annotate macros.xml @ 0:2d4e3aff9dc7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823

<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/>
        </requirements>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1101/gr.257246.119</citation>
            <yield />
        </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="Genome assembly fasta (that was used for STAR alignment)">
                <option value="history">From your history</option>
                <option value="cached">Use built-in Genome reference</option>
            </param>
            <when value="history">
                <param name="assembly" argument="-a" type="data" format="fasta" optional="@ASSEMBLY_OPTIONAL@" label="Genome assembly fasta"/>
            </when>
            <when value="cached">
                <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
                    <options from_data_table="all_fasta">
                        <validator type="no_options" message="No reference genomes are available" />
                    </options>
                </param>
            </when>
        </conditional>
    </xml>
    <xml name="gtf_source" token_assembly_optional="false" >
        <conditional name="genome_gtf">
            <param name="gtf_source" type="select" label="Genome GTF annotation source">
                <option value="history">From your history</option>
                <!-- <option value="cached">Use built-in Gtf annotation</option> -->
            </param>
            <when value="history">
                <param name="annotation" argument="-g" type="data" format="gtf" label="Gene annotation in GTF format"/>
            </when>
        </conditional>
    </xml>

    <token name="@GENOME_SOURCE@"><![CDATA[
#if str($genome.genome_source) == "history"
    #if $genome.assembly
        #set $genome_assembly = 'genome.fa'
        ln -sf '$genome.assembly' $genome_assembly &&
    #end if
#elif str($genome.genome_source) == "cached"
    #set $genome_assembly = $genome.ref_file.fields.fasta
#end if
    ]]></token>
    <token name="@GTF_SOURCE@"><![CDATA[
#if str($genome_gtf.gtf_source) == "history"
    #if $genome_gtf.annotation.is_of_type('gtf.gz')
        #set $genome_annotation = 'genome.gtf.gz'
    #else
        #set $genome_annotation = 'genome.gtf'
    #end if
    ln -sf '$genome_gtf.annotation' $genome_annotation &&
#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="--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,
                             in the sense that the coverage track is smooth and shows a visible increase in coverage after the fusion breakpoint.
                             However, the isoform with the highest coverage may not be the one that is involved in the fusion.
                             Often, genomic rearrangements lead to non-canonical isoforms being transcribed.
                             For this reason, it can make sense to rely on the transcript selection provided by the columns transcript_id1/2,
                             which reflect the actual isoforms involved in a fusion.
\                            As a third option, the transcripts that are annotated as canonical can be drawn.
                             Transcript isoforms tagged with appris_principal, appris_candidate, or CCDS are considered canonical.
                        </help>
                        <option value="coverage">coverage</option>
                        <option value="provided">provided</option>
                        <option value="canonical">canonical</option>
                    </param>
                    <param argument="--minConfidenceForCircosPlot" type="select" optional="true" label="Transcript selection">
                        <help>The fusion of interest is drawn as a solid line in the circos plot.
                              To give an impression of the overall degree of rearrangement,
                              all other fusions are drawn as semi-transparent lines in the background.
                              This option determines which other fusions should be included in the circos plot.
                              Values specify the minimum confidence a fusion must have to be included.
                              It usually makes no sense to include low-confidence fusions in circos plots,
                              because they are abundant and unreliable, and would clutter up the circos plot.
                              Default: medium
                        </help>
                        <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.
                              It makes sense to disable this feature, if breakpoints in introns are of importance.
                              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,
                              given that they overlap by the given fraction.
                              The description of the larger domain is used.
                              Default: 0.9
                        </help>
                    </param>
                    <param argument="--printExonLabels" type="select" optional="true" label="Print Exon Labels">
                        <help>By default the number of an exon is printed inside each exon,
                              which is taken from the attribute exon_number of the GTF annotation.
                              When a gene has many exons, the boxes may be too narrow to contain the labels,
                              resulting in unreadable exon labels. In these situations, i
                              it may be better to turn off exon labels.
                              Default: TRUE
                        </help>
                        <option value="TRUE">True</option>
                        <option value="FALSE">False</option>
                    </param>
                    <param argument="--render3dEffect" type="select" optional="true" label="Render 3D effect">
                        <help>Whether light and shadow should be rendered to give objects a 3D effect.
                              Default: TRUE
                        </help>
                        <option value="TRUE">True</option>
                        <option value="FALSE">False</option>
                    </param>
                    <param argument="--optimizeDomainColors" type="select" optional="true" label="Optimize Domain Colors">
                        <help>By default, the script colorizes domains according to the colors
                              specified in the file given in --annotation.
                              This way, coloring of domains is consistent across all proteins.
                              But since there are more distinct domains than colors,
                              this can lead to different domains having the same color.
                              If this option is set to TRUE, the colors are recomputed for each fusion separately.
                              This ensures that the colors have the maximum distance for each individual fusion,
                              but they are no longer consistent across different fusions.
                              Default: FALSE
                        </help>
                        <option value="TRUE">True</option>
                        <option value="FALSE">False</option>
                    </param>
                    <param argument="--color1" type="color" value="" optional="true"  label="Color of the 5' end of the fusion."/>
                    <param argument="--color2" type="color" value="" optional="true"  label="Color of the 3' end of the fusion."/>
                    <param argument="--pdfWidth" type="float" value="" min="1." optional="true" label="Width of PDF output file in inches"
                           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='$fusions'
    --alignments='Aligned.sortedByCoord.out.bam'
    --annotation='$genome_gtf.annotation'
    --output=fusions.pdf
    #if $visualization.cytobands
    --cytobands='$visualization.cytobands'
    #end if
    #if $protein_domains
    --proteinDomains='$protein_domains'
    #end if
    ## Visualization Options
    #if $visualization.options.transcriptSelection
        --transcriptSelection=$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
    #end if
    #if $visualization.options.color1
        --color1='$visualization.options.color1'
    #end if
    #if $visualization.options.color2
        --color2='$visualization.options.color2'
    #end if
    #if str($visualization.options.pdfWidth)
        --pdfWidth=$visualization.options.pdfWidth
    #end if
    #if str($visualization.options.pdfHeight)
        --pdfHeight=$visualization.options.pdfHeight
    #end if
    # fontFamily
    #if $visualization.options.fontFamily
        --fontFamily=$visualization.options.fontFamily
    #end if
    #if str($visualization.options.fontSize)
        --fontSize=$visualization.options.fontSize
    #end if
</token>
</macros>