| Previous changeset 30:ef2c525bd8cd (2019-11-06) Next changeset 32:8a7a42541080 (2021-12-01) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a" |
|
modified:
freebayes.xml leftalign.xml macros.xml |
| b |
| diff -r ef2c525bd8cd -r 57def2d7c093 freebayes.xml --- a/freebayes.xml Wed Nov 06 17:02:57 2019 -0500 +++ b/freebayes.xml Sat Nov 27 09:38:13 2021 +0000 |
| [ |
| b'@@ -1,5 +1,8 @@\n-<tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@">\n+<tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy1">\n <description>bayesian genetic variant detector</description>\n+ <xrefs>\n+ <xref type="bio.tools">freebayes</xref>\n+ </xrefs>\n <macros>\n <import>macros.xml</import>\n </macros>\n@@ -172,27 +175,25 @@\n \n ##INPUT FILTERS\n #if str( $options_type.input_filters.input_filters_selector ) == "set":\n+ $standard_filters\n ${options_type.input_filters.use_duplicate_reads}\n- -m ${options_type.input_filters.m}\n- -q ${options_type.input_filters.q}\n- -R ${options_type.input_filters.R}\n- -Y ${options_type.input_filters.Y}\n- -e ${options_type.input_filters.e}\n- -F ${options_type.input_filters.F}\n- -C ${options_type.input_filters.C}\n- -G ${options_type.input_filters.G}\n-\n+ --min-mapping-quality ${options_type.input_filters.min_mapping_quality}\n+ --min-base-quality ${options_type.input_filters.min_base_quality}\n+ --min-supporting-allele-qsum ${options_type.input_filters.min_supporting_allele_qsum}\n+ --min-supporting-mapping-qsum ${options_type.input_filters.min_supporting_mapping_qsum}\n #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set":\n- -Q ${options_type.input_filters.mismatch_filters.Q}\n- #if str($options_type.input_filters.mismatch_filters.U)\n- -U ${options_type.input_filters.mismatch_filters.U}\n+ --mismatch-base-quality-threshold ${options_type.input_filters.mismatch_filters.mismatch_base_quality_threshold}\n+ #if str($options_type.input_filters.mismatch_filters.read_mismatch_limit)\n+ --read-mismatch-limit ${options_type.input_filters.mismatch_filters.read_mismatch_limit}\n #end if\n- -z ${options_type.input_filters.mismatch_filters.z}\n-\n+ --read-max-mismatch-fraction ${options_type.input_filters.mismatch_filters.read_max_mismatch_fraction}\n --read-snp-limit ${options_type.input_filters.mismatch_filters.read_snp_limit}\n #end if\n-\n+ --read-indel-limit ${options_type.input_filters.read_indel_limit}\n+ --min-alternate-fraction ${options_type.input_filters.min_alternate_fraction}\n --min-alternate-qsum ${options_type.input_filters.min_alternate_qsum}\n+ --min-alternate-count ${options_type.input_filters.min_alternate_count}\n+ --min-alternate-total ${options_type.input_filters.min_alternate_total}\n #end if\n \n ## POPULATION AND MAPPABILITY PRIORS\n@@ -468,21 +469,23 @@\n \n <!-- input filters -->\n <conditional name="input_filters">\n- <param name="input_filters_selector" type="select" label="Input filters"\n- help="Sets -4, -m, -q, -R, -Y, -Q, -U, -z, -$, -e, -0, -F, -C, -3, -G, and -! options">\n+ <param name="input_filters_selector" type="select" label="Input filters">\n <option value="do_not_set" selected="true">No input filters (default)</option>\n <option value="set">Set input filters</option>\n </param>\n <when value="set">\n- <param name="use_duplicate_reads" argument="--use-duplicate-reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="false"\n+ <param argument="--standard-filters" type="boolean" truevalue="--standard-filters" falsevalue="" checked="false"\n+ label="Use stringent input base and mapping quality filters'..b'e="10"\n label="Count mismatches toward -U (option below) if the base quality of the mismatch is >=" />\n- <param name="U" type="integer" argument="--read-mismatch-limit" value="1000" optional="true"\n+ <param argument="--read-mismatch-limit" type="integer" value="1000" optional="true"\n label="Exclude reads with more than N mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (option above)"\n help="default=~unbounded" />\n- <param name="z" argument="--read-max-mismatch-fraction" type="float" value="1.0" min="0.0" max="1.0"\n+ <param argument="--read-max-mismatch-fraction" type="float" value="1.0" min="0.0" max="1.0"\n 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)" />\n <param name="read_snp_limit" argument="--read-snp-limit" type="integer" value="1000"\n label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= mismatch-base-quality-threshold (third option above)"\n@@ -504,19 +507,16 @@\n </when>\n <when value="do_not_set" />\n </conditional>\n- <param name="e" argument="--read-indel-limit" type="integer" value="1000"\n+ <param argument="--read-indel-limit" type="integer" value="1000"\n label="Exclude reads with more than this number of separate gaps"\n help="default=~unbounded" />\n- <param name="standard_filters" argument="--standard-filters" type="boolean" truevalue="-0" falsevalue="" checked="false"\n- label="Use stringent input base and mapping quality filters"\n- help="Equivalent to -m 30 -q 20 -R 0 -S 0" />\n- <param name="F" argument="--min-alternate-fraction" type="float" value="0.05"\n+ <param argument="--min-alternate-fraction" type="float" value="0.05"\n label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position" />\n- <param name="C" argument="--min-alternate-count" type="integer" value="2"\n+ <param argument="--min-alternate-qsum" type="integer" value="0"\n+ label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position" />\n+ <param argument="--min-alternate-count" type="integer" value="2"\n label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position" />\n- <param name="min_alternate_qsum" argument="--min-alternate-qsum" type="integer" value="0"\n- label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position" />\n- <param name="G" argument="--min-alternate-total" type="integer" value="1"\n+ <param argument="--min-alternate-total" type="integer" value="1"\n label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis" />\n </when>\n <when value="do_not_set" />\n' |
| b |
| diff -r ef2c525bd8cd -r 57def2d7c093 leftalign.xml --- a/leftalign.xml Wed Nov 06 17:02:57 2019 -0500 +++ b/leftalign.xml Sat Nov 27 09:38:13 2021 +0000 |
| b |
| @@ -1,6 +1,9 @@ <?xml version="1.0"?> -<tool id="bamleftalign" name="BamLeftAlign" version="@DEPENDENCY_VERSION@"> +<tool id="bamleftalign" name="BamLeftAlign" version="@TOOL_VERSION@"> <description> indels in BAM datasets</description> + <xrefs> + <xref type="bio.tools">freebayes</xref> + </xrefs> <macros> <import>macros.xml</import> </macros> |
| b |
| diff -r ef2c525bd8cd -r 57def2d7c093 macros.xml --- a/macros.xml Wed Nov 06 17:02:57 2019 -0500 +++ b/macros.xml Sat Nov 27 09:38:13 2021 +0000 |
| b |
| @@ -1,8 +1,8 @@ <macros> - <token name="@DEPENDENCY_VERSION@">1.3.1</token> + <token name="@TOOL_VERSION@">1.3.1</token> <xml name="requirements"> <requirements> - <requirement type="package" version="@DEPENDENCY_VERSION@">freebayes</requirement> + <requirement type="package" version="@TOOL_VERSION@">freebayes</requirement> <requirement type="package" version="1.9">samtools</requirement> <yield /> </requirements> |