comparison macros.xml @ 1:55ca46d68a57 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"

0:7345cb1bb772

<macros>
    <token name="@TOOL_VERSION@">2.2.1</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <xml name="requirements">
        <requirements>
        <requirement type="package" version="@TOOL_VERSION@">arriba</requirement>
            <yield/>

</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.
                             Alternatively, the transcript isoform that is provided in the columns
                             transcript_id1 and transcript_id2 in the given fusions file can be drawn.
                             Selecting the isoform with the highest coverage usually produces nicer plots,

                        <option value="none">none - only the fusion of interest is drawn</option>
                        <option value="low">low</option>
                        <option value="medium">medium</option>
                        <option value="high">high</option>
                    </param>
                    <param argument="--showIntergenicVicinity" type="integer" value="" min="0" optional="true" label="Intergenic Vicinity">
                        <help>This option only applies to intergenic breakpoints.
                              If it is set to a value greater than 0, then the script draws the genes
                              which are no more than the given distance away from an intergenic breakpoint.
                              Note that this option is incompatible with squishIntrons.
                              Default: 0
                        </help>
                    </param>
                    <param argument="--squishIntrons" type="select" optional="true" label="Squish introns">
                        <help>Exons usually make up only a small fraction of a gene.
                              They may be hard to see in the plot. i
                              Since introns are in most situations of no interest in the context of gene fusions,
                              this switch can be used to shrink the size of introns to a fixed, negligible size.

                              Default: TRUE
                        </help>
                        <option value="TRUE">True</option>
                        <option value="FALSE">False</option>
                    </param>

                    <param argument="--mergeDomainsOverlappingBy" type="float" value="" min="0." max="1.0" optional="true" label="Merge Domains Overlapping By">
                        <help>Occasionally, domains are annotated redundantly.
                              For example, tyrosine kinase domains are frequently annotated as
                              Protein tyrosine kinase and Protein kinase domain.
                              In order to simplify the visualization, such domains can be merged into one,

                           help="Default: 11.692"/>
                    <param argument="--pdfHeight" type="float" value="" min="1." optional="true" label="Height of PDF output file in inches"
                           help="Default: 8.267"/>
                    <param argument="--fontSize" type="float" value="" min="0." optional="true" label="Scale the size of text"
                           help="Default: 1.0"/>
                </section>
    </xml>
    <token name="@DRAW_FUSIONS@">
draw_fusions.R
    --fusions='$fusions'

        --transcriptSelection=$visualization.options.transcriptSelection
    #end if
    #if $visualization.options.minConfidenceForCircosPlot
        --minConfidenceForCircosPlot=$visualization.options.minConfidenceForCircosPlot
    #end if
    #if $visualization.options.showIntergenicVicinity
        --showIntergenicVicinity=$visualization.options.showIntergenicVicinity
    #end if
    #if $visualization.options.squishIntrons
        --squishIntrons=$visualization.options.squishIntrons
    #end if
    #if $visualization.options.mergeDomainsOverlappingBy
        --mergeDomainsOverlappingBy=$visualization.options.mergeDomainsOverlappingBy
    #end if
    #if $visualization.options.printExonLabels
        --printExonLabels=$visualization.options.printExonLabels
    #end if
    #if $visualization.options.render3dEffect
        --render3dEffect=$visualization.options.render3dEffect
    #end if
    #if $visualization.options.optimizeDomainColors
        --optimizeDomainColors=$visualization.options.optimizeDomainColors

        --pdfWidth=$visualization.options.pdfWidth
    #end if
    #if $visualization.options.pdfHeight
        --pdfHeight=$visualization.options.pdfHeight
    #end if
    #if $visualization.options.fontSize
        --fontSize=$visualization.options.fontSize
    #end if
</token>
</macros>

1:55ca46d68a57

<macros>
    <token name="@TOOL_VERSION@">2.3.0</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <xml name="requirements">
        <requirements>
        <requirement type="package" version="@TOOL_VERSION@">arriba</requirement>
            <yield/>

</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="--sampleName" type="text" value="" optional="true" label="Sample Name printed as the title on every page"/>
                    <param argument="--transcriptSelection" type="select" optional="true" label="Transcript selection">
                        <help>By default the transcript isoform with the highest coverage is drawn.
                             Alternatively, the transcript isoform that is provided in the columns
                             transcript_id1 and transcript_id2 in the given fusions file can be drawn.
                             Selecting the isoform with the highest coverage usually produces nicer plots,

                        <option value="none">none - only the fusion of interest is drawn</option>
                        <option value="low">low</option>
                        <option value="medium">medium</option>
                        <option value="high">high</option>
                    </param>
                    <param argument="--squishIntrons" type="select" optional="true" label="Squish introns">
                        <help>Exons usually make up only a small fraction of a gene.
                              They may be hard to see in the plot. i
                              Since introns are in most situations of no interest in the context of gene fusions,
                              this switch can be used to shrink the size of introns to a fixed, negligible size.

                              Default: TRUE
                        </help>
                        <option value="TRUE">True</option>
                        <option value="FALSE">False</option>
                    </param>
                    <param argument="--showIntergenicVicinity" type="text" value="" optional="true" label="Intergenic Vicinity">
                        <help>This option only applies to intergenic breakpoints.
                              If it is set to a value greater than 0, then the script draws the genes
                              which are no more than the given distance away from an intergenic breakpoint.
                              The keywords closestGene and closestProteinCodingGene instruct the script 
                              to dynamically determine the distance to the next (protein-coding) gene for each breakpoint. 
                              Alternatively, instead of specifying a single distance 
                              that is applied upstream and downstream of both breakpoints alike, 
                              more fine-grained control over the region to be shown is possible by specifying four comma-separated values. 
                              The first two values determine the region to the left and to the right of breakpoint 1; 
                              the third and fourth values determine the region to the left and to the right of breakpoint 2. 
                              Note that this option is incompatible with squishIntrons.
                              Default: 0
                        </help>
                        <option value="closestGene">closestGene</option>
                        <option value="closestProteinCodingGene">closestProteinCodingGene</option>
                        <validator type="regex" message="">^(closestGene|closestProteinCodingGene|\d+|\d+,\d+,\d+,\d+)$</validator>
                    </param>
                    <param argument="--mergeDomainsOverlappingBy" type="float" value="" min="0." max="1.0" optional="true" label="Merge Domains Overlapping By">
                        <help>Occasionally, domains are annotated redundantly.
                              For example, tyrosine kinase domains are frequently annotated as
                              Protein tyrosine kinase and Protein kinase domain.
                              In order to simplify the visualization, such domains can be merged into one,

                           help="Default: 11.692"/>
                    <param argument="--pdfHeight" type="float" value="" min="1." optional="true" label="Height of PDF output file in inches"
                           help="Default: 8.267"/>
                    <param argument="--fontSize" type="float" value="" min="0." optional="true" label="Scale the size of text"
                           help="Default: 1.0"/>
                    <param argument="--fontFamily" type="text" value="" optional="true" label="Font to use for all labels in the plots.">
                        <help>Default: Helvetica
                        </help>
                        <option value="serif">serif</option>
                        <option value="sans">sans</option>
                        <option value="mono">mono</option>
                        <option value="AvantGarde">AvantGarde</option>
                        <option value="Bookman">Bookman</option>
                        <option value="Courier">Courier</option>
                        <option value="Helvetica">Helvetica</option>
                        <option value="Helvetica-Narrow">Helvetica-Narrow</option>
                        <option value="NewCenturySchoolbook">NewCenturySchoolbook</option>
                        <option value="Palatino">Palatino</option>
                        <option value="Times">Times</option>
                        <option value="URWGothic">URWGothic</option>
                        <option value="URWBookman">URWBookman</option>
                        <option value="NimbusMon">NimbusMon</option>
                        <option value="NimbusSan">NimbusSan</option>
                        <option value="URWHelvetica">URWHelvetica</option>
                        <option value="NimbusSanCond">NimbusSanCond</option>
                        <option value="CenturySch">CenturySch</option>
                        <option value="URWPalladio">URWPalladio</option>
                        <option value="NimbusRom">NimbusRom</option>
                        <option value="URWTimes">URWTimes</option>
                        <option value="ArialMT">ArialMT</option>
                        <option value="Japan1">Japan1</option>
                        <option value="Japan1HeiMin">Japan1HeiMin</option>
                        <option value="Japan1GothicBBB">Japan1GothicBBB</option>
                        <option value="Japan1Ryumin">Japan1Ryumin</option>
                        <option value="Korea1">Korea1</option>
                        <option value="Korea1deb">Korea1deb</option>
                        <option value="CNS1">CNS1</option>
                        <option value="GB1">GB1</option>
                    </param>
                    <param argument="--fixedScale" type="integer" value="" min="0" optional="true" label="Apply a fixed scale to all fusions">
                        <help>By default, transcripts are scaled automatically to fill the entire page. 
                              This parameter enforces a fixed scale to be applied to all fusions, 
                              which is useful when a collection of fusions should be visualized and the sizes of all transcripts should be comparable. 
                              A common use case is the visualization of a gene that is found to be fused to multiple partners. 
                              By forcing all fusion plots to use the same scale, the fusions can be summarized as a collage 
                              in a single plot one above the other with matching scales. 
                              Note: The scale must be bigger than the sum of the biggest pair of transcripts to be drawn, 
                              or else dynamic scaling is applied, because display errors would occur otherwise. 
                              The default value is 0, which means that no fixed scale should be used 
                              and that the scale should be adapted dynamically for each fusion. Default: 0
                        </help>
                    </param>
                    <param argument="--coverageRange" type="text" value="" optional="true" label="Maximum coverage for plot">
                        <help>When the parameter --alignments is used, coverage plots are drawn above the transcripts of the fused genes. 
                              The plots can be cropped at a fixed level by passing a non-zero value to this parameter. 
                              When only a single value is given, both coverage plots (for gene1 and gene2) are cropped at the same level. 
                              When two comma-separated values are given, the cutoffs can be specified independently for the two plots. 
                              A value of 0 indicates that no cropping should be applied (i.e., the cutoff is set to the peak coverage) 
                              and that the coverage plots of both genes should be on the same scale. This is the default behavior. 
                              A value of 0,0 also indicates that no cropping should be applied, 
                              but the coverage plots of the two genes have different scales: 
                              each one is scaled individually to the peak coverage of the respective gene. 
                              Default: 0
                        </help>
                        <validator type="regex" message="">^\d+(,\d+)?$</validator>
                    </param>
                </section>
    </xml>
    <token name="@DRAW_FUSIONS@">
draw_fusions.R
    --fusions='$fusions'

        --transcriptSelection=$visualization.options.transcriptSelection
    #end if
    #if $visualization.options.minConfidenceForCircosPlot
        --minConfidenceForCircosPlot=$visualization.options.minConfidenceForCircosPlot
    #end if
    #if $visualization.options.squishIntrons
        --squishIntrons=$visualization.options.squishIntrons
        #if $visualization.options.squishIntrons == 'FALSE' and $visualization.options.showIntergenicVicinity
            --showIntergenicVicinity=$visualization.options.showIntergenicVicinity
        #end if
    #end if
    #if $visualization.options.mergeDomainsOverlappingBy
        --mergeDomainsOverlappingBy=$visualization.options.mergeDomainsOverlappingBy
    #end if
    #if $visualization.options.sampleName
        --sampleName=$visualization.options.sampleName
    #end if
    #if $visualization.options.printExonLabels
        --printExonLabels=$visualization.options.printExonLabels
    #end if
    #if $visualization.options.coverageRange
        --coverageRange="$visualization.options.coverageRange"
    #end if
    #if $visualization.options.render3dEffect
        --render3dEffect=$visualization.options.render3dEffect
    #end if
    #if $visualization.options.optimizeDomainColors
        --optimizeDomainColors=$visualization.options.optimizeDomainColors

        --pdfWidth=$visualization.options.pdfWidth
    #end if
    #if $visualization.options.pdfHeight
        --pdfHeight=$visualization.options.pdfHeight
    #end if
    # fontFamily
    #if $visualization.options.fontFamily
        --fontFamily=$visualization.options.fontFamily
    #end if
    #if $visualization.options.fontSize
        --fontSize=$visualization.options.fontSize
    #end if
</token>
</macros>