comparison macros.xml @ 3:d99788b71ce7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 91d5bae878afa54d8264c1ca89c79b2d26ef35ad

2:54aa421c2911

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">3.3.0</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">20.01</token>
    <xml name="biotools">
        <xrefs>
            <xref type="bio.tools">drep</xref>

            <param argument="--contamination_weight" type="float" value="5" label="Contamination weight"/>
            <param argument="--strain_heterogeneity_weight" type="float" value="1" min="0." max="1." label="Strain heterogeneity weight"/>
            <param argument="--N50_weight" type="float" value=".5" label="Weight of log(genome N50)"/>
            <param argument="--size_weight" type="float" value="0" label="Weight of log(genome size)"/>
            <param argument="--centrality_weight" type="float" value="1" label="Weight of (centrality - S_ani)"/>
        </section>
    </xml>
    <xml name="test_default_scoring_options">
        <section name="scoring">
            <param name="completeness_weight" value="1"/>

            <param name="N50_weight" value=".5" />
            <param name="size_weight" value="0"/>
            <param name="centrality_weight" value="1"/>
        </section>
    </xml>
    <token name="@SCORING_OPTIONS@"><![CDATA[
    --completeness_weight $scoring.completeness_weight
    --contamination_weight $scoring.contamination_weight
    --strain_heterogeneity_weight $scoring.strain_heterogeneity_weight
    --N50_weight $scoring.N50_weight
    --size_weight $scoring.size_weight
    --centrality_weight $scoring.centrality_weight
]]></token>

    <xml name="warning_options">
        <section name="warning" title="Warnings" expanded="false">
            <param argument="--warn_dist" type="float" value="0.25" min="0" max="1" label="How far from the threshold to throw cluster warnings"/>

                        strain heterogeneity weight (default: 1)
  -N50W N50_WEIGHT, --N50_weight N50_WEIGHT
                        weight of log(genome N50) (default: 0.5)
  -sizeW SIZE_WEIGHT, --size_weight SIZE_WEIGHT
                        weight of log(genome size) (default: 0)


]]></token>
    <token name="@TAXONOMY_HELP@"><![CDATA[
TAXONOMY:

3:d99788b71ce7

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">3.4.2</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">20.01</token>
    <xml name="biotools">
        <xrefs>
            <xref type="bio.tools">drep</xref>

            <param argument="--contamination_weight" type="float" value="5" label="Contamination weight"/>
            <param argument="--strain_heterogeneity_weight" type="float" value="1" min="0." max="1." label="Strain heterogeneity weight"/>
            <param argument="--N50_weight" type="float" value=".5" label="Weight of log(genome N50)"/>
            <param argument="--size_weight" type="float" value="0" label="Weight of log(genome size)"/>
            <param argument="--centrality_weight" type="float" value="1" label="Weight of (centrality - S_ani)"/>
            <param argument="--extra_weight_table" type="data" format="tabular" multiple="false" optional="true" label="Genome specific extra weight"/>
        </section>
    </xml>
    <xml name="test_default_scoring_options">
        <section name="scoring">
            <param name="completeness_weight" value="1"/>

            <param name="N50_weight" value=".5" />
            <param name="size_weight" value="0"/>
            <param name="centrality_weight" value="1"/>
        </section>
    </xml>
    <xml name="test_extra_weight_table_scoring_options">
        <section name="scoring">
            <param name="completeness_weight" value="1"/>
            <param name="contamination_weight" value="5"/>
            <param name="strain_heterogeneity_weight" value="1"/>
            <param name="N50_weight" value=".5" />
            <param name="size_weight" value="0"/>
            <param name="centrality_weight" value="1"/>
            <param name="extra_weight_table" ftype="tabular" value="extra_weight_table_test"/>
        </section>
    </xml>
    <token name="@SCORING_OPTIONS@"><![CDATA[
    --completeness_weight $scoring.completeness_weight
    --contamination_weight $scoring.contamination_weight
    --strain_heterogeneity_weight $scoring.strain_heterogeneity_weight
    --N50_weight $scoring.N50_weight
    --size_weight $scoring.size_weight
    --centrality_weight $scoring.centrality_weight
    #if str($extra_weight_table) != 'None'
    	--extra_weight_table $extra_weight_table
    #end if
    
]]></token>

    <xml name="warning_options">
        <section name="warning" title="Warnings" expanded="false">
            <param argument="--warn_dist" type="float" value="0.25" min="0" max="1" label="How far from the threshold to throw cluster warnings"/>

                        strain heterogeneity weight (default: 1)
  -N50W N50_WEIGHT, --N50_weight N50_WEIGHT
                        weight of log(genome N50) (default: 0.5)
  -sizeW SIZE_WEIGHT, --size_weight SIZE_WEIGHT
                        weight of log(genome size) (default: 0)
  -extraW EXTRA_WEIGHT_TABLE, --extra_weight_table EXTRA_WEIGHT_TABLE
  			Path to a tab-separated file with two-columns, no headers, listing genome and extra score to apply to that genome (optional)


]]></token>
    <token name="@TAXONOMY_HELP@"><![CDATA[
TAXONOMY: