + --ns + #elif $low_quality.qual_selector == "mask_reads": + --mask_reads + #end if + + #if $score_type.score_selector == "median": + --median + #elif $score_type.score_selector == "mean": + --mean + #end if + + $trim_reads + + -o output + + ]]></command> + <inputs> + <conditional name="data_type"> + <param name="type" type="select" label="Specify the read type."> + <option value="single">Single-end Data</option> + <option value="paired">Paired-end Data</option> + <option value="collection">Collection Paired-end Data</option> + </param> + <when value="single"> + <param name="fastq_input1" type="data" format="fastq" label="Single end read file(s)"/> + </when> + <when value="paired"> + <param name="fastq_input1" type="data" format="fastq" label="Forward paired-end read file"/> + <param name="fastq_input2" type="data" format="fastq" label="Reverse paired-end read file"/> + </when> + <when value="collection"> + <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastq" collection_type="paired" /> + </when> + </conditional> + <param name="mutation_db" type="data" format="tsv" optional="true" label="Mutation DB" help="Defaults to HIV mutation database." /> + <param name="reporting_threshold" type="integer" optional="true" min="1" max="100" value="1" label="Reporting threshold. Defaults to 1." help="Minimum mutation frequency to report." /> + <param name="consensus_pct" type="integer" optional="true" min="1" max="20" value="20" label="Consensus percentage" help="Minimum mutation frequency to report. Defaults to 20." /> + <param name="length_cutoff" type="integer" optional="true" min="1" max="1000" label="Length cutoff" value="100" help="Reads which fall short of the specified length will be filtered out. Defaults to 100." /> + <param name="score_cutoff" type="integer" optional="true" min="0" max="40" label="Score cutoff" value="30" help="Reads whose median or mean quality score (depending on the score type specified) is less than the specified score cutoff value will be filtered out. Defaults to 30." /> + <param name="error_rate" type="float" optional="true" min="0" max="1" label="Error rate" value="0.0021" help="Estimated sequencing error rate. Defaults to 0.0021."/> + <param name="min_variant_qual" type="integer" optional="true" min="1" max="100" label="Minimum quality" value="30" help="Minimum required quality for variant to be considered later on in the pipeline. Defaults to 30." /> + <param name="min_read_qual" type="integer" optional="true" min="1" max="100" label="Minimum quality" value="30" help="Minimum required quality for a position in a read not to be masked, is masking is enabled. Defaults to 30." /> + <param name="min_depth" type="integer" optional="true" min="0" max="5000" label="Minimum depth" value="100" help="Minimum required depth for variant to be considered later on in the pipeline. Defaults to 100." /> + <param name="min_ac" type="integer" optional="true" min="0" max="5000" label="Minimum allele count" value="5" help="Minimum required allele count for variant to be considered later on in the pipeline. Defaults to 5." /> + <param name="min_freq" type="float" optional="true" min="0" max="1" label="Minimum frequency" value="0.01" help="Minimum required frequency for variant to be considered later on in the pipeline. Defaults to 0.01." /> + <param name="trim_reads" type="boolean" optional="true" checked="false" truevalue="-tr" falsevalue="" label="Trim reads" help="Iteratively trim reads based on filter values if enabled." /> + <conditional name="consensus"> + <param name="consensus_bool" type="select" label="Generate consensus sequence." multiple="false" display="radio"> + <option value="true_consensus">True</option> + <option selected="true" value="false_consensus">False</option> + </param> + <when value="true_consensus"> + <conditional name="fasta_id"> + <param name="type" type="select" label="Specify consensus fasta identifier" multiple="false" display="radio"> + <option value="default" >Use fasta dataset name</option> + <option value="custom">Use custom name</option> + </param> + <when value="default"> + </when> + <when value="custom"> + <param name="custom_id" type="text" optional="false" value="custom_id" label="Fasta identifier" help="Type in a fasta identifier."/> + </when> + </conditional> + </when> + <when value="false_consensus"> + </when> + </conditional> + <conditional name="low_quality"> + <param name="qual_selector" type="select" label="Filter out regions masked, or mask low coverage regions with n's." multiple="false" display="radio"> + <option value="filter_ns">Filter out regions with n's</option> + <option value="mask_reads">Mask low coverage regions with n's</option> + <option value="neither" selected="true">Do not filter or mask low coverage regions.</option> + </param> + <when value="filter_ns"> + </when> + <when value="mask_reads"> + </when> + <when value="neither"> + </when> + </conditional> + <conditional name="score_type"> + <param name="score_selector" type="select" label="Use either median score (default) or mean score for the score cutoff value." multiple="false" display="radio"> + <option value="median" selected="true">Use median score</option> + <option value="mean">Use mean score</option> + </param> + <when value="median"> + </when> + <when value="mean"> + </when> + </conditional> + </inputs> + <outputs> + <data format="bam" label="HyDRA: alignment bam output" name="output_bam" from_work_dir="output/align.bam" /> + <data format="csv" label="HyDRA: coverage output" name="output_coverage" from_work_dir="output/coverage_file.csv" /> + <data format="csv" label="HyDRA: drug resistance output" name="output_dr" from_work_dir="output/dr_report.csv" /> + <data format="fastq" label="HyDRA: filtered reads output" name="output_filtered" from_work_dir="output/filtered.fastq" /> + <data format="vcf" label="HyDRA: variants output" name="output_hydra" from_work_dir="output/hydra.vcf" /> + <data format="txt" label="HyDRA: aa mutations output" name="output_aa_mt" from_work_dir="output/mutation_report.aavf" /> + <data format="txt" label="HyDRA: stats output" name="output_stats" from_work_dir="output/stats.txt" /> + <data format="fasta" label="HyDRA: consensus output" name="output_consensus" from_work_dir="output/consensus.fasta" > + <filter>consensus['consensus_bool'] == "true_consensus"</filter> + </data> + </outputs> + <tests> + <test> + <param name="type" value="single"/> + <param name="fastq_input1" value="forward.fastq" /> + <param name="score_selector" value="mean" /> + <output name="output_coverage"> + <assert_contents> + <has_text text="frame: 0" /> + <has_text text="1,0" /> + <has_text text="948,0" /> + </assert_contents> + </output> + <output name="output_dr"> + <assert_contents> + <has_text text="Chromosome,Gene,Category,Surveillance,Wildtype,Position,Mutation,Mutation Frequency,Coverage" /> + <has_text text="hxb2_pol,RT,NNRTI,Yes,K,101,P,14.23,1574" /> + <has_text text="hxb2_pol,RT,NNRTI,Yes,K,103,N,5.49,1912" /> + <has_text text="hxb2_pol,RT,NNRTI,Yes,Y,181,C,24.07,4557" /> + <has_text text="hxb2_pol,RT,NNRTI,Yes,Y,181,I,18.04,4557" /> + <has_text text="hxb2_pol,RT,NNRTI,Yes,Y,181,V,20.08,4557" /> + <has_text text="hxb2_pol,RT,NNRTI,Yes,Y,188,C,2.81,3454" /> + <has_text text="hxb2_pol,RT,NNRTI,Yes,G,190,A,5.20,3233" /> + <has_text text="hxb2_pol,RT,NNRTI,Yes,G,190,S,6.68,3233" /> + </assert_contents> + </output> + <output name="output_hydra"> + <assert_contents> + <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"/> + <has_text_matching expression="hxb2_pol\s576\s.\sa\sg\s100\sPASS\sDP=805;AC=245;AF=0.3043" /> + <has_text_matching expression="hxb2_pol\s958\s.\sc\sa\s100\sPASS\sDP=2503;AC=28;AF=0.0112" /> + </assert_contents> + </output> + <output name="output_aa_mt"> + <assert_contents> + <has_text_matching expression="#CHROM\tGENE\tPOS\tREF\tALT\tFILTER\tALT_FREQ\tCOVERAGE\tINFO"/> + <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" /> + <has_text_matching expression="hxb2_pol\tRT\t101\tK\tT\tmf0.01\t0.0013\t1574\tRC=aaa;AC=aCa;ACF=0.0013;CAT=.;SRVL=." /> + </assert_contents> + </output> + + <output name="output_stats"> + <assert_contents> + <has_text text="Input Size: 25000"/> + <has_text text="Number of reads filtered due to length: 15074"/> + <has_text text="Number of reads filtered due to average quality score: 501"/> + <has_text text="Number of reads filtered due to presence of Ns: 0"/> + <has_text text="Number of reads filtered due to excess coverage: 0"/> + <has_text text="Number of reads filtered due to poor mapping: 12"/> + <has_text text="Percentage of reads filtered: 62.35"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + +HyDRA - HIV Drug Resistance Analyzer +==================================== + +The HyDRA pipeline provides a pipeline for identifying drug resistance within a Next Generation Sequencing dataset. The pipeline takes as input the raw reads produced by a Next Generation Sequencer and produces a report detailing found drug resistance per sample. + +Authors +------- + +The HyDRA pipeline was developed by Eric Enns and David Peddle. + +Stages +------ + +The HyDRA pipleine proceeds through the following stages: + +1. Quality Control/Filtering +2. Reference mapping using bowtie2. +3. Variant Calling and filtering using a Poisson distribution. +4. AA Mutation Calling and filtering. +5. Drug Resistance report generation. + +Details +------- + +The following is an example for running the pipeline, using our included test dataset: + * Output directory name: "/tmp/hydra_out" + * Forward reads: "reads_w_K103N.fastq" + +### Output ### + +The detailed output directory tree looks as follows: + + /tmp/hydra_out/ + * align.bam + * coverage_file.csv + * dr_report.csv + * filtered.fastq + * hydra.vcf + * mutation_report.aavf + * stats.txt + +The description of each of these directories/files are as follows: + +* __run.conf__: The configuration used when this output was produced. +* __reads_w_K103N/__: The results directory for the input file reads_w_K103N.fastq + * __align.bam__: The alignment file in bam format. + * __coverage_file.csv__: A file with one entry per line with the AA position and the coverage at the position. + * __dr_report.csv__: A report detailing the drug resistant mutations found, above the reporting threshold (default: 1%). + * __filtered.fastq__: The reads remaining after the filtering stage. + * __hydra.vcf__: The variants found by the pipeline. + * __mutation_report.aavf__: The AA mutations found by the pipeline. + * __stats.txt__: A log file detailing size after filtering and major stages. + +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. + +Example: __dr_report.csv__ + + Gene,Category,Surveillance,Wildtype,Position,Mutation,Mutation Frequency,Coverage + RT,NNRTI,Yes,K,103,N,9.03,155 + +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. + +Example: __mutation_report.aavf__ + + ##fileformat=AAVFv1.0 + ##fileDate=20220615 + ##source=quasitools:hydra + ##reference=hxb2_pol.fas + ##INFO=<ID=RC,Number=1,Type=String,Description="Reference Codon"> + ##INFO=<ID=AC,Number=.,Type=String,Description="Alternate Codon"> + ##INFO=<ID=ACF,Number=.,Type=Float,Description="Alternate Codon Frequency,for each Alternate Codon,in the same order aslisted."> + ##INFO=<ID=CAT,Number=.,Type=String,Description="Drug Resistance Category"> + ##INFO=<ID=SRVL,Number=.,Type=String,Description="Drug Resistance Surveillance"> + ##FILTER=<ID=af0.01,Description="Set if True; alt_freq<0.01"> + #CHROM GENE POS REF ALT FILTER ALT_FREQ COVERAGE INFO + hxb2_pol RT 101 K P PASS 0.1423 1574 RC=aaa;AC=CCa;ACF=0.1423;CAT=NNRTI;SRVL=Yes + + ]]></help> + <expand macro="citations" /> +</tool>