Mercurial > repos > iuc > bcftools_filter
diff bcftools_filter.xml @ 25:5d8b9dd955c6 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
| author | iuc |
|---|---|
| date | Tue, 02 Dec 2025 07:56:38 +0000 |
| parents | 0bb5f14a9955 |
| children |
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--- a/bcftools_filter.xml Sun Aug 18 09:56:05 2024 +0000 +++ b/bcftools_filter.xml Tue Dec 02 07:56:38 2025 +0000 @@ -4,11 +4,10 @@ <token name="@EXECUTABLE@">filter</token> <import>macros.xml</import> </macros> - <expand macro="bio_tools" /> - <expand macro="requirements" /> - <expand macro="version_command" /> + <expand macro="bio_tools"/> + <expand macro="requirements"/> + <expand macro="version_command"/> <command detect_errors="aggressive"><![CDATA[ -@PREPARE_ENV@ @PREPARE_INPUT_FILE@ #set $section = $sec_restrict @PREPARE_TARGETS_FILE@ @@ -51,16 +50,16 @@ ]]> </command> <inputs> - <expand macro="macro_input" /> + <expand macro="macro_input"/> <section name="sec_restrict" expanded="false" title="Restrict to"> - <expand macro="macro_restrict" /> - <expand macro="macro_restrict" type="target" label_type="Target" /> - <expand macro="macro_include" /> - <expand macro="macro_exclude" /> + <expand macro="macro_region_restrict"/> + <expand macro="macro_target_restrict"/> + <expand macro="macro_include"/> + <expand macro="macro_exclude"/> </section> <section name="sec_filter" expanded="false" title="Filter Options"> - <param name="SnpGap" type="integer" label="Snpgap" optional="True" help="(-g) Filter SNPs within <int> base pairs of an indel" /> - <param name="IndelGap" type="integer" label="Indelgap" optional="True" help="(-G) Filter clusters of indels separated by <int> or fewer base pairs allowing only one to pass" /> + <param name="SnpGap" type="integer" label="Snpgap" optional="True" help="(-g) Filter SNPs within <int> base pairs of an indel"/> + <param name="IndelGap" type="integer" label="Indelgap" optional="True" help="(-G) Filter clusters of indels separated by <int> or fewer base pairs allowing only one to pass"/> <param name="mode" type="select" label="Mode FILTER annotation" optional="true" multiple="true" display="checkboxes"> <help>(-m) The default mode replaces existing filters of failed sites with a new FILTER string @@ -82,193 +81,233 @@ Annotate FILTER column with STRING or, with +, a unique filter name generated by the program ("Filter%d"). ]]></help> </param> - <expand macro="macro_restrict" type="mask" label_type="Mask"/> + <expand macro="macro_mask_restrict"/> </when> </conditional> - - <param name="select_set_GTs" type="select" label="Set genotypes of failed samples" optional="true" help="(-S)"> + <param name="select_set_GTs" type="select" label="Set genotypes of failed samples" optional="true" help="(-S)"> <option value=".">to missing (.)</option> <option value="0">to REF (0)</option> </param> </section> - <expand macro="macro_select_output_type" /> + <expand macro="macro_select_output_type"/> </inputs> <outputs> <expand macro="macro_vcf_output"/> </outputs> <tests> <test> - <param name="input_file" ftype="vcf" value="filter.1.vcf" /> - <param name="mode" value="x" /> - <param name="SnpGap" value="2" /> - <param name="IndelGap" value="2" /> - <param name="output_type" value="v" /> + <param name="input_file" ftype="vcf" value="filter.1.vcf"/> + <section name="sec_filter"> + <param name="mode" value="x"/> + </section> + <section name="sec_filter"> + <param name="SnpGap" value="2"/> + <param name="IndelGap" value="2"/> + </section> + <param name="output_type" value="v"/> <output name="output_file"> <assert_contents> - <has_text text="PASS" /> - <not_has_text text="1006" /> + <has_text text="PASS"/> + <not_has_text text="1006"/> </assert_contents> </output> </test> <test> - <param name="input_file" ftype="vcf" value="filter.2.vcf" /> - <param name="exclude" value="QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))" /> - <param name="soft_filter" value="Modified" /> - <param name="select_set_GTs" value="." /> - <param name="output_type" value="v" /> + <param name="input_file" ftype="vcf" value="filter.2.vcf"/> + <section name="sec_restrict"> + <param name="exclude" value="QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))"/> + </section> + <section name="sec_filter"> + <param name="mode" value="+"/> + <conditional name="conditional_soft_filter"> + <param name="selector" value="enabled"/> + <param name="soft_filter" value="Modified"/> + </conditional> + <param name="select_set_GTs" value="."/> + </section> + <param name="output_type" value="v"/> <output name="output_file"> <assert_contents> - <has_text text="genotypes" /> - <has_text text="AN=2;AC=1" /> - <has_text_matching expression="TAAAA\tTA,T\t61.5\tPASS" /> + <has_text text="genotypes"/> + <has_text text="AN=2;AC=1"/> + <has_text_matching expression="TAAAA\s.*TA,T\s.*61.5\s.*Modified.+"/> </assert_contents> </output> </test> <test> - <param name="input_file" ftype="vcf" value="filter.3.vcf" /> - <param name="exclude" value="INFO/DP=19" /> - <param name="output_type" value="v" /> + <param name="input_file" ftype="vcf" value="filter.3.vcf"/> + <section name="sec_restrict"> + <param name="exclude" value="INFO/DP=19"/> + </section> + <param name="output_type" value="v"/> <output name="output_file"> <assert_contents> - <not_has_text text="3162006" /> - <has_text text="3162007" /> + <not_has_text text="3162006"/> + <has_text text="3162007"/> </assert_contents> </output> </test> - <test> - <param name="input_file" ftype="vcf" value="filter.3.vcf" /> - <param name="exclude" value="INFO/DP=19" /> + <param name="input_file" ftype="vcf" value="filter.3.vcf"/> + <section name="sec_restrict"> + <param name="exclude" value="INFO/DP=19"/> + </section> <section name="sec_filter"> <conditional name="conditional_soft_filter"> <param name="selector" value="enabled"/> - <param name="soft_filter" value="XX" /> + <param name="soft_filter" value="XX"/> </conditional> </section> - <param name="output_type" value="v" /> + <param name="output_type" value="v"/> <output name="output_file"> <assert_contents> - <has_text_matching expression="\tXX\tDP=19" /> - <has_text_matching expression="\tq20\tAO" /> + <has_text_matching expression="\t238\tXX\tDP=19.+"/> + <has_text_matching expression="\tq20\tAO.+"/> </assert_contents> </output> </test> <test> - <param name="input_file" ftype="vcf" value="filter.3.vcf" /> - <param name="exclude" value="INFO/DP=19" /> + <param name="input_file" ftype="vcf" value="filter.3.vcf"/> + <section name="sec_restrict"> + <param name="exclude" value="INFO/DP=19"/> + </section> <section name="sec_filter"> + <param name="mode" value="+"/> <conditional name="conditional_soft_filter"> <param name="selector" value="enabled"/> - <param name="soft_filter" value="XX" /> - <param name="mode" value="+" /> + <param name="soft_filter" value="XX"/> </conditional> </section> - <param name="output_type" value="v" /> + <param name="output_type" value="v"/> <output name="output_file"> <assert_contents> - <has_text_matching expression="238\tXX\tDP=19" /> - <has_text_matching expression="\tq20\tAO" /> + <has_text_matching expression="238\tq20;XX\tDP=19"/> + <has_text_matching expression="\tq20\tAO"/> </assert_contents> </output> </test> <test> - <param name="input_file" ftype="vcf" value="filter.3.vcf" /> - <param name="exclude" value="INFO/DP=19" /> + <param name="input_file" ftype="vcf" value="filter.3.vcf"/> + <section name="sec_restrict"> + <param name="exclude" value="INFO/DP=19"/> + </section> <section name="sec_filter"> + <param name="mode" value="+"/> <conditional name="conditional_soft_filter"> <param name="selector" value="enabled"/> - <param name="soft_filter" value="XX" /> - <param name="mode" value="+" /> + <param name="soft_filter" value="XX"/> </conditional> </section> - <param name="output_type" value="v" /> + <param name="output_type" value="v"/> <output name="output_file"> <assert_contents> - <has_text_matching expression="\tXX\tDP=19" /> - <has_text_matching expression="\tq20\tAO=52101" /> + <has_text_matching expression="\tq20;XX\tDP=19"/> + <has_text_matching expression="\tq20\tAO=52101"/> </assert_contents> </output> </test> <test> - <param name="input_file" ftype="vcf" value="filter.3.vcf" /> - <param name="exclude" value="INFO/DP=19" /> + <param name="input_file" ftype="vcf" value="filter.3.vcf"/> + <section name="sec_restrict"> + <param name="exclude" value="INFO/DP=19"/> + </section> <section name="sec_filter"> + <param name="mode" value="+"/> <conditional name="conditional_soft_filter"> <param name="selector" value="enabled"/> - <param name="soft_filter" value="XX" /> - <param name="mode" value="+" /> + <param name="soft_filter" value="XX"/> </conditional> </section> - <param name="output_type" value="v" /> + <param name="output_type" value="v"/> <output name="output_file"> <assert_contents> - <has_text_matching expression="\t238\tXX\tDP=19" /> - <has_text_matching expression="\t238\tq20\tAO" /> + <has_text_matching expression="\t238\tq20;XX\tDP=19"/> + <has_text_matching expression="\t238\tq20\tAO"/> </assert_contents> </output> </test> <test> - <param name="input_file" ftype="vcf" value="filter.3.vcf" /> - <param name="exclude" value="FMT/GT="0/2"" /> - <param name="output_type" value="v" /> + <param name="input_file" ftype="vcf" value="filter.3.vcf"/> + <section name="sec_restrict"> + <param name="exclude" value="FMT/GT="0/2""/> + </section> + <param name="output_type" value="v"/> <output name="output_file"> <assert_contents> - <not_has_text text="3162006" /> - <has_text text="3162007" /> + <not_has_text text="3162006"/> + <has_text text="3162007"/> </assert_contents> </output> </test> <test> - <param name="input_file" ftype="vcf" value="filter.2.vcf" /> - <param name="include" value="FMT/GT="0/0" && AC[*]=2" /> - <param name="output_type" value="v" /> + <param name="input_file" ftype="vcf" value="filter.2.vcf"/> + <section name="sec_restrict"> + <param name="include" value="FMT/GT="0/0" && AC[*]=2"/> + </section> + <param name="output_type" value="v"/> <output name="output_file"> <assert_contents> - <has_text text="AN=4;AC=2" /> - <not_has_text text="AN=4;AC=0" /> + <has_text text="AN=4;AC=2"/> + <not_has_text text="AN=4;AC=0"/> </assert_contents> </output> </test> <!-- Test region overlap --> <test> - <param name="input_file" ftype="vcf" value="filter.2.vcf" /> - <param name="include" value="FMT/GT="0/0" && AC[*]=2" /> - <param name="output_type" value="v" /> + <param name="input_file" ftype="vcf" value="filter.2.vcf"/> + <section name="sec_restrict"> + <param name="include" value="FMT/GT="0/0" && AC[*]=2"/> + </section> + <param name="output_type" value="v"/> <section name="sec_restrict"> - <param name="regions_overlap" value="1"/> + <conditional name="regions"> + <param name="regions_src" value="regions" /> + <repeat name="region_specs"> + <param name="chrom" value="1" /> + </repeat> + </conditional> </section> <output name="output_file"> <assert_contents> - <has_text text="AN=4;AC=2" /> - <not_has_text text="AN=4;AC=0" /> + <has_text text="AN=4;AC=2"/> + <not_has_text text="AN=4;AC=0"/> </assert_contents> </output> <assert_command> - <has_text text="--regions-overlap" /> + <has_text text="--regions-overlap"/> </assert_command> </test> <!-- Test mask options--> <test> - <param name="input_file" ftype="vcf" value="filter.3.vcf" /> - <param name="exclude" value="INFO/DP=19" /> + <param name="input_file" ftype="vcf" value="filter.3.vcf"/> + <section name="sec_restrict"> + <param name="exclude" value="INFO/DP=19"/> + </section> <section name="sec_filter"> - <param name="mode" value="+,x" /> + <param name="mode" value="+,x"/> <conditional name="conditional_soft_filter"> <param name="selector" value="enabled"/> - <param name="soft_filter" value="XX" /> - <param name="masks_overlap" value="1"/> + <param name="soft_filter" value="XX"/> + <conditional name="masks"> + <param name="masks_src" value="masks" /> + <repeat name="mask_specs"> + <param name="chrom" value="1" /> + <param name="start" value="1" /> + <param name="stop" value="1000" /> + </repeat> + <param name="masks_overlap" value="1"/> + </conditional> </conditional> </section> - - <param name="output_type" value="v" /> + <param name="output_type" value="v"/> <output name="output_file"> <assert_contents> - <has_text_matching expression="\tq20;XX\tDP=19" /> - <has_text_matching expression="\tPASS\tAO" /> + <has_text_matching expression="\tq20;XX\tDP=19"/> + <has_text_matching expression="\tPASS\tAO"/> </assert_contents> </output> <assert_command> - <has_text text="--mask-overlap" /> + <has_text text="--mask-overlap"/> </assert_command> </test> </tests> @@ -286,8 +325,8 @@ @BCFTOOLS_MANPAGE@#@EXECUTABLE@ -@BCFTOOLS_WIKI@ +@BCFTOOLS_HOWTOS@ ]]> </help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>