Mercurial > repos > jjohnson > arriba
changeset 13:1d459aaa5765 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
| author | jjohnson |
|---|---|
| date | Mon, 13 Jun 2022 12:09:32 +0000 |
| parents | 73fd7703a743 |
| children | |
| files | arriba.xml macros.xml |
| diffstat | 2 files changed, 147 insertions(+), 15 deletions(-) [+] |
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--- a/arriba.xml Tue Apr 26 20:35:35 2022 +0000 +++ b/arriba.xml Mon Jun 13 12:09:32 2022 +0000 @@ -13,6 +13,10 @@ <expand macro="version_command" /> <command detect_errors="exit_code"><![CDATA[ @GENOME_SOURCE@ +#set $filter_list = [] +#if $options.filters + #set $filter_list = $options.filters.split(',') +#end if #if $blacklist #if $blacklist.is_of_type('tabular.gz') #set $blacklist_file = 'blacklist.tsv.gz' @@ -20,7 +24,12 @@ #else #set $blacklist_file = $blacklist #end if +#else + #if 'blacklist' not in $filter_list + #silent $filter_list.append('blacklist') + #end if #end if +#set $filters = ','.join($filter_list) #if $known_fusions #if $known_fusions.is_of_type('tabular.gz') #set $known_fusions_file = 'known_fusions.tsv.gz' @@ -106,8 +115,9 @@ -g '$genome_annotation' #if $blacklist -b '$blacklist_file' - #else - -f 'blacklist' + #end if + #if $filters + -f '$filters' #end if #if $protein_domains -p '$protein_domains' @@ -317,6 +327,46 @@ Default: AC_* NC_* </help> </param> + <param name="filters" argument="-f" type="select" optional="true" multiple="true" label="Diable filters"> + <help>By default all filters are enabled.</help> + <option value="top_expressed_viral_contigs">top_expressed_viral_contigs</option> + <option value="viral_contigs">viral_contigs</option> + <option value="low_coverage_viral_contigs">low_coverage_viral_contigs</option> + <option value="uninteresting_contigs">uninteresting_contigs</option> + <option value="no_genomic_support">no_genomic_support</option> + <option value="short_anchor">short_anchor</option> + <option value="select_best">select_best</option> + <option value="many_spliced">many_spliced</option> + <option value="long_gap">long_gap</option> + <option value="merge_adjacent">merge_adjacent</option> + <option value="hairpin">hairpin</option> + <option value="small_insert_size">small_insert_size</option> + <option value="same_gene">same_gene</option> + <option value="genomic_support">genomic_support</option> + <option value="read_through">read_through</option> + <option value="no_coverage">no_coverage</option> + <option value="mismatches">mismatches</option> + <option value="homopolymer">homopolymer</option> + <option value="low_entropy">low_entropy</option> + <option value="multimappers">multimappers</option> + <option value="inconsistently_clipped">inconsistently_clipped</option> + <option value="duplicates">duplicates</option> + <option value="homologs">homologs</option> + <option value="blacklist">blacklist</option> + <option value="mismappers">mismappers</option> + <option value="spliced">spliced</option> + <option value="relative_support">relative_support</option> + <option value="min_support">min_support</option> + <option value="known_fusions">known_fusions</option> + <option value="end_to_end">end_to_end</option> + <option value="non_coding_neighbors">non_coding_neighbors</option> + <option value="isoforms">isoforms</option> + <option value="intronic">intronic</option> + <option value="in_vitro">in_vitro</option> + <option value="intragenic_exonic">intragenic_exonic</option> + <option value="internal_tandem_duplication">internal_tandem_duplication</option> + </param> + <param name="max_evalue" argument="-E" type="float" value="" optional="true" label="Max e-value threahold"> <help>Arriba estimates the number of fusions with a given number of supporting reads which one would expect to see by random chance. If the expected number @@ -560,6 +610,7 @@ <param name="arriba_ref" value="GRCh38+ENSEMBL93"/> </conditional> <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/> + <param name="output_fusions_vcf" value="false"/> <conditional name="visualization"> <param name="do_viz" value="no"/> <param name="cytobands" ftype="tabular" value="cytobands.tsv"/>
--- a/macros.xml Tue Apr 26 20:35:35 2022 +0000 +++ b/macros.xml Mon Jun 13 12:09:32 2022 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">2.2.1</token> + <token name="@TOOL_VERSION@">2.3.0</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> @@ -49,6 +49,7 @@ <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 @@ -81,14 +82,6 @@ <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 @@ -100,7 +93,24 @@ <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 @@ -151,6 +161,67 @@ 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@"> @@ -172,18 +243,24 @@ #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 + #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 @@ -202,6 +279,10 @@ #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