Mercurial > repos > iuc > bcftools_filter
diff bcftools_filter.xml @ 16:e7452697afd9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
author | iuc |
---|---|
date | Tue, 20 Sep 2022 13:17:14 +0000 |
parents | e4988fd4d503 |
children | 46fcafba49ec |
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--- a/bcftools_filter.xml Sat Jul 23 13:39:59 2022 +0000 +++ b/bcftools_filter.xml Tue Sep 20 13:17:14 2022 +0000 @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='utf-8'?> -<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@"> +<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Apply fixed-threshold filters</description> <macros> <token name="@EXECUTABLE@">filter</token> @@ -29,8 +29,9 @@ #set $mode = str($section.mode).replace(',','') --mode '$mode' #end if -#if $section.soft_filter: - --soft-filter "${section.soft_filter}" +#if $section.conditional_soft_filter.selector == 'enabled': + --soft-filter '${section.conditional_soft_filter.soft_filter}' + @MASK@ #end if #if $section.select_set_GTs: --set-GTs "${section.select_set_GTs}" @@ -70,11 +71,22 @@ <option value="+">(+) append new FILTER strings of failed sites instead of replacing them</option> <option value="x">(x) resets filters of sites which pass to "PASS"</option> </param> - <param name="soft_filter" type="text" value="" label="Soft Filter" optional="true"> - <help><![CDATA[ (-s) - Annotate FILTER column with STRING or, with +, a unique filter name generated by the program ("Filter%d"). - ]]></help> - </param> + <conditional name="conditional_soft_filter"> + <param name="selector" type="select" label="Perform soft filtering"> + <option value="disabled">Disabled</option> + <option value="enabled">Enabled</option> + </param> + <when value="disabled"/> + <when value="enabled"> + <param argument="--soft-filter" type="text" value="" label="Soft Filter" optional="true"> + <help><![CDATA[ (-s) + 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"/> + </when> + </conditional> + <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> @@ -107,9 +119,9 @@ <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> - <has_text text="Modified" /> + <has_text text="genotypes" /> <has_text text="AN=2;AC=1" /> - <has_text_matching expression="TAAAA\tTA,T\t61.5\tModified" /> + <has_text_matching expression="TAAAA\tTA,T\t61.5\tPASS" /> </assert_contents> </output> </test> @@ -128,7 +140,12 @@ <test> <param name="input_file" ftype="vcf" value="filter.3.vcf" /> <param name="exclude" value="INFO/DP=19" /> - <param name="soft_filter" value="XX" /> + <section name="sec_filter"> + <conditional name="conditional_soft_filter"> + <param name="selector" value="enabled"/> + <param name="soft_filter" value="XX" /> + </conditional> + </section> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> @@ -140,12 +157,17 @@ <test> <param name="input_file" ftype="vcf" value="filter.3.vcf" /> <param name="exclude" value="INFO/DP=19" /> - <param name="soft_filter" value="XX" /> - <param name="mode" value="+" /> + <section name="sec_filter"> + <conditional name="conditional_soft_filter"> + <param name="selector" value="enabled"/> + <param name="soft_filter" value="XX" /> + <param name="mode" value="+" /> + </conditional> + </section> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> - <has_text_matching expression="\tq20;XX\tDP=19" /> + <has_text_matching expression="238\tXX\tDP=19" /> <has_text_matching expression="\tq20\tAO" /> </assert_contents> </output> @@ -153,26 +175,36 @@ <test> <param name="input_file" ftype="vcf" value="filter.3.vcf" /> <param name="exclude" value="INFO/DP=19" /> - <param name="soft_filter" value="XX" /> - <param name="mode" value="x" /> + <section name="sec_filter"> + <conditional name="conditional_soft_filter"> + <param name="selector" value="enabled"/> + <param name="soft_filter" value="XX" /> + <param name="mode" value="+" /> + </conditional> + </section> <param name="output_type" value="v" /> <output name="output_file"> <assert_contents> <has_text_matching expression="\tXX\tDP=19" /> - <has_text_matching expression="\tPASS\tAO" /> + <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="soft_filter" value="XX" /> - <param name="mode" value="+,x" /> + <section name="sec_filter"> + <conditional name="conditional_soft_filter"> + <param name="selector" value="enabled"/> + <param name="soft_filter" value="XX" /> + <param name="mode" value="+" /> + </conditional> + </section> <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="\t238\tXX\tDP=19" /> + <has_text_matching expression="\t238\tq20\tAO" /> </assert_contents> </output> </test> @@ -198,6 +230,48 @@ </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" /> + <section name="sec_restrict"> + <param name="regions_overlap" value="1"/> + </section> + <output name="output_file"> + <assert_contents> + <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" /> + </assert_command> + </test> + <!-- Test mask options--> + <test> + <param name="input_file" ftype="vcf" value="filter.3.vcf" /> + <param name="exclude" value="INFO/DP=19" /> + <section name="sec_filter"> + <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"/> + </conditional> + </section> + + <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" /> + </assert_contents> + </output> + <assert_command> + <has_text text="--mask-overlap" /> + </assert_command> + </test> </tests> <help><![CDATA[ =====================================