comparison bcftools_consensus.xml @ 8:70b8e9908ea8 draft

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

7:2363ef414c9b

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@">
    <description>Create consensus sequence by applying VCF variants to a reference fasta file</description>
    <macros>
        <token name="@EXECUTABLE@">consensus</token>
        <import>macros.xml</import>
    </macros>

    </expand>
    <expand macro="version_command" />
    <command detect_errors="aggressive"><![CDATA[
@PREPARE_ENV@
@PREPARE_INPUT_FILE@
#set $section = $sec_default
@PREPARE_FASTA_REF@

bcftools @EXECUTABLE@

## Default section
#set $section = $sec_default
@FASTA_REF@

${section.iupac_codes}

#if $section.mask:
  --mask "${section.mask}"

@INPUT_FILE@
]]>
    </command>
    <inputs>
        <expand macro="macro_input" />
        <section name="sec_default" expanded="true" title="Default Options">
            <expand macro="macro_fasta_ref" />
            <param name="mask" type="data" format="tabular" label="Mask" optional="True" help="Replace regions with N" />

            <param name="iupac_codes" type="boolean" truevalue="--iupac-codes" falsevalue="" label="Iupac Codes" 
                   help="Output variants in the form of IUPAC ambiguity codes" />
            <expand macro="macro_sample" />
            <param name="select_haplotype" type="select" optional="true">
                <option value="1">1</option>

            <filter>chain</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="fasta_ref" ftype="fasta" value="consensus.fa" />
            <param name="input_file" ftype="vcf" value="consensus.vcf" />
            <param name="mask" ftype="tabular" value="consensus.tab" />
            <param name="chain" value="True" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="NNNNNNNNNNNNNNNNNNNNNNNNNN" />

8:70b8e9908ea8

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1">
    <description>Create consensus sequence by applying VCF variants to a reference fasta file</description>
    <macros>
        <token name="@EXECUTABLE@">consensus</token>
        <import>macros.xml</import>
    </macros>

    </expand>
    <expand macro="version_command" />
    <command detect_errors="aggressive"><![CDATA[
@PREPARE_ENV@
@PREPARE_INPUT_FILE@
#set $section = $reference_source
@PREPARE_FASTA_REF@

bcftools @EXECUTABLE@

@FASTA_REF@

## Default section
#set $section = $sec_default

${section.iupac_codes}

#if $section.mask:
  --mask "${section.mask}"

@INPUT_FILE@
]]>
    </command>
    <inputs>
        <expand macro="macro_input" />
        <expand macro="macro_fasta_ref" />
        <section name="sec_default" expanded="true" title="Default Options">
            <param name="mask" type="data" format="tabular" label="Mask" optional="True" help="Replace regions with N" />
            <param name="iupac_codes" type="boolean" truevalue="--iupac-codes" falsevalue="" label="Iupac Codes" 
                   help="Output variants in the form of IUPAC ambiguity codes" />
            <expand macro="macro_sample" />
            <param name="select_haplotype" type="select" optional="true">
                <option value="1">1</option>

            <filter>chain</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <expand macro="test_using_reference" ref="consensus.fa" />
            <param name="input_file" ftype="vcf" value="consensus.vcf" />
            <param name="mask" ftype="tabular" value="consensus.tab" />
            <param name="chain" value="True" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="NNNNNNNNNNNNNNNNNNNNNNNNNN" />
                </assert_contents>
            </output>
            <output name="chain_file">
                <assert_contents>
                    <has_text text="chain 497 1 501 + 1 501 1 502 + 1 502 1" />
                </assert_contents>
            </output>
        </test>
        <test>
            <expand macro="test_using_reference" select_from="cached" ref="consensus" />
            <param name="input_file" ftype="vcf" dbkey="?" value="consensus.vcf" />
            <param name="mask" ftype="tabular" value="consensus.tab" />
            <param name="chain" value="True" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="NNNNNNNNNNNNNNNNNNNNNNNNNN" />