Mercurial > repos > devteam > freebayes
diff freebayes.xml @ 3:9f3d6c3098ac draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
| author | devteam |
|---|---|
| date | Mon, 09 Nov 2015 11:37:39 -0500 |
| parents | 14f952d2a9db |
| children | c171daf263dd |
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--- a/freebayes.xml Thu Dec 11 18:38:34 2014 -0500 +++ b/freebayes.xml Mon Nov 09 11:37:39 2015 -0500 @@ -1,7 +1,7 @@ <?xml version="1.0"?> -<tool id="freebayes" name="FreeBayes" version="0.3"> +<tool id="freebayes" name="FreeBayes" version="0.4.1"> <requirements> - <requirement type="package" version="0.9.18_0059bdf">freebayes</requirement> + <requirement type="package" version="0_9_20_b040236">freebayes</requirement> <requirement type="package" version="0.1.18">samtools</requirement> </requirements> <description> - bayesian genetic variant detector</description> @@ -76,21 +76,55 @@ --min-coverage "${options_type.min_coverage}" ## Command line direct text entry is not allowed at this time for security reasons - -## #elif str( $options_type.options_type_selector ) == "cline": - -## ${options_type.cline} - -## @optional_inputs_outputs@ #elif str( $options_type.options_type_selector ) == "full": - -##optional inputs and outputs + + #if $options_type.optional_inputs.optional_inputs_selector: + + ${options_type.optional_inputs.report_monomorphic} - @optional_inputs_outputs@ + #if $options_type.optional_inputs.output_trace_option: + --trace "${output_trace}" + #end if + + #if $options_type.optional_inputs.output_failed_alleles_option: + --failed-alleles "${output_failed_alleles_bed}" + #end if + + #if $options_type.optional_inputs.samples: + --samples "${options_type.optional_inputs.samples}" + #end if + + #if $options_type.optional_inputs.populations: + --populations "${options_type.optional_inputs.populations}" + #end if + + #if $options_type.optional_inputs.A: + --cnv-map "${options_type.optional_inputs.A}" + #end if + + #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf": + --variant-input "input_variant_vcf.vcf.gz" ## input_variant_vcf.vcf.gz is symlinked to a galaxy-generated dataset in "Tabixize optional input_varinat_vcf file" section of the command line above + ${options_type.optional_inputs.input_variant_type.only_use_input_alleles} + #end if + + #if $options_type.optional_inputs.haplotype_basis_alleles: + --haplotype-basis-alleles "${options_type.optional_inputs.haplotype_basis_alleles}" + #end if + + #if $options_type.optional_inputs.observation_bias: + --observation-bias "${options_type.optional_inputs.observation_bias}" + #end if + + #if $options_type.optional_inputs.contamination_estimates: + --contamination-estimates "${options_type.optional_inputs.contamination_estimates}" + #end if + + #end if ## REPORTING - + + #if str( $options_type.reporting.reporting_selector ) == "True": --pvar ${options_type.reporting.pvar} #end if @@ -193,87 +227,6 @@ </command> - <macros> - <token name="@optional_inputs_outputs@"> - ## This token gets injected in commane in two instances: when options_type.options_type_selector == "full" and "cline" ( cline is not supported at this time ) - - #if $options_type.optional_inputs.optional_inputs_selector: - - #if $options_type.optional_inputs.output_trace_option: - --trace "${output_trace}" - #end if - - #if $options_type.optional_inputs.output_failed_alleles_option: - --failed-alleles "${output_failed_alleles_bed}" - #end if - - #if $options_type.optional_inputs.samples: - --samples "${options_type.optional_inputs.samples}" - #end if - - #if $options_type.optional_inputs.populations: - --populations "${options_type.optional_inputs.populations}" - #end if - - #if $options_type.optional_inputs.A: - --cnv-map "${options_type.optional_inputs.A}" - #end if - - #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf": - --variant-input "input_variant_vcf.vcf.gz" ## input_variant_vcf.vcf.gz is symlinked to a galaxy-generated dataset in "Tabixize optional input_varinat_vcf file" section of the command line above - ${options_type.optional_inputs.input_variant_type.only_use_input_alleles} - #end if - - #if $options_type.optional_inputs.haplotype_basis_alleles: - --haplotype-basis-alleles "${options_type.optional_inputs.haplotype_basis_alleles}" - #end if - - #if $options_type.optional_inputs.observation_bias: - --observation-bias "${options_type.optional_inputs.observation_bias}" - #end if - - #if $options_type.optional_inputs.contamination_estimates: - --contamination-estimates "${options_type.optional_inputs.contamination_estimates}" - #end if - - #end if - </token> - <xml name="optional_file_inputs"> - <conditional name="optional_inputs"> - <param name="optional_inputs_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Do you want to provide additional inputs?" help="Sets --samples, --populations, --cnv-map, --trace, --failed-alleles, --varinat-input, --only-use-input-alleles, --haplotype-basis-alleles, --report-all-haplotype-alleles, --report-monomorphic options, --observation-bias, and --contamination-estimates" /> - <when value="set"> - <param name="output_failed_alleles_option" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="False" label="Write out failed alleles file" help="--failed-alleles" /> - <param name="output_trace_option" type="boolean" truevalue="--trace" falsevalue="" checked="False" label="Write out algorithm trace file" help="--trace"/> - <param name="samples" type="data" format="txt" label="Limit analysis to samples listed (one per line) in the FILE" optional="True" help="-s --samples; default=By default FreeBayes will analyze all samples in its input BAM files"/> - <param name="populations" type="data" format="txt" label="Populations File" optional="True" help="--populations; default=False. Each line of FILE should list a sample and a population which it is part of. The population-based bayesian inference model will then be partitioned on the basis of the populations" /> - <param name="A" type="data" format="bed" label="Read a copy number map from the BED file FILE" optional="True" help="-A --cnv-map; default=copy number is set to as specified by --ploidy. Read a copy number map from the BED file FILE, which has the format: reference sequence, start, end, sample name, copy number ... for each region in each sample which does not have the default copy number as set by --ploidy."/> - <conditional name="input_variant_type"> - <param name="input_variant_type_selector" type="select" label="Provide variants file"> - <option value="do_not_provide" selected="True">Do not provide</option> - <option value="provide_vcf">Provide VCF file</option> - </param> - <when value="do_not_provide"> - <!-- Do nothing here --> - </when> - <when value="provide_vcf"> - <param name="input_variant_vcf" type="data" format="vcf_bgzip" label="Use variants reported in VCF file as input to the algorithm"> - <conversion name="Tabixized_input" type="tabix" /> - </param> - <param name="only_use_input_alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="False" label="Only provide variant calls and genotype likelihoods for sites in VCF" /> - </when> - </conditional> - <param name="haplotype_basis_alleles" type="data" format="vcf" label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" optional="True" help="--haplotype-basis-alleles" /> - <param name="report_monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="False" label="Report even loci which appear to be monomorphic, and report all considered alleles, even those which are not in called genotypes." help="--report-monomorphic " /> - <param name="observation_bias" optional="True" type="data" format="tabular" label="Load read length-dependent allele observation biases from" help="--observation-bias; The format is [length] [alignment efficiency relative to reference] where the efficiency is 1 if there is no relative observation bias" /> - <param name="contamination_estimates" optional="True" type="data" format="tabular" label="Upload per-sample estimates of contamination from" help="--contamination-estimates; The format should be: sample p(read=R|genotype=AR) p(read=A|genotype=AA) Sample '*' can be used to set default contamination estimates." /> - </when> - <when value="do_not_set"> - <!-- do nothing --> - </when> - </conditional> - </xml> - </macros> - <inputs> <conditional name="reference_source"> <param name="reference_source_selector" type="select" label="Load reference genome from"> @@ -332,8 +285,39 @@ --> </param> <when value="full"> - - <expand macro="optional_file_inputs" /> <!-- see macros section --> + + <conditional name="optional_inputs"> + <param name="optional_inputs_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Do you want to provide additional inputs?" help="Sets --samples, --populations, --cnv-map, --trace, --failed-alleles, --varinat-input, --only-use-input-alleles, --haplotype-basis-alleles, --report-all-haplotype-alleles, --report-monomorphic options, --observation-bias, and --contamination-estimates" /> + <when value="set"> + <param name="output_failed_alleles_option" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="False" label="Write out failed alleles file" help="--failed-alleles" /> + <param name="output_trace_option" type="boolean" truevalue="--trace" falsevalue="" checked="False" label="Write out algorithm trace file" help="--trace"/> + <param name="samples" type="data" format="txt" label="Limit analysis to samples listed (one per line) in the FILE" optional="True" help="-s --samples; default=By default FreeBayes will analyze all samples in its input BAM files"/> + <param name="populations" type="data" format="txt" label="Populations File" optional="True" help="--populations; default=False. Each line of FILE should list a sample and a population which it is part of. The population-based bayesian inference model will then be partitioned on the basis of the populations" /> + <param name="A" type="data" format="bed" label="Read a copy number map from the BED file FILE" optional="True" help="-A --cnv-map; default=copy number is set to as specified by --ploidy. Read a copy number map from the BED file FILE, which has the format: reference sequence, start, end, sample name, copy number ... for each region in each sample which does not have the default copy number as set by --ploidy."/> + <conditional name="input_variant_type"> + <param name="input_variant_type_selector" type="select" label="Provide variants file"> + <option value="do_not_provide" selected="True">Do not provide</option> + <option value="provide_vcf">Provide VCF file</option> + </param> + <when value="do_not_provide"> + <!-- Do nothing here --> + </when> + <when value="provide_vcf"> + <param name="input_variant_vcf" type="data" format="vcf_bgzip" label="Use variants reported in VCF file as input to the algorithm"> + <conversion name="Tabixized_input" type="tabix" /> + </param> + <param name="only_use_input_alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="False" label="Only provide variant calls and genotype likelihoods for sites in VCF" /> + </when> + </conditional> + <param name="haplotype_basis_alleles" type="data" format="vcf" label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" optional="True" help="--haplotype-basis-alleles" /> + <param name="report_monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="False" label="Report even loci which appear to be monomorphic, and report all considered alleles, even those which are not in called genotypes." help="--report-monomorphic " /> + <param name="observation_bias" optional="True" type="data" format="tabular" label="Load read length-dependent allele observation biases from" help="--observation-bias; The format is [length] [alignment efficiency relative to reference] where the efficiency is 1 if there is no relative observation bias" /> + <param name="contamination_estimates" optional="True" type="data" format="tabular" label="Upload per-sample estimates of contamination from" help="--contamination-estimates; The format should be: sample p(read=R|genotype=AR) p(read=A|genotype=AA) Sample '*' can be used to set default contamination estimates." /> + </when> + <when value="do_not_set"> + <!-- do nothing --> + </when> + </conditional> <!-- reporting --> @@ -368,7 +352,7 @@ <param name="reference_allele_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Use reference allele?" help="Sets --use-reference-allele and --reference-quality options " /> <when value="set"> <param name="Z" type="boolean" truevalue="-Z" falsevalue="" checked="False" label="Include the reference allele in the analysis as if it is another sample from the same population" help="-Z --use-reference-allele; default=False" /> - <param name="reference_quality" type="text" size="8" value="100,60" label="Assign mapping quality of MQ (100) to the reference allele at each site and base quality of BQ (60)" help="--reference-quality; default=100,60 " /> + <param name="reference_quality" type="text" value="100,60" label="Assign mapping quality of MQ (100) to the reference allele at each site and base quality of BQ (60)" help="--reference-quality; default=100,60 " /> </when> <when value="do_not_set"> <!-- do nothing --> @@ -471,7 +455,7 @@ <param name="report_genotype_likelihood_max" type="boolean" truevalue="--report-genotype-likelihood-max" falsevalue="" checked="False" label="Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods." help="--report-genotype-likelihood-max; default=False" /> <param name="B" type="integer" value="1000" label="Iterate no more than N times during genotyping step" help="-B --genotyping-max-iterations; default=1000." /> <param name="genotyping_max_banddepth" type="integer" value="6" label="Integrate no deeper than the Nth best genotype by likelihood when genotyping" help="--genotyping-max-banddepth; default=6" /> - <param name="W" type="text" size="8" value="1,3" label="Integrate all genotype combinations in our posterior space which include no more than N (1) samples with their Mth (3) best data likelihood" help="-W --posterior-integration-limits; default=1,3" /> + <param name="W" type="text" value="1,3" label="Integrate all genotype combinations in our posterior space which include no more than N (1) samples with their Mth (3) best data likelihood" help="-W --posterior-integration-limits; default=1,3" /> <param name="N" type="boolean" truevalue="--exclude-unobserved-genotypes" falsevalue="" checked="False" label="Skip sample genotypings for which the sample has no supporting reads" help="-N --exclude-unobserved-genotypes; default=False" /> <conditional name="genotype_variant_threshold"> <param name="genotype_variant_threshold_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Do you want to to limit posterior integration" help="-S --genotype-variant-threshold" /> @@ -506,28 +490,10 @@ <!-- do nothing build command line using haplotype-length 0 min-alternate-count 1 min-alternate-fraction 0 pooled-continuous report-monomorphic standard-filters--> <param name="min_coverage" type="integer" value="0" label="Require at least this coverage to process a site" help="-! --min-coverage; default=0 " /> </when> - - <!-- We will not allow command line textboxes at this time - <when value="cline"> - - <expand macro="optional_file_inputs" /> - - <param name="cline" size="60" type="text" value="-m 20 -q 30" label="Type command line tags here" help="All paremeters that DO NOT involve filenames can be typed here. Use "Do you want to provide additional inputs?" section above to control input and output files. For full syntax check help section below"> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - </valid> - <mapping initial="none"> - <add source="'" target="__sq__"/> - </mapping> - </sanitizer> - </param> - </when> - --> - </conditional> </inputs> + <outputs> <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" /> <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)"> @@ -545,6 +511,14 @@ <param name="options_type_selector" value="simple"/> <output name="output_vcf" file="freebayes-phix174-test1.vcf" compare="contains"/> </test> + <test> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/> + <param name="input_bam" ftype="bam" value="freebayes-phix174.bam"/> + <param name="options_type_selector" value="naive_w_filters"/> + <param name="min_coverage" value="14"/> + <output name="output_vcf" file="freebayes-phix174-test2.vcf" compare="contains"/> + </test> </tests> <stdio> <exit_code range="1:" /> @@ -556,7 +530,7 @@ See https://github.com/ekg/freebayes for details on FreeBayes. -This Galaxy instance of FreeBayes corresponds to release 0.9.18 +This Galaxy instance of FreeBayes corresponds to release 0.9.20 ------