comparison bcftools_mpileup.xml @ 4:256e65e460b7 draft

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

3:4e1d23e5c691

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1">
    <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description>
    <macros>
        <token name="@EXECUTABLE@">mpileup</token>
        <import>macros.xml</import>
        <xml name="bam_flag_options">

                <when value="no_limit" />
            </conditional>
        </section>

        <section name="sec_restrict" expanded="false" title="Restrict to">
            <expand macro="macro_regions" />
            <expand macro="macro_targets" />
        </section>
        <section name="sec_subset" expanded="false" title="Subset Options">
            <expand macro="macro_samples" />
        </section>

            </output>
        </test>
        <test>
            <param name="input_number" value="single" />
            <param name="input_bam" ftype="bam" value="mpileup.1.bam" />
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" />
            <param name="quality_settings" value="adjust" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="mpileup" />

        <test>
            <param name="input_number" value="multiple" />
            <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam" />
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" />
            <param name="regions_src" value="regions" />
            <param name="regions" value="17:100-110" />
            <param name="output_tags" value="DP,INFO/AD,DV" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="mpileup" />

        <test>
            <param name="input_number" value="multiple" />
            <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam" />
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" />
            <param name="regions_src" value="regions_file" />
            <param name="regions_file" ftype="bed" value="mpileup.regions.bed" />
            <param name="targets_src" value="targets" />
            <param name="targets" value="17:100-104" />
            <param name="output_tags" value="DP,INFO/AD,DV" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="mpileup" />

        <test>
            <param name="input_number" value="multiple" />
            <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam" />
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" />
            <param name="regions_src" value="regions" />
            <param name="regions" value="17:1050-1060" />
            <param name="filter_flags" value="filter" />
            <param name="exclude_flags" value="4,16" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>

4:256e65e460b7

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy2">
    <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description>
    <macros>
        <token name="@EXECUTABLE@">mpileup</token>
        <import>macros.xml</import>
        <xml name="bam_flag_options">

                <when value="no_limit" />
            </conditional>
        </section>

        <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_invert_targets" />
            </expand>
        </section>
        <section name="sec_subset" expanded="false" title="Subset Options">
            <expand macro="macro_samples" />
        </section>

            </output>
        </test>
        <test>
            <param name="input_number" value="single" />
            <param name="input_bam" ftype="bam" value="mpileup.1.bam" />
            <param name="reference_source_selector" value="cached" />
            <param name="ref_file" value="mpileup" />
            <param name="quality_settings" value="adjust" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="mpileup" />

        <test>
            <param name="input_number" value="multiple" />
            <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam" />
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" />
            <section name="sec_restrict">
                <conditional name="regions">
                    <param name="regions_src" value="regions" />
                    <repeat name="regions">
                        <param name="chrom" value="17" />
                        <param name="start" value="100" />
                        <param name="stop" value="110" />
                    </repeat>
                </conditional>
            </section>
            <param name="output_tags" value="DP,INFO/AD,DV" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="mpileup" />

        <test>
            <param name="input_number" value="multiple" />
            <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam" />
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" />
            <section name="sec_restrict">
                <conditional name="targets">
                    <param name="targets_src" value="targets" />
                    <repeat name="targets">
                        <param name="chrom" value="17" />
                        <param name="start" value="100" />
                        <param name="stop" value="104" />
                    </repeat>
                </conditional>
            </section>
            <param name="output_tags" value="DP,INFO/AD,DV" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="mpileup" />

        <test>
            <param name="input_number" value="multiple" />
            <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam" />
            <param name="reference_source_selector" value="history" />
            <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" />
            <section name="sec_restrict">
                <conditional name="regions">
                    <param name="regions_src" value="regions" />
                    <repeat name="regions">
                        <param name="chrom" value="17" />
                        <param name="start" value="1050" />
                        <param name="stop" value="1060" />
                    </repeat>
                </conditional>
            </section>
            <param name="filter_flags" value="filter" />
            <param name="exclude_flags" value="4,16" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>