comparison macros.xml @ 2:f923c54a17ee draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit 30718e775cd7cd2a7746608a0c99e86521cf8d7b"

1:2c6349fb175c

<macros>
    <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy1</token>
    <token name="@TOOL_VERSION@">11.6</token>
    <xml name="reference_interface">
        <conditional name="reference_source">
            <param name="ref_selector" type="select" label="Choose the source for the reference genome">
                <option value="cached">Locally cached</option>
                <option value="history">History</option>

            </when>
            <when value="history">
                <param argument="--ref" type="data" format="fasta" label="Reference" help="Reference sequence" />
            </when>
        </conditional>
    </xml>
    <xml name="WGS">
        <param name="degree" type="select" label="Degree of polynomial" help="">
            <option value="34" selected="True">GC-content based normalization, WGS (3&amp;4)</option>
            <option value="1">control-read-count-based normalization, WES (1)</option>

            <param name="maxExpectedGC" type="float" label="Maximal expected value of the GC-content" value="0.55" min="0" max="1" help="Maximal expected value of the GC-content for the prior evaluation of &quot;Read Count ~ GC-content&quot; dependency. Change only if you run Control-FREEC on a bacterial genome." />
            <param name="ploidy" type="text" value="2" label="Genome ploidy" help="In case of doubt, you can set different values and Control-FREEC will select the one that explains most observed CNAs. Ex: 2 or 2,3,4" />
            <param name="sex" type="select" label="Sample sex" help="&quot;XX&quot; will exclude chr Y from the analysis. &quot;XY&quot; will not annotate one copy of chr X and Y as a loss.">
                <option value="XY" selected="True">XY</option>
                <option value="XX">XX</option>
                <option value="no value"></option>
            </param>
            <param name="telocentromeric" type="integer" value="50000" label="Length of pre-telomeric and pre-centromeric regions" help="Control-FREEC will not output small CNAs and LOH found within these regions (they are likely to be false because of mappability/genome assembly issues). 50000 is OK for human/mouse genomes. Use smaller values for yeasts and flies. Do not set anything for exome-seq data." />
            <!-- uniqueMatch if true -> gemMappabilityFile is needed-->
        <!-- BAF parameters -->
            <!-- makePileup: path to a BED or VCF file with SNP positions -->

    </xml>
    <xml name="input_control_sample">
        <param name="input_sample_file" type="data" format="bam" multiple="false" label="Sample file" help="Sample file in .BAM format." />
        <param name="input_control_file" type="data" format="bam" multiple="false" label="Control file" help="Control file in .BAM format." />
    </xml>
    <xml name="wes_input_files">
        <expand macro="input_control_sample" />
        <param name="input_capture_file" optional="true" type="data" format="bed" multiple="false" label="BED file with capture regions" help="Capture regions in .BED format." />
        <expand macro="mateOrientation_selector" />
    </xml>
    <xml name="def_input_files">
        <expand macro="input_control_sample" />
        <expand macro="mateOrientation_selector" />
    </xml>
    <xml name="output_section">
        <section name="output_section" title="Outputs" expanded="false">
            <param name="BedGraphOutput" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="BedGraph Output for UCSC genome browser" help="Set &quot;Yes&quot; if you want an additional output in BedGraph format for the UCSC genome browser." />

2:f923c54a17ee

<macros>
    <token name="@VERSION_SUFFIX@">2</token>
    <token name="@TOOL_VERSION@">11.6</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="5.0.1">gawk</requirement>
            <requirement type="package" version="@TOOL_VERSION@">control-freec</requirement>
        </requirements>
    </xml>
    <xml name="reference_interface">
        <conditional name="reference_source">
            <param name="ref_selector" type="select" label="Choose the source for the reference genome">
                <option value="cached">Locally cached</option>
                <option value="history">History</option>

            </when>
            <when value="history">
                <param argument="--ref" type="data" format="fasta" label="Reference" help="Reference sequence" />
            </when>
        </conditional>
    </xml>
    <xml name="xrefs">
        <xrefs>
            <xref type="bio.tools">freec</xref>
        </xrefs>
    </xml>
    <xml name="WGS">
        <param name="degree" type="select" label="Degree of polynomial" help="">
            <option value="34" selected="True">GC-content based normalization, WGS (3&amp;4)</option>
            <option value="1">control-read-count-based normalization, WES (1)</option>

            <param name="maxExpectedGC" type="float" label="Maximal expected value of the GC-content" value="0.55" min="0" max="1" help="Maximal expected value of the GC-content for the prior evaluation of &quot;Read Count ~ GC-content&quot; dependency. Change only if you run Control-FREEC on a bacterial genome." />
            <param name="ploidy" type="text" value="2" label="Genome ploidy" help="In case of doubt, you can set different values and Control-FREEC will select the one that explains most observed CNAs. Ex: 2 or 2,3,4" />
            <param name="sex" type="select" label="Sample sex" help="&quot;XX&quot; will exclude chr Y from the analysis. &quot;XY&quot; will not annotate one copy of chr X and Y as a loss.">
                <option value="XY" selected="True">XY</option>
                <option value="XX">XX</option>
                <option value="no value">Do not expecify sex</option>
            </param>
            <param name="telocentromeric" type="integer" value="50000" label="Length of pre-telomeric and pre-centromeric regions" help="Control-FREEC will not output small CNAs and LOH found within these regions (they are likely to be false because of mappability/genome assembly issues). 50000 is OK for human/mouse genomes. Use smaller values for yeasts and flies. Do not set anything for exome-seq data." />
            <!-- uniqueMatch if true -> gemMappabilityFile is needed-->
        <!-- BAF parameters -->
            <!-- makePileup: path to a BED or VCF file with SNP positions -->

    </xml>
    <xml name="input_control_sample">
        <param name="input_sample_file" type="data" format="bam" multiple="false" label="Sample file" help="Sample file in .BAM format." />
        <param name="input_control_file" type="data" format="bam" multiple="false" label="Control file" help="Control file in .BAM format." />
    </xml>
    <xml name="input_control_sample_wgs">
        <param name="input_sample_file" type="data" format="bam" multiple="false" label="Sample file" help="Sample file in .BAM format." />
        <param name="input_control_file" type="data" format="bam" multiple="false" optional="true" label="Control file" help="Control file in .BAM format." />
    </xml>
    <xml name="wes_input_files">
        <expand macro="input_control_sample" />
        <param name="input_capture_file" optional="true" type="data" format="bed" multiple="false" label="BED file with capture regions" help="Capture regions in .BED format." />
        <expand macro="mateOrientation_selector" />
    </xml>
    <xml name="wgs_input_files">
        <expand macro="input_control_sample_wgs" />
        <expand macro="mateOrientation_selector" />
    </xml>
    <xml name="output_section">
        <section name="output_section" title="Outputs" expanded="false">
            <param name="BedGraphOutput" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="BedGraph Output for UCSC genome browser" help="Set &quot;Yes&quot; if you want an additional output in BedGraph format for the UCSC genome browser." />