comparison bcftools_stats.xml @ 8:e3c64225cbe6 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5

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@

@PREPARE_INPUT_FILES@
#set $section = $sec_restrict
@PREPARE_TARGETS_FILE@
@PREPARE_REGIONS_FILE@
## Stats section
#set $section = $sec_default
@PREPARE_FASTA_REF@
@PREPARE_EXONS_FILE@

bcftools @EXECUTABLE@

## 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

        <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" />
            <expand macro="macro_targets" />
            <expand macro="macro_include" />
            <expand macro="macro_exclude" />
        </section>
        <section name="sec_default" expanded="true" title="Stats Options">
            <param name="first_allele_only" type="boolean" truevalue="--1st-allele-only" falsevalue="" label="1St Allele Only" 

                    <param name="depth_min" type="integer" value="0" min="0" label="Depth min"/> 
                    <param name="depth_max" type="integer" value="500" min="1" label="Depth max" />
                    <param name="depth_bin_size" type="integer" value="1" min="1" label="Depth bin size" />
                </when>
            </conditional>
            <expand macro="macro_fasta_ref" />
            <expand macro="macro_exons_file" />
            <param name="split_by_ID" type="boolean" truevalue="--split-by-ID" falsevalue="" label="Split By Id (Ignored on multiple inputs)" 
                   help="Collect stats for sites with ID separately (known vs novel)" />
            <param name="user_tstv" type="text" value="" optional="true" label="User Tstv" 
                   help="Collect Ts/Tv stats for any tag using the given binning: TAG[:min:max:binsize]" >

                </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"/>

8:e3c64225cbe6

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1">
    <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"/>
        <expand macro="matplotlib_requirement" />
        <requirement type="package" version="0.1.11">tectonic</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.reference_source
@PREPARE_FASTA_REF@
#set $section = $sec_default
@PREPARE_EXONS_FILE@

bcftools @EXECUTABLE@

## Stats section
#set $section = $sec_default.reference_source
@FASTA_REF@
#set $section = $sec_default
@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

        <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_restrict" />
            <expand macro="macro_restrict" type="target" label_type="Target" />
            <expand macro="macro_include" />
            <expand macro="macro_exclude" />
        </section>
        <section name="sec_default" expanded="true" title="Stats Options">
            <param name="first_allele_only" type="boolean" truevalue="--1st-allele-only" falsevalue="" label="1St Allele Only" 

                    <param name="depth_min" type="integer" value="0" min="0" label="Depth min"/> 
                    <param name="depth_max" type="integer" value="500" min="1" label="Depth max" />
                    <param name="depth_bin_size" type="integer" value="1" min="1" label="Depth bin size" />
                </when>
            </conditional>
            <conditional name="reference_source">
                <param name="reference_source_selector" type="select" label="Choose a reference genome">
                    <option value="">Run without a reference genome</option>
                    <option value="cached">Use a built-in genome</option>
                    <option value="history">Use a genome from the history</option>
                </param>
                <when value="" />
                <when value="cached">
                    <param name="fasta_ref" type="select" label="Reference genome">
                        <options from_data_table="fasta_indexes">
                            <filter type="data_meta" column="1" key="dbkey" ref="input_file" />
                            <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
                        </options>
                    </param>
                </when>
                <when value="history">
                    <param name="fasta_ref" type="data" format="fasta" label="Reference genome" />
                </when>
            </conditional>
            <expand macro="macro_exons_file" />
            <param name="split_by_ID" type="boolean" truevalue="--split-by-ID" falsevalue="" label="Split By Id (Ignored on multiple inputs)" 
                   help="Collect stats for sites with ID separately (known vs novel)" />
            <param name="user_tstv" type="text" value="" optional="true" label="User Tstv" 
                   help="Collect Ts/Tv stats for any tag using the given binning: TAG[:min:max:binsize]" >

                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_file" ftype="vcf" value="mpileup.vcf" />
            <section name="sec_default">
                <expand macro="test_using_reference" select_from="cached" ref="mpileup" />
            </section>
            <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>
        <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"/>