| Previous changeset 12:73fd7703a743 (2022-04-26) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d" |
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modified:
arriba.xml macros.xml |
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| diff -r 73fd7703a743 -r 1d459aaa5765 arriba.xml --- a/arriba.xml Tue Apr 26 20:35:35 2022 +0000 +++ b/arriba.xml Mon Jun 13 12:09:32 2022 +0000 |
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| @@ -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"/> |
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| diff -r 73fd7703a743 -r 1d459aaa5765 macros.xml --- a/macros.xml Tue Apr 26 20:35:35 2022 +0000 +++ b/macros.xml Mon Jun 13 12:09:32 2022 +0000 |
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| b'@@ -1,5 +1,5 @@\n <macros>\n- <token name="@TOOL_VERSION@">2.2.1</token>\n+ <token name="@TOOL_VERSION@">2.3.0</token>\n <token name="@VERSION_SUFFIX@">0</token>\n <xml name="requirements">\n <requirements>\n@@ -49,6 +49,7 @@\n <xml name="visualization_options">\n <param name="cytobands" argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/>\n <section name="options" expanded="false" title="Draw Fusion Options">\n+ <param argument="--sampleName" type="text" value="" optional="true" label="Sample Name printed as the title on every page"/>\n <param argument="--transcriptSelection" type="select" optional="true" label="Transcript selection">\n <help>By default the transcript isoform with the highest coverage is drawn.\n Alternatively, the transcript isoform that is provided in the columns\n@@ -81,14 +82,6 @@\n <option value="medium">medium</option>\n <option value="high">high</option>\n </param>\n- <param argument="--showIntergenicVicinity" type="integer" value="" min="0" optional="true" label="Intergenic Vicinity">\n- <help>This option only applies to intergenic breakpoints.\n- If it is set to a value greater than 0, then the script draws the genes\n- which are no more than the given distance away from an intergenic breakpoint.\n- Note that this option is incompatible with squishIntrons.\n- Default: 0\n- </help>\n- </param>\n <param argument="--squishIntrons" type="select" optional="true" label="Squish introns">\n <help>Exons usually make up only a small fraction of a gene.\n They may be hard to see in the plot. i\n@@ -100,7 +93,24 @@\n <option value="TRUE">True</option>\n <option value="FALSE">False</option>\n </param>\n-\n+ <param argument="--showIntergenicVicinity" type="text" value="" optional="true" label="Intergenic Vicinity">\n+ <help>This option only applies to intergenic breakpoints.\n+ If it is set to a value greater than 0, then the script draws the genes\n+ which are no more than the given distance away from an intergenic breakpoint.\n+ The keywords closestGene and closestProteinCodingGene instruct the script \n+ to dynamically determine the distance to the next (protein-coding) gene for each breakpoint. \n+ Alternatively, instead of specifying a single distance \n+ that is applied upstream and downstream of both breakpoints alike, \n+ more fine-grained control over the region to be shown is possible by specifying four comma-separated values. \n+ The first two values determine the region to the left and to the right of breakpoint 1; \n+ the third and fourth values determine the region to the left and to the right of breakpoint 2. \n+ Note that this option is incompatible with squishIntrons.\n+ Default: 0\n+ </help>\n+ <option value="closestGene">closestGene</option>\n+ <option value="closestProteinCodingGene">closestProteinCodingGene</option>\n+ <validator type="regex" message="">^(closestGene|closestProteinCodingGene|\\d+|\\d+,\\d+,\\d+,\\d+)$</validator>\n+ </param>\n <param argument="--mergeDomainsOverlappi'..b'common use case is the visualization of a gene that is found to be fused to multiple partners. \n+ By forcing all fusion plots to use the same scale, the fusions can be summarized as a collage \n+ in a single plot one above the other with matching scales. \n+ Note: The scale must be bigger than the sum of the biggest pair of transcripts to be drawn, \n+ or else dynamic scaling is applied, because display errors would occur otherwise. \n+ The default value is 0, which means that no fixed scale should be used \n+ and that the scale should be adapted dynamically for each fusion. Default: 0\n+ </help>\n+ </param>\n+ <param argument="--coverageRange" type="text" value="" optional="true" label="Maximum coverage for plot">\n+ <help>When the parameter --alignments is used, coverage plots are drawn above the transcripts of the fused genes. \n+ The plots can be cropped at a fixed level by passing a non-zero value to this parameter. \n+ When only a single value is given, both coverage plots (for gene1 and gene2) are cropped at the same level. \n+ When two comma-separated values are given, the cutoffs can be specified independently for the two plots. \n+ A value of 0 indicates that no cropping should be applied (i.e., the cutoff is set to the peak coverage) \n+ and that the coverage plots of both genes should be on the same scale. This is the default behavior. \n+ A value of 0,0 also indicates that no cropping should be applied, \n+ but the coverage plots of the two genes have different scales: \n+ each one is scaled individually to the peak coverage of the respective gene. \n+ Default: 0\n+ </help>\n+ <validator type="regex" message="">^\\d+(,\\d+)?$</validator>\n+ </param>\n </section>\n </xml>\n <token name="@DRAW_FUSIONS@">\n@@ -172,18 +243,24 @@\n #if $visualization.options.minConfidenceForCircosPlot\n --minConfidenceForCircosPlot=$visualization.options.minConfidenceForCircosPlot\n #end if\n- #if $visualization.options.showIntergenicVicinity\n- --showIntergenicVicinity=$visualization.options.showIntergenicVicinity\n- #end if\n #if $visualization.options.squishIntrons\n --squishIntrons=$visualization.options.squishIntrons\n+ #if $visualization.options.squishIntrons == \'FALSE\' and $visualization.options.showIntergenicVicinity\n+ --showIntergenicVicinity=$visualization.options.showIntergenicVicinity\n+ #end if\n #end if\n #if $visualization.options.mergeDomainsOverlappingBy\n --mergeDomainsOverlappingBy=$visualization.options.mergeDomainsOverlappingBy\n #end if\n+ #if $visualization.options.sampleName\n+ --sampleName=$visualization.options.sampleName\n+ #end if\n #if $visualization.options.printExonLabels\n --printExonLabels=$visualization.options.printExonLabels\n #end if\n+ #if $visualization.options.coverageRange\n+ --coverageRange="$visualization.options.coverageRange"\n+ #end if\n #if $visualization.options.render3dEffect\n --render3dEffect=$visualization.options.render3dEffect\n #end if\n@@ -202,6 +279,10 @@\n #if $visualization.options.pdfHeight\n --pdfHeight=$visualization.options.pdfHeight\n #end if\n+ # fontFamily\n+ #if $visualization.options.fontFamily\n+ --fontFamily=$visualization.options.fontFamily\n+ #end if\n #if $visualization.options.fontSize\n --fontSize=$visualization.options.fontSize\n #end if\n' |