Mercurial > repos > devteam > freebayes
diff freebayes.xml @ 5:949ac66308a7
Update FreeBayes to 0.9.6_9608597d12e127c847ae03aa03440ab63992fedf.
| author | Daniel Blankenberg <dan@bx.psu.edu> |
|---|---|
| date | Fri, 24 Aug 2012 16:00:21 -0400 |
| parents | e54bb199a47b |
| children | fcb60273c710 |
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--- a/freebayes.xml Wed Aug 15 10:43:46 2012 -0400 +++ b/freebayes.xml Fri Aug 24 16:00:21 2012 -0400 @@ -1,8 +1,8 @@ <?xml version="1.0"?> -<tool id="freebayes" name="FreeBayes" version="0.0.2"> +<tool id="freebayes" name="FreeBayes" version="0.0.3"> <requirements> - <requirement type="package" version="0.9.4_a46483351fd0196637614121868fb5c386612b55">freebayes</requirement> - <requirement type="package" version="0.1.18">samtools</requirement> + <requirement type="package" version="0.9.6_9608597d12e127c847ae03aa03440ab63992fedf">freebayes</requirement> + <requirement type="package">samtools</requirement> </requirements> <description> - Bayesian genetic variant detector</description> <command> @@ -59,6 +59,10 @@ --variant-input "${options_type.input_variant_type.input_variant_vcf}" ${options_type.input_variant_type.only_use_input_alleles} #end if + #if $options_type.haplotype_basis_alleles: + --haplotype-basis-alleles "${options_type.haplotype_basis_alleles}" + #end if + ##reporting #if str( $options_type.section_reporting_type.section_reporting_type_selector ) == "set": @@ -98,12 +102,12 @@ ##input filters #if str( $options_type.section_input_filters_type.section_input_filters_type_selector ) == "set": ${options_type.section_input_filters_type.use_duplicate_reads} - #if str( $options_type.section_input_filters_type.no_filter_type.no_filter_type_selector ) == "apply_filters": - --min-mapping-quality "${options_type.section_input_filters_type.no_filter_type.min_mapping_quality}" - --min-base-quality "${options_type.section_input_filters_type.no_filter_type.min_base_quality}" - --min-supporting-quality "${options_type.section_input_filters_type.no_filter_type.min_supporting_quality_mq},${options_type.section_input_filters_type.no_filter_type.min_supporting_quality_bq}" - #else: - --no-filters + #if str( $options_type.section_input_filters_type.quality_filter_type.quality_filter_type_selector ) == "apply_filters": + --min-mapping-quality "${options_type.section_input_filters_type.quality_filter_type.min_mapping_quality}" + --min-base-quality "${options_type.section_input_filters_type.quality_filter_type.min_base_quality}" + --min-supporting-quality "${options_type.section_input_filters_type.quality_filter_type.min_supporting_quality_mq},${options_type.section_input_filters_type.quality_filter_type.min_supporting_quality_bq}" + #elif str( $options_type.section_input_filters_type.quality_filter_type.quality_filter_type_selector ) == "standard_filters": + --standard-filters #end if --mismatch-base-quality-threshold "${options_type.section_input_filters_type.mismatch_base_quality_threshold}" #if $options_type.section_input_filters_type.read_mismatch_limit: @@ -233,7 +237,7 @@ <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" /> <!-- reporting --> <conditional name="section_reporting_type"> @@ -316,17 +320,17 @@ </when> <when value="set"> <param name="use_duplicate_reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="False" label="Include duplicate-marked alignments in the analysis" /> - <conditional name="no_filter_type"> - <param name="no_filter_type_selector" type="select" label="Apply filters"> - <option value="apply_filters" selected="True">Apply</option> - <option value="no_filters">Do not apply</option> + <conditional name="quality_filter_type"> + <param name="quality_filter_type_selector" type="select" label="Apply Quality filters"> + <option value="standard_filters" selected="True">Apply standard</option> + <option value="apply_filters">Apply specified</option> </param> - <when value="no_filters"> - <!-- Do nothing here --> <!-- no-filters --> + <when value="standard_filters"> + <!-- Do nothing here --> <!-- standard-filters --> </when> <when value="apply_filters"> - <param name="min_mapping_quality" type="integer" label="Exclude alignments from analysis if they have a mapping quality less than" value="30" /> - <param name="min_base_quality" type="integer" label="Exclude alleles from analysis if their supporting base quality less than" value="20" /> + <param name="min_mapping_quality" type="integer" label="Exclude alignments from analysis if they have a mapping quality less than" value="0" /> + <param name="min_base_quality" type="integer" label="Exclude alleles from analysis if their supporting base quality less than" value="0" /> <param name="min_supporting_quality_mq" type="integer" label="In order to consider an alternate allele, at least one supporting alignment must have mapping quality" value="0" /> <param name="min_supporting_quality_bq" type="integer" label="In order to consider an alternate allele, at least one supporting alignment must have base quality" value="0" /> </when> @@ -423,8 +427,6 @@ <param name="input_bam" ftype="bam" value="fake_phiX_reads_1.bam"/> <param name="options_type_selector" value="basic"/> <output name="output_vcf" file="freebayes_out_1.vcf.contains" compare="contains"/> - <!-- <output name="output_failed_alleles_bed" file="empty_file.dat" /> - <output name="output_trace" file="freebayes_out_1.output_trace" /> --> </test> </tests> <help> @@ -494,6 +496,10 @@ and alleles which are provided in the VCF input, and provide output in the VCF for all input alleles, not just those which have support in the data. + --haplotype-basis-alleles VCF + When specified, only variant alleles provided in this input + VCF will be used for the construction of complex or haplotype + alleles. reporting: @@ -577,8 +583,8 @@ -e --read-indel-limit N Exclude reads with more than N separate gaps. default: ~unbounded - -0 --no-filters Do not use any input base and mapping quality filters - Equivalent to -m 0 -q 0 -R 0 -S 0 + -0 --standard-filters Use stringent input base and mapping quality filters + Equivalent to -m 30 -q 20 -R 0 -S 0 -x --indel-exclusion-window Ignore portions of alignments this many bases from a putative insertion or deletion allele. default: 0 @@ -662,7 +668,7 @@ **Citation** -For the underlying tool, please cite `FreeBayes <http://bioinformatics.bc.edu/marthlab/FreeBayes>`_. +For the underlying tool, please cite `Erik Garrison and Gabor Marth. Haplotype-based variant detection from short-read sequencing <http://arxiv.org/abs/1207.3907>`_. If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*