Mercurial > repos > devteam > freebayes
diff freebayes.xml @ 31:57def2d7c093 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
| author | iuc |
|---|---|
| date | Sat, 27 Nov 2021 09:38:13 +0000 |
| parents | ef2c525bd8cd |
| children | 8a7a42541080 |
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--- a/freebayes.xml Wed Nov 06 17:02:57 2019 -0500 +++ b/freebayes.xml Sat Nov 27 09:38:13 2021 +0000 @@ -1,5 +1,8 @@ -<tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@"> +<tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy1"> <description>bayesian genetic variant detector</description> + <xrefs> + <xref type="bio.tools">freebayes</xref> + </xrefs> <macros> <import>macros.xml</import> </macros> @@ -172,27 +175,25 @@ ##INPUT FILTERS #if str( $options_type.input_filters.input_filters_selector ) == "set": + $standard_filters ${options_type.input_filters.use_duplicate_reads} - -m ${options_type.input_filters.m} - -q ${options_type.input_filters.q} - -R ${options_type.input_filters.R} - -Y ${options_type.input_filters.Y} - -e ${options_type.input_filters.e} - -F ${options_type.input_filters.F} - -C ${options_type.input_filters.C} - -G ${options_type.input_filters.G} - + --min-mapping-quality ${options_type.input_filters.min_mapping_quality} + --min-base-quality ${options_type.input_filters.min_base_quality} + --min-supporting-allele-qsum ${options_type.input_filters.min_supporting_allele_qsum} + --min-supporting-mapping-qsum ${options_type.input_filters.min_supporting_mapping_qsum} #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set": - -Q ${options_type.input_filters.mismatch_filters.Q} - #if str($options_type.input_filters.mismatch_filters.U) - -U ${options_type.input_filters.mismatch_filters.U} + --mismatch-base-quality-threshold ${options_type.input_filters.mismatch_filters.mismatch_base_quality_threshold} + #if str($options_type.input_filters.mismatch_filters.read_mismatch_limit) + --read-mismatch-limit ${options_type.input_filters.mismatch_filters.read_mismatch_limit} #end if - -z ${options_type.input_filters.mismatch_filters.z} - + --read-max-mismatch-fraction ${options_type.input_filters.mismatch_filters.read_max_mismatch_fraction} --read-snp-limit ${options_type.input_filters.mismatch_filters.read_snp_limit} #end if - + --read-indel-limit ${options_type.input_filters.read_indel_limit} + --min-alternate-fraction ${options_type.input_filters.min_alternate_fraction} --min-alternate-qsum ${options_type.input_filters.min_alternate_qsum} + --min-alternate-count ${options_type.input_filters.min_alternate_count} + --min-alternate-total ${options_type.input_filters.min_alternate_total} #end if ## POPULATION AND MAPPABILITY PRIORS @@ -468,21 +469,23 @@ <!-- input filters --> <conditional name="input_filters"> - <param name="input_filters_selector" type="select" label="Input filters" - help="Sets -4, -m, -q, -R, -Y, -Q, -U, -z, -$, -e, -0, -F, -C, -3, -G, and -! options"> + <param name="input_filters_selector" type="select" label="Input filters"> <option value="do_not_set" selected="true">No input filters (default)</option> <option value="set">Set input filters</option> </param> <when value="set"> - <param name="use_duplicate_reads" argument="--use-duplicate-reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="false" + <param argument="--standard-filters" type="boolean" truevalue="--standard-filters" falsevalue="" checked="false" + label="Use stringent input base and mapping quality filters" + help="--min-mapping-quality 30 --min-base-quality 20, --min-supporting-allele-qsum 0 --genotype-variant-threshold 0"/> + <param argument="--use-duplicate-reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="false" label="Include duplicate-marked alignments in the analysis" /> - <param name="m" argument="--min-mapping-quality" type="integer" value="1" + <param argument="--min-mapping-quality" type="integer" value="1" label="Exclude alignments from analysis if they have a mapping quality less than" /> - <param name="q" argument="--min-base-quality" type="integer" value="0" + <param argument="--min-base-quality" type="integer" value="0" label="Exclude alleles from analysis if their supporting base quality less than" /> - <param name="R" argument="--min-supporting-allele-qsum" type="integer" value="0" + <param argument="--min-supporting-allele-qsum" type="integer" value="0" label="Consider any allele in which the sum of qualities of supporting observations is at least" /> - <param name="Y" argument="--min-supporting-mapping-qsum" type="integer" value="0" + <param argument="--min-supporting-mapping-qsum" type="integer" value="0" label="Consider any allele in which and the sum of mapping qualities of supporting reads is at least" /> <conditional name="mismatch_filters"> <param name="mismatch_filters_selector" type="select" label="Mismatch filters" @@ -491,12 +494,12 @@ <option value="set">Set mismatch filters</option> </param> <when value="set"> - <param name="Q" argument="--mismatch-base-quality-threshold" type="integer" value="10" + <param argument="--mismatch-base-quality-threshold" type="integer" value="10" label="Count mismatches toward -U (option below) if the base quality of the mismatch is >=" /> - <param name="U" type="integer" argument="--read-mismatch-limit" value="1000" optional="true" + <param argument="--read-mismatch-limit" type="integer" value="1000" optional="true" label="Exclude reads with more than N mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (option above)" help="default=~unbounded" /> - <param name="z" argument="--read-max-mismatch-fraction" type="float" value="1.0" min="0.0" max="1.0" + <param argument="--read-max-mismatch-fraction" type="float" value="1.0" min="0.0" max="1.0" label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (second option above)" /> <param name="read_snp_limit" argument="--read-snp-limit" type="integer" value="1000" label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= mismatch-base-quality-threshold (third option above)" @@ -504,19 +507,16 @@ </when> <when value="do_not_set" /> </conditional> - <param name="e" argument="--read-indel-limit" type="integer" value="1000" + <param argument="--read-indel-limit" type="integer" value="1000" label="Exclude reads with more than this number of separate gaps" help="default=~unbounded" /> - <param name="standard_filters" argument="--standard-filters" type="boolean" truevalue="-0" falsevalue="" checked="false" - label="Use stringent input base and mapping quality filters" - help="Equivalent to -m 30 -q 20 -R 0 -S 0" /> - <param name="F" argument="--min-alternate-fraction" type="float" value="0.05" + <param argument="--min-alternate-fraction" type="float" value="0.05" label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position" /> - <param name="C" argument="--min-alternate-count" type="integer" value="2" + <param argument="--min-alternate-qsum" type="integer" value="0" + label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position" /> + <param argument="--min-alternate-count" type="integer" value="2" label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position" /> - <param name="min_alternate_qsum" argument="--min-alternate-qsum" type="integer" value="0" - label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position" /> - <param name="G" argument="--min-alternate-total" type="integer" value="1" + <param argument="--min-alternate-total" type="integer" value="1" label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis" /> </when> <when value="do_not_set" />