comparison bcftools_stats.xml @ 7:baa8823f8073 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69

6:b641062a2587

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@">
    <description>Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats</description>
    <macros>
        <token name="@EXECUTABLE@">stats</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <expand macro="samtools_requirement"/>
        <requirement type="package" version="2.0.0">matplotlib</requirement>
    </expand>
    <expand macro="version_command" />
    <command detect_errors="aggressive"><![CDATA[
@PREPARE_ENV@
@PREPARE_INPUT_FILES@
#set $section = $sec_restrict
@PREPARE_TARGETS_FILE@
@PREPARE_REGIONS_FILE@
## Stats section

#set $section = $sec_default
@FASTA_REF@
@EXONS_FILE@
${section.first_allele_only}
#if $section.depth.set_depth == 'yes':
  --depth "${section.depth.depth_min},${section.depth.depth_max},${section.depth.depth_bin_size}"
#end if
#if $section.user_tstv:
  --user-tstv "${section.user_tstv}"
#end if
#if $section.afbins.afbins_select == 'af_bins_list':
  --af-bins $section.afbins.af_bins_list
#elif $section.afbins.afbins_select == 'af_bins_file':
  --af-bins $section.afbins.af_bins_file
#end if
#if $section.af_tag:
  --af-tag "${section.af_tag}"
#end if
#if len($input_vcfs) == 1:
${section.split_by_ID}
#end if
${section.verbose}

## Stats section
#set $section = $sec_restrict

@INCLUDE@
@EXCLUDE@

## Primary Input/Outputs
@INPUT_FILES@
> $output_file
## requires: matplotlib and pdflatex
#if $plot_title:
&& plot-vcfstats -p 'plot_tmp/' -T $plot_title -s $output_file
#end if
]]>
    </command>
    <inputs>
        <expand macro="macro_inputs" />
        <section name="sec_restrict" expanded="false" title="Restrict to">
            <expand macro="macro_samples" />
            <expand macro="macro_apply_filters" />
            <expand macro="macro_collapse" />
            <expand macro="macro_regions" />

            <validator type="regex" message="">^\w.*\w$</validator>
        </param>
    </inputs>
    <outputs>
        <data name="output_file" format="txt"/>
        <data name="output_pdf" format="pdf">
            <filter>plot_title</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input_files" ftype="vcf" value="stats.b.vcf,stats.a.vcf" />
            <output name="output_file">
                <assert_contents>
                    <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>
                    <has_text_matching expression="SN\t1\tnumber of samples:\t3"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_files" ftype="vcf" value="mpileup.vcf" />
            <output name="output_file">
                <assert_contents>
                    <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>
                    <has_text_matching expression="SN\t0\tnumber of records:\t4103"/>
                    <has_text_matching expression="ST\t0\tA>C\t16"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
=====================================
 bcftools @EXECUTABLE@

Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats. 

When two files are given, the program generates separate stats for intersection and the complements. 
By default only sites are compared, -s/-S must given to include also sample columns.

@COLLAPSE_HELP@
@REGIONS_HELP@
@TARGETS_HELP@
@EXPRESSIONS_HELP@

7:baa8823f8073

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@">
    <description>Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats</description>
    <macros>
        <token name="@EXECUTABLE@">stats</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <expand macro="samtools_requirement"/>
        <requirement type="package" version="3.0.2">matplotlib</requirement>
        <requirement type="package" version="0.1.11">tectonic</requirement>
    </expand>
    <expand macro="version_command" />
    <command detect_errors="aggressive"><![CDATA[
@PREPARE_ENV@
#set $input_files = [$input_file]
#if $inputB_file:
    #silent $input_files.append($inputB_file)
#end if
@PREPARE_INPUT_FILES@
#set $section = $sec_restrict
@PREPARE_TARGETS_FILE@
@PREPARE_REGIONS_FILE@
## Stats section

#set $section = $sec_default
@FASTA_REF@
@EXONS_FILE@
${section.first_allele_only}
#if $section.depth.set_depth == 'yes':
    --depth ${section.depth.depth_min},${section.depth.depth_max},${section.depth.depth_bin_size}
#end if
#if $section.user_tstv:
    --user-tstv '${section.user_tstv}'
#end if
#if $section.afbins.afbins_select == 'af_bins_list':
    --af-bins '$section.afbins.af_bins_list'
#elif $section.afbins.afbins_select == 'af_bins_file':
    --af-bins '$section.afbins.af_bins_file'
#end if
#if $section.af_tag:
    --af-tag '${section.af_tag}'
#end if
#if len($input_vcfs) == 1:
    ${section.split_by_ID}
#end if
${section.verbose}

## Stats section
#set $section = $sec_restrict

@INCLUDE@
@EXCLUDE@

## Primary Input/Outputs
@INPUT_FILES@
> '$output_file'
#if $plot_title:
    && plot-vcfstats
    -p 'plot_tmp/'
    -T '$plot_title'
    -s
    '$output_file'
    || (printf "The content of plot_tmp/plot-vcfstats.log is:\n" >&2 && cat plot_tmp/plot-vcfstats.log >&2 && exit 1)
#end if
    ]]></command>
    <inputs>
        <expand macro="macro_input" />
        <param name="inputB_file" type="data" format="vcf,vcf_bgzip,bcf" optional="true" label="Optional VCF/BCF Data to compare against" help="When this second dataset is also specified, separate stats for intersection and the complements are generated" />
        <section name="sec_restrict" expanded="false" title="Restrict to">
            <expand macro="macro_samples" />
            <expand macro="macro_apply_filters" />
            <expand macro="macro_collapse" />
            <expand macro="macro_regions" />

            <validator type="regex" message="">^\w.*\w$</validator>
        </param>
    </inputs>
    <outputs>
        <data name="output_file" format="txt"/>
        <data name="output_pdf" format="pdf" from_work_dir="plot_tmp/summary.pdf">
            <filter>plot_title</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="vcf" value="stats.b.vcf" />
            <param name="inputB_file" ftype="vcf" value="stats.a.vcf" />
            <output name="output_file">
                <assert_contents>
                    <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>
                    <has_text_matching expression="SN\t1\tnumber of samples:\t3"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_file" ftype="vcf" value="mpileup.vcf" />
            <param name="plot_title" value="Plot for mpileup.vcf" />
            <output name="output_file">
                <assert_contents>
                    <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>
                    <has_text_matching expression="SN\t0\tnumber of records:\t4103"/>
                    <has_text_matching expression="ST\t0\tA>C\t16"/>
                </assert_contents>
            </output>
            <output name="output_pdf" file="summary.pdf" compare="sim_size" delta="20000" />
        </test>
    </tests>
    <help><![CDATA[
=====================================
 bcftools @EXECUTABLE@

Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats. 

When two files are given, the program generates separate stats for intersection and the complements. 
By default only sites are compared, -s/-S must given to include also sample columns.

When one VCF file is specified, then stats by non-reference allele frequency, depth distribution, stats by quality and per-sample counts, singleton stats, etc. are printed. When two VCF files are given, then stats such as concordance (Genotype concordance by non-reference allele frequency, Genotype concordance by sample, Non-Reference Discordance) and correlation are also printed. Per-site discordance (PSD) is also printed in --verbose mode.

@COLLAPSE_HELP@
@REGIONS_HELP@
@TARGETS_HELP@
@EXPRESSIONS_HELP@