comparison variant.xml @ 10:9fb055604648 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"

9:43815fa60f3a

<?xml version="1.0"?>
<tool id="medaka_variant" name="medaka variant tool" version="@TOOL_VERSION@+galaxy7" profile="@PROFILE@">
    <description>Probability decoding</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="1.4.1">scipy</requirement>
    </expand>

    <expand macro="version_command"/>

    <configfiles>
        <configfile name="convert_fasta">

    --debug
    #if $regions
        --regions '${regions}'
    #end if
    $verbose
    ## required
    reference.fa
    #for $current in $pool.inputs
        '$current'
    #end for
    '$out_result' ## output

    2>&1 | tee '$out_log'
#elif $pool.pool_mode == "No":
    ## run
    medaka variant
    ## optional
    --debug
    #if $regions
        --regions '${regions}'
    #end if
    $verbose
    ## required
    reference.fa
    '$pool.input'
    '$out_result' ##output
    2>&1 | tee '$out_log'
#end if

#if $out_annotated:
    ## medaka annotate errors out if the reference is lower case at a position it's annotating because it checks vs the ref base in the vcf
    && python '$convert_fasta' reference.fa  upper_reference.fa
    && ln -s '$output_annotated.in_bam' in.bam
    && ln -s '$output_annotated.in_bam.metadata.bam_index' in.bai
    && medaka tools annotate --pad $output_annotated.pad '$out_result' upper_reference.fa in.bam tmp.vcf
    && '$__tool_directory__/convert_VCF_info_fields.py' tmp.vcf '$out_annotated'
#end if
    ]]></command>
    <inputs>
        <conditional name="pool">
            <param name="pool_mode"  type="select" label="Are you pooling HDF5 datasets?">
                <option value="No" selected="True">No</option>
                <option value="Yes">Yes</option>
            </param>
            <when value="Yes">
                <param name="inputs" type="data" format="h5" multiple="true" label="Select consensus file(s)"/>
            </when>

                    <add value="."/>
                </valid>
            </sanitizer>
        </param>
        <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Populate VCF info fields?"/>
        <conditional name="output_annotated">
            <param name="output_annotated_select" type="select" label="Output annotated VCF?" help="Annotate allele frequency, depth of coverage, etc for each variant (requires BAM file)">
                <option value="true" selected="true">Output annotated VCF</option>
                <option value="false">Don't output annotated VCF</option>
            </param>

                <param name="pool_mode" value="Yes"/>
                <param name="inputs" value="medaka_test.hdf,medaka_test.hdf"/>
            </conditional>
            <conditional name="reference_source">
                <param name="reference_source_selector" value="history"/>
                <param name="ref_file" value="ref.fasta"/>
            </conditional>
            <conditional name="output_annotated">
                <param name="output_annotated_select" value="true"/>
                <param name="in_bam" value="medaka_test.bam"/>
            </conditional>
            <param name="output_log_bool" value="true"/>

                    <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
                </assert_contents>
            </output>
            <output name="out_annotated">
                <assert_contents>
                    <has_n_lines n="22"/>
                    <has_line line="##fileformat=VCFv4.1" />
                    <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
                    <has_line_matching expression="##convert_VCF_info_fields=[0-9]+\.[0-9]+" />
                </assert_contents>
            </output>

            </conditional>
            <conditional name="reference_source">
                <param name="reference_source_selector" value="history"/>
                <param name="ref_file" value="ref.fasta.gz" ftype="fasta.gz"/>
            </conditional>
            <conditional name="output_annotated">
                <param name="output_annotated_select" value="true"/>
                <param name="in_bam" value="medaka_test.bam"/>
            </conditional>
            <param name="output_log_bool" value="true"/>

                    <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
                </assert_contents>
            </output>
            <output name="out_annotated">
                <assert_contents>
                    <has_n_lines n="22"/>
                    <has_line line="##fileformat=VCFv4.1" />
                    <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
                    <has_line_matching expression="##convert_VCF_info_fields=[0-9]+\.[0-9]+" />
                </assert_contents>
            </output>

10:9fb055604648

<?xml version="1.0"?>
<tool id="medaka_variant" name="medaka variant tool" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
    <description>Probability decoding</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

    <expand macro="version_command"/>

    <configfiles>
        <configfile name="convert_fasta">

    --debug
    #if $regions
        --regions '${regions}'
    #end if
    $verbose
    ${ambig_ref}
    ${gvcf}
    ## required
    reference.fa
    #for $current in $pool.inputs
        '$current'
    #end for
    '$out_result' ## output
    2>&1 | tee '$out_log'
#elif $pool.pool_mode == "No":
    ## run
    medaka variant
    ## optional
    --debug
    #if $regions
        --regions '${regions}'
    #end if
    $verbose
    ${ambig_ref}
    ${gvcf}
    ## required
    reference.fa
    '$pool.input'
    '$out_result' ##output
    2>&1 | tee '$out_log'
#end if
#if $out_annotated:
    ## medaka annotate errors out if the reference is lower case at a position it's annotating because it checks vs the ref base in the vcf
    && python '$convert_fasta' reference.fa  upper_reference.fa
    && ln -s '$output_annotated.in_bam' in.bam
    && ln -s '$output_annotated.in_bam.metadata.bam_index' in.bai
    && medaka tools annotate --dpsp --pad $output_annotated.pad '$out_result' upper_reference.fa in.bam tmp.vcf
    && python '$__tool_directory__/convert_VCF_info_fields.py' tmp.vcf '$out_annotated'
#end if
    ]]></command>
    <inputs>
        <conditional name="pool">
            <param name="pool_mode"  type="select" label="Are you pooling HDF5 datasets?">
                <option value="No" selected="true">No</option>
                <option value="Yes">Yes</option>
            </param>
            <when value="Yes">
                <param name="inputs" type="data" format="h5" multiple="true" label="Select consensus file(s)"/>
            </when>

                    <add value="."/>
                </valid>
            </sanitizer>
        </param>
        <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Populate VCF info fields?"/>
        <param argument="--ambig_ref" type="boolean" truevalue="--ambig_ref" falsevalue="" label="Decode variants at ambiguous reference positions?" checked="false"/>
        <param argument="--gvcf" type="boolean" truevalue="--gvcf" falsevalue="" label="Output VCF records for reference loci predicted to be non-variant?" checked="false"/>
        <conditional name="output_annotated">
            <param name="output_annotated_select" type="select" label="Output annotated VCF?" help="Annotate allele frequency, depth of coverage, etc for each variant (requires BAM file)">
                <option value="true" selected="true">Output annotated VCF</option>
                <option value="false">Don't output annotated VCF</option>
            </param>

                <param name="pool_mode" value="Yes"/>
                <param name="inputs" value="medaka_test.hdf,medaka_test.hdf"/>
            </conditional>
            <conditional name="reference_source">
                <param name="reference_source_selector" value="history"/>
                <param name="ref_file" value="ref.fasta.gz"/>
            </conditional>
            <param name="ambig_ref" value="true"/>
            <conditional name="output_annotated">
                <param name="output_annotated_select" value="true"/>
                <param name="in_bam" value="medaka_test.bam"/>
            </conditional>
            <param name="output_log_bool" value="true"/>

                    <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
                </assert_contents>
            </output>
            <output name="out_annotated">
                <assert_contents>
                    <has_n_lines n="23"/>
                    <has_line line="##fileformat=VCFv4.1" />
                    <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
                    <has_line_matching expression="##convert_VCF_info_fields=[0-9]+\.[0-9]+" />
                </assert_contents>
            </output>

            </conditional>
            <conditional name="reference_source">
                <param name="reference_source_selector" value="history"/>
                <param name="ref_file" value="ref.fasta.gz" ftype="fasta.gz"/>
            </conditional>
            <param name="ambig_ref" value="true"/>
            <conditional name="output_annotated">
                <param name="output_annotated_select" value="true"/>
                <param name="in_bam" value="medaka_test.bam"/>
            </conditional>
            <param name="output_log_bool" value="true"/>

                    <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
                </assert_contents>
            </output>
            <output name="out_annotated">
                <assert_contents>
                    <has_n_lines n="23"/>
                    <has_line line="##fileformat=VCFv4.1" />
                    <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
                    <has_line_matching expression="##convert_VCF_info_fields=[0-9]+\.[0-9]+" />
                </assert_contents>
            </output>