Mercurial > repos > nml > quasitools
changeset 9:18aad692772a draft default tip
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 | |
| files | aacoverage.xml callaavar.xml callcodonvar.xml callntvar.xml complexity_bam.xml complexity_fasta.xml consensus.xml distance.xml dnds.xml drmutations.xml hydra.xml macros.xml quality.xml |
| diffstat | 13 files changed, 140 insertions(+), 200 deletions(-) [+] |
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--- a/aacoverage.xml Tue Aug 06 08:50:28 2019 -0400 +++ b/aacoverage.xml Mon Jun 20 20:06:36 2022 +0000 @@ -1,13 +1,15 @@ -<tool id="aacoverage" name="Amino Acid Coverage" version="0.7.0"> +<tool id="aacoverage" name="Amino Acid Coverage" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>Builds an aa census and returns its coverage</description> - <requirements> - <requirement type="package" version="0.7.0">quasitools</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ - ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && + ln -s $input_bam '${input_bam.name}' && + ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' && - quasitools aacoverage $input_bam $ref_file $input_genes -o output.csv + quasitools aacoverage '${input_bam.name}' $ref_file $input_genes -o output.csv ]]></command> <inputs> @@ -44,14 +46,5 @@ A file with one entry per line with the AA position and the coverage at the position. ]]></help> - <citations> - <citation type="bibtex"> - @misc{GitHubquasitoolsaacoverage, - title = {quasitools aacoverage}, - publisher = {phac-nml}, - journal = {GitHub repository}, - url = {https://github.com/phac-nml/quasitools}, - } - </citation> - </citations> + <expand macro="citations" /> </tool>
--- a/callaavar.xml Tue Aug 06 08:50:28 2019 -0400 +++ b/callaavar.xml Mon Jun 20 20:06:36 2022 +0000 @@ -1,12 +1,15 @@ -<tool id="aavariants" name="Amino Acid Variants" version="0.7.0"> +<tool id="aavariants" name="Amino Acid Variants" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>Identifies amino acid mutations</description> - <requirements> - <requirement type="package" version="0.7.0">quasitools</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ - ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && - quasitools call aavar $input_bam $ref_file $input_genes + ln -s $input_bam '${input_bam.name}' && + ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' && + + quasitools call aavar '${input_bam.name}' $ref_file $input_genes #if $var_file: $var_file @@ -69,14 +72,5 @@ ]]></help> - <citations> - <citation type="bibtex"> - @misc{GitHubquasitoolscallaavar, - title = {quasitools callaavar}, - publisher = {phac-nml}, - journal = {GitHub repository}, - url = {https://github.com/phac-nml/quasitools}, - } - </citation> - </citations> + <expand macro="citations" /> </tool>
--- a/callcodonvar.xml Tue Aug 06 08:50:28 2019 -0400 +++ b/callcodonvar.xml Mon Jun 20 20:06:36 2022 +0000 @@ -1,14 +1,17 @@ -<tool id="callcodonvar" name="Codon Variants" version="0.7.0"> +<tool id="callcodonvar" name="Codon Variants" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>Identifies codon variants and non-synonymous/synonymous mutations</description> - <requirements> - <requirement type="package" version="0.7.0">quasitools</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ cat $input_genes && - ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && - quasitools call codonvar $input_bam $ref_file $offset $input_genes + ln -s $input_bam '${input_bam.name}' && + ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' && + + quasitools call codonvar '${input_bam.name}' $ref_file $offset $input_genes #if $var_file: $var_file @@ -56,14 +59,5 @@ a synonymous or non-synonymous mutation. ]]></help> - <citations> - <citation type="bibtex"> - @misc{GitHubquasitoolscallcodonvar, - title = {quasitools callcodonvar}, - publisher = {phac-nml}, - journal = {GitHub repository}, - url = {https://github.com/phac-nml/quasitools}, - } - </citation> - </citations> + <expand macro="citations" /> </tool>
--- a/callntvar.xml Tue Aug 06 08:50:28 2019 -0400 +++ b/callntvar.xml Mon Jun 20 20:06:36 2022 +0000 @@ -1,12 +1,15 @@ -<tool id="callntvar" name="Nucleotide Variants" version="0.7.0"> +<tool id="callntvar" name="Nucleotide Variants" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>Identifies nucleotide variants</description> - <requirements> - <requirement type="package" version="0.7.0">quasitools</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ - ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && - quasitools call ntvar $input_bam $ref_file + ln -s $input_bam '${input_bam.name}' && + ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' && + + quasitools call ntvar '${input_bam.name}' $ref_file #if $error_rate: -e $error_rate @@ -45,14 +48,5 @@ Call nucleotide variants for a given BAM file and a supplied reference file. ]]></help> - <citations> - <citation type="bibtex"> - @misc{GitHubquasitoolscallntvar, - title = {quasitools callntvar}, - publisher = {phac-nml}, - journal = {GitHub repository}, - url = {https://github.com/phac-nml/quasitools}, - } - </citation> - </citations> + <expand macro="citations" /> </tool>
--- a/complexity_bam.xml Tue Aug 06 08:50:28 2019 -0400 +++ b/complexity_bam.xml Mon Jun 20 20:06:36 2022 +0000 @@ -1,12 +1,14 @@ -<tool id="complexity_bam" name="Complexity BAM" version="0.7.0"> - <requirements> - <requirement type="package" version="0.7.0">quasitools</requirement> - </requirements> +<tool id="complexity_bam" name="Complexity BAM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ - ln -f -s '${input_bam.metadata.bam_index}' '${input_bam}.bai' && + ln -s $input_bam '${input_bam.name}' && + ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' && - quasitools complexity bam '$ref_file' '$input_bam' $k -f '$filter_size' -o output.csv + quasitools complexity bam '$ref_file' '${input_bam.name}' $k -f '$filter_size' -o output.csv ]]></command> <inputs> @@ -44,14 +46,5 @@ ]]></help> - <citations> - <citation type="bibtex"> - @misc{GitHubquasitoolscomplexity, - title = {quasitools complexity}, - publisher = {phac-nml}, - journal = {GitHub repository}, - url = {https://github.com/phac-nml/quasitools}, - } - </citation> - </citations> + <expand macro="citations" /> </tool>
--- a/complexity_fasta.xml Tue Aug 06 08:50:28 2019 -0400 +++ b/complexity_fasta.xml Mon Jun 20 20:06:36 2022 +0000 @@ -1,7 +1,8 @@ -<tool id="complexity_fasta" name="Complexity FASTA" version="0.7.0"> - <requirements> - <requirement type="package" version="0.7.0">quasitools</requirement> - </requirements> +<tool id="complexity_fasta" name="Complexity FASTA" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ quasitools complexity fasta '$input_fasta' -o output.csv @@ -38,14 +39,5 @@ ]]></help> - <citations> - <citation type="bibtex"> - @misc{GitHubquasitoolscomplexity, - title = {quasitools complexity}, - publisher = {phac-nml}, - journal = {GitHub repository}, - url = {https://github.com/phac-nml/quasitools}, - } - </citation> - </citations> + <expand macro="citations" /> </tool>
--- a/consensus.xml Tue Aug 06 08:50:28 2019 -0400 +++ b/consensus.xml Mon Jun 20 20:06:36 2022 +0000 @@ -1,12 +1,15 @@ -<tool id="consensus" name="Consensus Sequence" version="0.7.0"> +<tool id="consensus" name="Consensus Sequence" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>Generate a consensus sequence from a BAM file</description> - <requirements> - <requirement type="package" version="0.7.0">quasitools</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ - ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && - quasitools consensus $input_bam $ref_file + ln -s $input_bam '${input_bam.name}' && + ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' && + + quasitools consensus '${input_bam.name}' $ref_file #if $fasta_id.type == 'default': -i '${input_bam.element_identifier}' @@ -88,14 +91,5 @@ When there is zero coverage or no bases meet the percentage threshold (only when percentage is < 100) a n will be incorporated. ]]></help> - <citations> - <citation type="bibtex"> - @misc{GitHubquasitoolsconsensus, - title = {quasitools consensus}, - publisher = {phac-nml}, - journal = {GitHub repository}, - url = {https://github.com/phac-nml/quasitools}, - } - </citation> - </citations> + <expand macro="citations" /> </tool>
--- a/distance.xml Tue Aug 06 08:50:28 2019 -0400 +++ b/distance.xml Mon Jun 20 20:06:36 2022 +0000 @@ -1,8 +1,9 @@ -<tool id="distance" name="Quasispecies Distance" version="0.7.0"> +<tool id="distance" name="Quasispecies Distance" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>Calculate the evolutionary distance between viral quasispecies.</description> - <requirements> - <requirement type="package" version="0.7.0">quasitools</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ #for $bam_file in $bam_files @@ -114,14 +115,5 @@ A CSV file containing a matrix of similarities or distances, as requested by the user. ]]></help> - <citations> - <citation type="bibtex"> - @misc{GitHubquasitoolsdistance, - title = {quasitools distance}, - publisher = {phac-nml}, - journal = {GitHub repository}, - url = {https://github.com/phac-nml/quasitools}, - } - </citation> - </citations> + <expand macro="citations" /> </tool>
--- a/dnds.xml Tue Aug 06 08:50:28 2019 -0400 +++ b/dnds.xml Mon Jun 20 20:06:36 2022 +0000 @@ -1,8 +1,9 @@ -<tool id="dnds" name="dNdS Report" version="0.7.0"> +<tool id="dnds" name="dNdS Report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>Calculate the dN/dS value for each region in a bed file</description> - <requirements> - <requirement type="package" version="0.7.0">quasitools</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ quasitools dnds $csv_file $ref_file $offset -o output.csv @@ -36,14 +37,5 @@ Determines the dNdS ratio for each codon variant in a supplied csv file (codon variants). ]]></help> - <citations> - <citation type="bibtex"> - @misc{GitHubquasitoolsdnds, - title = {quasitools dnds}, - publisher = {phac-nml}, - journal = {GitHub repository}, - url = {https://github.com/phac-nml/quasitools}, - } - </citation> - </citations> + <expand macro="citations" /> </tool>
--- a/drmutations.xml Tue Aug 06 08:50:28 2019 -0400 +++ b/drmutations.xml Mon Jun 20 20:06:36 2022 +0000 @@ -1,12 +1,15 @@ -<tool id="drmutations" name="Drug Resistance Mutations" version="0.7.0"> +<tool id="drmutations" name="Drug Resistance Mutations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description></description> - <requirements> - <requirement type="package" version="0.7.0">quasitools</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ - ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && - quasitools drmutations $input_bam $ref_file $var_file $input_genes + ln -s $input_bam '${input_bam.name}' && + ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' && + + quasitools drmutations '${input_bam.name}' $ref_file $var_file $input_genes #if $mutation_db: $mutation_db @@ -81,14 +84,5 @@ A CSV file containing the drug resistant mutations found. ]]></help> - <citations> - <citation type="bibtex"> - @misc{GitHubquasitoolsdrmutations, - title = {quasitools drmutations}, - publisher = {phac-nml}, - journal = {GitHub repository}, - url = {https://github.com/phac-nml/quasitools}, - } - </citation> - </citations> + <expand macro="citations" /> </tool>
--- a/hydra.xml Tue Aug 06 08:50:28 2019 -0400 +++ b/hydra.xml Mon Jun 20 20:06:36 2022 +0000 @@ -1,8 +1,9 @@ -<tool id="hydra" name="Hydra pipeline" version="0.5.1"> +<tool id="hydra" name="Hydra pipeline" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>Identifies drug resistance within an NGS dataset</description> - <requirements> - <requirement type="package" version="0.5.1">quasitools</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ quasitools hydra @@ -181,7 +182,7 @@ <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="vcf" label="HyDRA: aa mutations output" name="output_aa_mt" from_work_dir="output/mutation_report.hmcf" /> + <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> @@ -221,9 +222,9 @@ </output> <output name="output_aa_mt"> <assert_contents> - <has_text_matching expression="#CHROM\sGENE\sTYPE\sWILDTYPE\sPOS\sMUTANT\sFILTER\sMUTANT_FREQ\sCOVERAGE\sINFO"/> - <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" /> - <has_text_matching expression="hxb2_pol\sRT\smutation\sH\s221\sN\sPASS\s0.0113\s2475\sWC=cat;MC=Aat;MCF=0.0113;CAT=.;SRVL=." /> + <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> @@ -280,7 +281,7 @@ * dr_report.csv * filtered.fastq * hydra.vcf - * mutation_report.hmcf + * mutation_report.aavf * stats.txt The description of each of these directories/files are as follows: @@ -292,7 +293,7 @@ * __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.hmcf__: The AA mutations 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. @@ -302,30 +303,23 @@ Gene,Category,Surveillance,Wildtype,Position,Mutation,Mutation Frequency,Coverage RT,NNRTI,Yes,K,103,N,9.03,155 -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. +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.hmcf__ +Example: __mutation_report.aavf__ - ##fileformat=HMCFv1 - ##fileDate=20150008 - ##source=HyDRA - ##reference=/home/ericenns/hydra/var/hxb2_pol.fas - ##INFO=<ID=MC,Number=.,Description="String"> - ##INFO=<ID=MCF,Number=.,Description="String"> - ##INFO=<ID=WC,Number=.,Description="String"> - ##FILTER=<ID=mf0.01,Description="Mutant freq below 0.01"> - #GENE CATEGORY SURVEILLANCE TYPE WILDTYPE POS MUTANT FILTER MUTANT_FREQ COVERAGE INFO - RT NNRTI Yes mutation K 103 N PASS 0.0903 155 WC=aaa;MC=aaC;MCF=0.0903 + ##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> - <citations> - <citation type="bibtex"> - @misc{GitHubquasitoolshydra, - title = {quasitools hydra}, - publisher = {phac-nml}, - journal = {GitHub repository}, - url = {https://github.com/phac-nml/quasitools}, - } - </citation> - </citations> + <expand macro="citations" /> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Jun 20 20:06:36 2022 +0000 @@ -0,0 +1,22 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">quasitools</requirement> + </requirements> + </xml> + <token name="@TOOL_VERSION@">0.7.0</token> + <token name="@VERSION_SUFFIX@">1</token> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{GitHubquasitools, + title = {quasitools}, + publisher = {phac-nml}, + journal = {GitHub repository}, + url = {https://github.com/phac-nml/quasitools}, + } + </citation> + </citations> + </xml> +</macros>
--- a/quality.xml Tue Aug 06 08:50:28 2019 -0400 +++ b/quality.xml Mon Jun 20 20:06:36 2022 +0000 @@ -1,8 +1,9 @@ -<tool id="quality" name="Quality control" version="0.7.0"> +<tool id="quality" name="Quality control" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>Performs quality control on FASTQ reads.</description> - <requirements> - <requirement type="package" version="0.7.0">quasitools</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ quasitools quality @@ -167,14 +168,5 @@ =============== Perform quality control on FASTQ reads.]]></help> - <citations> - <citation type="bibtex"> - @misc{GitHubquasitoolsquality, - title = {quasitools quality}, - publisher = {phac-nml}, - journal = {GitHub repository}, - url = {https://github.com/phac-nml/quasitools}, - } - </citation> - </citations> + <expand macro="citations" /> </tool>