Mercurial > repos > nml > quasitools
changeset 4:8cdffc02d2e2 draft
planemo upload for repository https://github.com/phac-nml/quasitools commit 19e0f266ee455b82432e2d7b987b35de8c7a14d5
| author | nml |
|---|---|
| date | Wed, 25 Apr 2018 10:38:00 -0400 |
| parents | 8dacd75ca8f1 |
| children | b69e898b8109 |
| files | aacoverage.xml callaavar.xml callcodonvar.xml callntvar.xml consensus.xml distance.xml dnds.xml drmutations.xml hydra.xml test-data/quasi1.bai test-data/quasi1.bam test-data/quasi2.bai test-data/quasi2.bam |
| diffstat | 13 files changed, 171 insertions(+), 13 deletions(-) [+] |
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--- a/aacoverage.xml Mon Mar 26 15:38:19 2018 -0400 +++ b/aacoverage.xml Wed Apr 25 10:38:00 2018 -0400 @@ -1,7 +1,7 @@ <tool id="aacoverage" name="Amino Acid Coverage" version="0.1.0"> <description>Builds an aa census and returns its coverage</description> <requirements> - <requirement type="package" version="0.2.3">quasitools</requirement> + <requirement type="package" version="0.3.1">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[
--- a/callaavar.xml Mon Mar 26 15:38:19 2018 -0400 +++ b/callaavar.xml Wed Apr 25 10:38:00 2018 -0400 @@ -1,7 +1,7 @@ <tool id="aavariants" name="Amino Acid Variants" version="0.1.0"> <description>Identifies amino acid mutations</description> <requirements> - <requirement type="package" version="0.2.3">quasitools</requirement> + <requirement type="package" version="0.3.1">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[
--- a/callcodonvar.xml Mon Mar 26 15:38:19 2018 -0400 +++ b/callcodonvar.xml Wed Apr 25 10:38:00 2018 -0400 @@ -1,7 +1,7 @@ <tool id="callcodonvar" name="Codon Variants" version="0.1.0"> <description>Identifies codon variants and non-synonymous/synonymous mutations</description> <requirements> - <requirement type="package" version="0.2.3">quasitools</requirement> + <requirement type="package" version="0.3.1">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[
--- a/callntvar.xml Mon Mar 26 15:38:19 2018 -0400 +++ b/callntvar.xml Wed Apr 25 10:38:00 2018 -0400 @@ -1,7 +1,7 @@ <tool id="callntvar" name="Nucleotide Variants" version="0.1.0"> <description>Identifies nucleotide variants</description> <requirements> - <requirement type="package" version="0.2.3">quasitools</requirement> + <requirement type="package" version="0.3.1">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[
--- a/consensus.xml Mon Mar 26 15:38:19 2018 -0400 +++ b/consensus.xml Wed Apr 25 10:38:00 2018 -0400 @@ -1,7 +1,7 @@ <tool id="consensus" name="Consensus Sequence" version="0.2.0"> <description>Generate a consensus sequence from a BAM file</description> <requirements> - <requirement type="package" version="0.2.3">quasitools</requirement> + <requirement type="package" version="0.3.1">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/distance.xml Wed Apr 25 10:38:00 2018 -0400 @@ -0,0 +1,127 @@ +<tool id="distance" name="Quasispecies Distance" version="0.1.0"> + <description>Calculate the evolutionary distance between viral quasispecies.</description> + <requirements> + <requirement type="package" version="0.3.1">quasitools</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + + #for $bam_file in $bam_files + ln -s $bam_file '${bam_file.name}' && + ln -s $bam_file.metadata.bam_index '${bam_file.name}.bai' && + #end for + + quasitools distance $ref_file + + #for $bam_file in $bam_files + '${bam_file.name}' + #end for + + -o matrix.csv + + $normalize + + #if $low_coverage.coverage_selector == 'keep': + -k + #else if $low_coverage.coverage_selector == 'remove': + -r + #else if $low_coverage.coverage_selector == 'truncate': + -t + #end if + + #if $select_range.manual_input == 'select_range': + -s $select_range.start + -e $select_range.end + #end if + + $output_similarity + + ]]></command> + <inputs> + <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" /> + <param name="bam_files" type="data" format="bam" optional="false" multiple="true" label="BAM files" min="2" help="At least two BAM files are required to perform quasispecies distance comparison."/> + <param name="normalize" type="boolean" truevalue="-n" falsevalue="-dn" checked="True" label="Normalize pileups" help="Normalize read count data so that the read counts per 4-tuple (A, C, T, G) sum to one."/> + <param name="output_similarity" type="boolean" truevalue="-os" falsevalue="-od" checked="False" label="Output cosine similarity instead of angular cosine distance." help="Cosine similarity is not a distance metric." /> + <conditional name="low_coverage"> + <param name="coverage_selector" type="select" label="Choose how to treat zero coverage positions."> + <option value="remove" selected = "true">Remove all zero coverage positions.</option> + <option value="keep">Keep all zero coverage positions.</option> + <option value="truncate">Truncate zero coverage positions at start and end of pileup.</option> + </param> + <when value="remove"> + </when> + <when value="keep"> + </when> + <when value="truncate"> + </when> + </conditional> + <conditional name="select_range"> + <param name="manual_input" type="select" label="Select pileup range." help="Currently only supports selection of custom start and end position for one single reference."> + <option value="keep_range" selected = "true">Use original pileup for distance calculation.</option> + <option value="select_range">Manually select pileup's start and end position for distance calculation.</option> + </param> + <when value="select_range"> + <param name="start" type="integer" optional="false" min="1" value="1" label="Select one-indexed start base position." help="Positions before start position will be ignored in the distance calculation." /> + <param name="end" type="integer" optional="false" min="1" value="1" label="Select one-indexed end base position." help="Positions after end position will be ignored in the distance calculation." /> + </when> + <when value="keep_range"> + </when> + </conditional> + </inputs> + <outputs> + <data format="csv" name="matrix" from_work_dir="matrix.csv" /> + </outputs> + <tests> + <test> + <param name="ref_file" value="hxb2_pol.fas" /> + <param name="bam_files" value="quasi1.bam,quasi2.bam" /> + <param name="normalize" value="-n" /> + <param name="coverage_selector" value="truncate" /> + <param name="manual_input" value="keep_range" /> + <param name="output_similarity" value="-od" /> + <output name="matrix" ftype="csv" > + <assert_contents> + <has_text_matching expression="Quasispecies"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + +Quasispecies Distance +===================== + +Determines the evolutionary distance between viral quasispecies. +Uses the angular cosine distance function by default. + +------ +Inputs +------ + +1. FASTA Consensus file +2. Two or more BAM files (otherwise tool will throw an error) + +---------- +Parameters +---------- +1. Normalize pileup (True or False) +2. Select custom start and end position. Currently only supports selection of custom start and end position for one single reference. +3. Choose how to treat zero coverage regions (keep, remove all, or truncate) + +------- +Outputs +------- + +CSV containing distance matrix. + + ]]></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> +</tool>
--- a/dnds.xml Mon Mar 26 15:38:19 2018 -0400 +++ b/dnds.xml Wed Apr 25 10:38:00 2018 -0400 @@ -1,7 +1,7 @@ <tool id="dnds" name="dNdS Report" version="0.1.0"> <description>Calculate the dN/dS value for each region in a bed file</description> <requirements> - <requirement type="package" version="0.2.3">quasitools</requirement> + <requirement type="package" version="0.3.1">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[
--- a/drmutations.xml Mon Mar 26 15:38:19 2018 -0400 +++ b/drmutations.xml Wed Apr 25 10:38:00 2018 -0400 @@ -1,7 +1,7 @@ <tool id="drmutations" name="Drug Resistance Mutations" version="0.1.0"> <description></description> <requirements> - <requirement type="package" version="0.2.3">quasitools</requirement> + <requirement type="package" version="0.3.1">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[
--- a/hydra.xml Mon Mar 26 15:38:19 2018 -0400 +++ b/hydra.xml Wed Apr 25 10:38:00 2018 -0400 @@ -1,7 +1,7 @@ -<tool id="hydra" name="Hydra pipeline" version="0.1.0"> +<tool id="hydra" name="Hydra pipeline" version="0.2.0"> <description>Identifies drug resistance within an NGS dataset</description> <requirements> - <requirement type="package" version="0.2.3">quasitools</requirement> + <requirement type="package" version="0.3.1">quasitools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ @@ -64,8 +64,19 @@ -mf '$min_freq' #end if - #if $generate_consensus: + #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 $filter_ns: @@ -103,7 +114,27 @@ <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="generate_consensus" type="boolean" truevalue="--generate_consensus" falsevalue="" checked="False" label="Generate consensus" /> + <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> <param name="filter_ns" type="boolean" truevalue="--ns" falsevalue="" checked="False" label="Filter out n's" /> </inputs> <outputs> @@ -115,8 +146,8 @@ <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: 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>generate_consensus</filter> + <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>