Mercurial > repos > iuc > bcftools_filter
diff bcftools_filter.xml @ 0:061729be105d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
| author | iuc |
|---|---|
| date | Wed, 06 Jul 2016 07:03:12 -0400 |
| parents | |
| children | 6981feb1d742 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bcftools_filter.xml Wed Jul 06 07:03:12 2016 -0400 @@ -0,0 +1,218 @@ +<?xml version='1.0' encoding='utf-8'?> +<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0"> + <description>Apply fixed-threshold filters</description> + <macros> + <token name="@EXECUTABLE@">filter</token> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command detect_errors="aggressive"><![CDATA[ +@PREPARE_ENV@ +@PREPARE_INPUT_FILE@ +#set $section = $sec_restrict +@PREPARE_TARGETS_FILE@ + +bcftools @EXECUTABLE@ + +## Filter section +#set $section = $sec_filter +#if $section.SnpGap: + --SnpGap "${section.SnpGap}" +#end if +#if $section.IndelGap: + --IndelGap "${section.IndelGap}" +#end if +#if $section.mode: + #set $mode = str($section.mode).replace(',','') + --mode '$mode' +#end if +#if $section.soft_filter: + --soft-filter "${section.soft_filter}" +#end if +#if $section.select_set_GTs: + --set-GTs "${section.select_set_GTs}" +#end if + +#set $section = $sec_restrict +@REGIONS@ +@TARGETS@ +@INCLUDE@ +@EXCLUDE@ + +@OUTPUT_TYPE@ +@THREADS@ + +## Primary Input/Outputs +@INPUT_FILE@ +> "$output_file" +]]> + </command> + <inputs> + <expand macro="macro_input" /> + <section name="sec_restrict" expanded="false" title="Restrict to"> + <expand macro="macro_regions" /> + <expand macro="macro_targets" /> + <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="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 + while leaving sites which pass untouched when non-empty + and setting to "PASS" when the FILTER string is absent. + </help> + <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> + <param name="select_set_GTs" type="select" ladel="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" /> + </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" /> + <output name="output_file"> + <assert_contents> + <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" /> + <output name="output_file"> + <assert_contents> + <has_text text="Modified" /> + <has_text text="AN=2;AC=1" /> + <has_text_matching expression="TAAAA\tTA,T\t61.5\tModified" /> + </assert_contents> + </output> + </test> + <test> + <param name="input_file" ftype="vcf" value="filter.3.vcf" /> + <param name="exclude" value="DP=19" /> + <param name="output_type" value="v" /> + <output name="output_file"> + <assert_contents> + <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="DP=19" /> + <param name="soft_filter" value="XX" /> + <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" /> + </assert_contents> + </output> + </test> + <test> + <param name="input_file" ftype="vcf" value="filter.3.vcf" /> + <param name="exclude" value="DP=19" /> + <param name="soft_filter" value="XX" /> + <param name="mode" value="+" /> + <param name="output_type" value="v" /> + <output name="output_file"> + <assert_contents> + <has_text_matching expression="\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="DP=19" /> + <param name="soft_filter" value="XX" /> + <param name="mode" value="x" /> + <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" /> + </assert_contents> + </output> + </test> + <test> + <param name="input_file" ftype="vcf" value="filter.3.vcf" /> + <param name="exclude" value="DP=19" /> + <param name="soft_filter" value="XX" /> + <param name="mode" value="+,x" /> + <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> + </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" /> + <output name="output_file"> + <assert_contents> + <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" /> + <output name="output_file"> + <assert_contents> + <has_text text="AN=4;AC=2" /> + <not_has_text text="AN=4;AC=0" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +===================================== + bcftools @EXECUTABLE@ +===================================== + +Apply fixed-threshold filters. + +@REGIONS_HELP@ +@TARGETS_HELP@ +@EXPRESSIONS_HELP@ + + +@BCFTOOLS_MANPAGE@#@EXECUTABLE@ + +@BCFTOOLS_WIKI@ +]]> + </help> + <expand macro="citations" /> +</tool>