comparison macros.xml @ 9:8c4c97fd0555 draft

"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"

8:1a56888ddb7d

<macros>
    <token name="@TOOL_VERSION@">2.1.0</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <xml name="requirements">
        <requirements>
        <requirement type="package" version="@TOOL_VERSION@">arriba</requirement>
            <yield/>
        </requirements>

        </citations>
    </xml>
    <xml name="version_command">
        <version_command>arriba -h | grep Version | sed 's/^.* //'</version_command>
    </xml>
    <xml name="visualization_options">
                <param name="cytobands" argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/>
                <section name="options" expanded="false" title="Draw Fusion Options">
                    <param argument="--transcriptSelection" type="select" optional="true" label="Transcript selection">
                        <help>By default the transcript isoform with the highest coverage is drawn.

    </xml>
    <token name="@DRAW_FUSIONS@">
draw_fusions.R
    --fusions='$fusions'
    --alignments='Aligned.sortedByCoord.out.bam'
    --annotation='$annotation'
    --output=fusions.pdf
    #if $visualization.cytobands
    --cytobands='$visualization.cytobands'
    #end if
    #if $protein_domains

9:8c4c97fd0555

<macros>
    <token name="@TOOL_VERSION@">2.1.0</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <xml name="requirements">
        <requirements>
        <requirement type="package" version="@TOOL_VERSION@">arriba</requirement>
            <yield/>
        </requirements>

        </citations>
    </xml>
    <xml name="version_command">
        <version_command>arriba -h | grep Version | sed 's/^.* //'</version_command>
    </xml>
    <xml name="genome_source" token_assembly_optional="false" >
        <conditional name="genome">
            <param name="genome_source" type="select" label="Arriba Genome assembly and annotation source">
                <option value="history">From your history</option>
                <option value="cached">Use built-in Arriba</option>
            </param>
            <when value="history">
                <param name="assembly" argument="-a" type="data" format="fasta" optional="@ASSEMBLY_OPTIONAL@" label="Genome assembly fasta"/>
                <param name="annotation" argument="-g" type="data" format="gtf" label="Gene annotation in GTF format"/>
            </when>
            <when value="cached">
                <param name="arriba_ref" type="select" label="Arriba Genome assembly and annotation">
                    <options from_data_table="arriba_indexes">
                    </options>
                </param>
            </when>
        </conditional>
    </xml>
    <token name="@GENOME_SOURCE@">
#if str($genome.genome_source) == "history"
    #if $genome.assembly
        #set $genome_assembly = $genome.assembly
    #end if
    #set $genome_annotation = $genome.annotation
#else
    #set $genome_assembly = $genome.arriba_ref.fields.fasta
    #set $genome_annotation = $genome.arriba_ref.fields.gtf
#end if
</token>

    <xml name="visualization_options">
                <param name="cytobands" argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/>
                <section name="options" expanded="false" title="Draw Fusion Options">
                    <param argument="--transcriptSelection" type="select" optional="true" label="Transcript selection">
                        <help>By default the transcript isoform with the highest coverage is drawn.

    </xml>
    <token name="@DRAW_FUSIONS@">
draw_fusions.R
    --fusions='$fusions'
    --alignments='Aligned.sortedByCoord.out.bam'
    --annotation='$genome.annotation'
    --output=fusions.pdf
    #if $visualization.cytobands
    --cytobands='$visualization.cytobands'
    #end if
    #if $protein_domains