| Previous changeset 22:a730269af659 (2024-08-18) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc |
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modified:
bcftools_plugin_setgt.xml macros.xml |
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| diff -r a730269af659 -r 394dbf428c7b bcftools_plugin_setgt.xml --- a/bcftools_plugin_setgt.xml Sun Aug 18 10:17:20 2024 +0000 +++ b/bcftools_plugin_setgt.xml Tue Dec 02 08:08:25 2025 +0000 |
| [ |
| @@ -9,7 +9,6 @@ <expand macro="requirements" /> <expand macro="version_command" /> <command detect_errors="aggressive"><![CDATA[ -@PREPARE_ENV@ @PREPARE_INPUT_FILE@ #set $section = $sec_restrict @PREPARE_TARGETS_FILE@ @@ -42,8 +41,8 @@ <inputs> <expand macro="macro_input" /> <section name="sec_restrict" title="Restrict to"> - <expand macro="macro_restrict" /> - <expand macro="macro_restrict" type="target" label_type="Target" /> + <expand macro="macro_region_restrict" /> + <expand macro="macro_target_restrict" /> <expand macro="macro_include" /> <expand macro="macro_exclude" /> </section> @@ -60,6 +59,7 @@ <option value=".">. missing (. or ./., keeps ploidy)</option> <option value="0">0 reference allele (e.g. 0/0 or 0, keeps ploidy)</option> <option value="c:GT">c:GT custom genotype (e.g. 0/0, 0, 0/1, m/M, overrides ploidy)</option> + <option value="c:./.">c:./. missing genotype with arbitrary ploidy</option> <option value="M">M major allele</option> <option value="m">m minor (the second most common) allele (e.g. 1/1 or 1, keeps ploidy)</option> <option value="p">p phased genotype</option> @@ -74,8 +74,10 @@ <tests> <test> <param name="input_file" ftype="vcf" value="plugin1.vcf" /> - <param name="target_gt" value="." /> - <param name="new_gt" value="0" /> + <section name="sec_plugin"> + <param name="target_gt" value="." /> + <param name="new_gt" value="0" /> + </section> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> @@ -100,6 +102,20 @@ </assert_contents> </output> </test> + <test> + <param name="input_file" ftype="vcf" value="plugin1.vcf" /> + <section name="sec_plugin"> + <param name="target_gt" value="." /> + <param name="new_gt" value="c:./." /> + </section> + <param name="output_type" value="v" /> + <output name="output_file"> + <assert_contents> + <has_text text="GT" /> + <has_text text="DP4=1,2,3,4;INDEL;STR=test" /> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ ===================================== |
| b |
| diff -r a730269af659 -r 394dbf428c7b macros.xml --- a/macros.xml Sun Aug 18 10:17:20 2024 +0000 +++ b/macros.xml Tue Dec 02 08:08:25 2025 +0000 |
| [ |
| b'@@ -1,7 +1,7 @@\n <macros>\n- <token name="@TOOL_VERSION@">1.15.1</token>\n- <token name="@VERSION_SUFFIX@">4</token>\n- <token name="@PROFILE@">20.01</token>\n+ <token name="@TOOL_VERSION@">1.22</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ <token name="@PROFILE@">24.1</token>\n <xml name="bio_tools">\n <xrefs>\n <xref type="bio.tools">bcftools</xref>\n@@ -10,15 +10,15 @@\n <xml name="requirements">\n <requirements>\n <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement>\n- <requirement type="package" version="1.15.1">htslib</requirement>\n+ <requirement type="package" version="1.22.1">htslib</requirement>\n <yield />\n </requirements>\n </xml>\n <xml name="samtools_requirement">\n- <requirement type="package" version="1.15.1">samtools</requirement>\n+ <requirement type="package" version="1.22.1">samtools</requirement>\n </xml>\n <xml name="matplotlib_requirement">\n- <requirement type="package" version="3.5.3">matplotlib</requirement>\n+ <requirement type="package" version="3.10.7">matplotlib</requirement>\n </xml>\n <xml name="version_command">\n <version_command>bcftools 2>&1 | grep \'Version:\'</version_command>\n@@ -30,16 +30,11 @@\n <yield />\n </citations>\n </xml>\n- <token name="@BCFTOOLS_WIKI@">https://github.com/samtools/bcftools/wiki</token>\n- <token name="@BCFTOOLS_MANPAGE@">http://samtools.github.io/bcftools/bcftools.html</token>\n+ <token name="@BCFTOOLS_HOWTOS@">https://samtools.github.io/bcftools/howtos/index.html</token>\n+ <token name="@BCFTOOLS_MANPAGE@">https://www.htslib.org/doc/bcftools.html</token>\n <token name="@THREADS@">\n --threads \\${GALAXY_SLOTS:-4}\n </token>\n- <token name="@PREPARE_ENV@">\n-<![CDATA[\n-export BCFTOOLS_PLUGINS=`which bcftools | sed \'s,bin/bcftools,libexec/bcftools,\'`;\n-]]>\n- </token>\n <xml name="macro_input">\n <!-- \n REQUIRES https://github.com/galaxyproject/galaxy/pull/14605/files\n@@ -294,8 +289,8 @@\n help="inverts the query/filtering applied by the targets" />\n </xml>\n \n- <xml name="macro_restriction_spec" token_type="region" token_label_type="Region">\n- <repeat name="@TYPE@s" title="@LABEL_TYPE@ Filter" default="1" min="1">\n+ <xml name="macro_restriction_spec" tokens="type,label_type">\n+ <repeat name="@TYPE@_specs" title="@LABEL_TYPE@ Filter" default="1" min="1">\n <param name="chrom" type="text" label="@LABEL_TYPE@ chromosome">\n <validator type="expression" message="A chromosome identifier is required when specifying a @LABEL_TYPE@ filter">value.strip()</validator>\n </param>\n@@ -305,36 +300,85 @@\n <param name="stop" type="text" label="@LABEL_TYPE@ end position">\n <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>\n </param>\n- <yield />\n </repeat>\n </xml>\n \n- <xml name="macro_restrictions_file" token_type="region" token_label_type="Region">\n+ <xml name="macro_restrictions_file" tokens="type,label_type">\n <param name="@TYPE@s_file" type="data" format="tabular" label="@LABEL_TYPE@s File" help="restrict to @LABEL_TYPE@s listed in a file" />\n </xml>\n \n- <xml name="macro_restrict" token_type="region" token_label_type="Region" >\n+ <xml name="__macro_restrict__" tokens="type,label_select,label_type,pos_is_default,rec_is_default">\n <conditional name="@TYPE@s">\n- <param name="@TYPE@s_src" type="select" label="@LABEL_TYPE@s">\n- <option value="__none__">Do not restrict to @LABEL_TYPE@s</option>\n- <option value="@TYPE@s">Specify one or more @LABEL_TYPE@(s) directly</option>\n- <option value="@TYPE@s_file">Operate on @LABEL_TYPE@s specified in a history dataset</option>\n+ <param name="@TYPE@s_src" type="select" label="@LABEL_SELECT@">\n+ <option value="__none__">Do not restrict to @LABEL_TYPE@s</option>\n+ <option value="@TYPE@s">Specify one or more @LABEL_TYPE@'..b'intervals = $section.targets.target_specs\n+ @PARSE_INTERVALS@\n+ --targets \'${section.targets.invert_targets_file}$intervals_spec\'\n+ #elif $section.targets.targets_src == \'targets_file\':\n+ #if $targets_path:\n+ --targets-file \'${section.targets.invert_targets_file}${targets_path}\'\n+ #else:\n+ --targets-file \'${section.targets.invert_targets_file}${section.targets.targets_file}\'\n+ #end if\n+ #end if\n+ #if \'targets_overlap\' in $section.targets:\n+ --targets-overlap $section.targets.targets_overlap\n+ #end if\n #end if\n ]]>\n </token>\n@@ -417,7 +462,7 @@\n <![CDATA[\n #set $regions_path = None\n #if \'regions\' in $section\n- #if $section.regions.regions_src == \'regions_file\' and $section.regions.regions_file:\n+ #if $section.regions.regions_src == \'regions_file\':\n #if $section.regions.regions_file.ext.startswith(\'bed\'):\n #set $regions_path = \'regions_file.bed\'\n ln -s \'$section.regions.regions_file\' $regions_path &&\n@@ -461,11 +506,31 @@\n </param>\n <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"\n help="Inverts the query/filtering applied by Samples (adds "^" prefix to exclude)" />\n- <param argument="--samples_file" type="data" format="tabular" optional="true" label="Samples file"\n- help="File of samples to include" />\n+ <param argument="--samples_file" type="data" format="tabular" optional="true" label="Samples file" help="File of samples to include" />\n <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples file"\n help="inverts the query/filtering applied by Samples file" />\n </xml>\n+\n+ <xml name="macro_samples_enhanced" token_all_samples="" token_file_help="File listing samples to include one per line.">\n+ <conditional name="specify_samples">\n+ <param name="how" type="select" label="How do you want to select samples?">\n+ <option value="-s">Specify samples manually</option>\n+ <option value="-S">Provide sample file</option>\n+ <option value="@ALL_SAMPLES@" selected="true">No selection; just use all samples found in input</option>\n+ </param>\n+ <when value="-s">\n+ <param argument="--samples" name="samples_spec" type="text" optional="false" label="Sample(s)" help="Specify a single sample by name or a comma-separated list of sample names.">\n+ <validator type="expression" message="Please specify a single sample by name or a comma-separated list of sample names">value.strip() and value[0] not in "^," and ",," not in value</validator>\n+ </param>\n+ <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" label="Exclude these samples instead of including them?" help="Equivalent to prefixing the list of samples with "^" on the command line."/>\n+ </when>\n+ <when value="-S">\n+ <param argument="--samples_file" type="data" format="tabular" optional="@IS_OPTIONAL@" label="Samples file" help="@FILE_HELP@" />\n+ <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" label="Exclude the samples listed in the file instead of including them?" help="Equivalent to prefixing the file with "^" on the command line."/>\n+ </when>\n+ <when value="@ALL_SAMPLES@" />\n+ </conditional>\n+ </xml>\n <token name="@SAMPLES@">\n #set $samples_defined = False\n #if str($section.samples) != \'\':\n@@ -478,8 +543,8 @@\n #end if\n </token>\n \n- <xml name="macro_sample">\n- <param name="sample" type="text" optional="true" label="Sample" help="Apply variants of the given sample" />\n+ <xml name="macro_sample" token_help="Apply variants of the given sample">\n+ <param name="sample" type="text" optional="true" label="Sample" help="@HELP@" />\n </xml>\n <token name="@SAMPLE@">\n #if $section.sample:\n' |