| Previous changeset 5:005b200c8841 (2021-10-10) Next changeset 7:25d207f7ff83 (2021-10-11) |
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Commit message:
"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea" |
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modified:
arriba.xml |
| b |
| diff -r 005b200c8841 -r 7253b367c082 arriba.xml --- a/arriba.xml Sun Oct 10 13:00:45 2021 +0000 +++ b/arriba.xml Mon Oct 11 01:47:22 2021 +0000 |
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| b'@@ -70,10 +70,83 @@\n #if $tags\n -t \'$tags\'\n #end if\n+ #if str($wgs.use_wgs) == "yes"\n+ -d \'$wgs.wgs\'\n+ #if $wgs.max_genomic_breakpoint_distance\n+ -D $wgs.max_genomic_breakpoint_distance\n+ #end if\n+ #end if\n -o fusions.tsv\n #if $output_fusions_discarded\n -O fusions.discarded.tsv \n #end if\n+## Arriba options\n+ #if $options.gtf_features\n+ -G $options.gtf_features\n+ #end if\n+ #if $options.strandedness\n+ -s $options.strandedness\n+ #end if\n+ #if $options.genome_contigs\n+ -i $options.genome_contigs\n+ #end if\n+ #if $options.viral_contigs\n+ -v $options.viral_contigs\n+ #end if\n+ #if $options.max_evalue\n+ -E $options.max_evalue\n+ #end if\n+ #if $options.min_supporting_reads\n+ -S $options.min_supporting_reads\n+ #end if\n+ #if $options.max_mismappers\n+ -m $options.max_mismappers\n+ #end if\n+ #if $options.max_homolog_identity\n+ -L $options.max_homolog_identity\n+ #end if\n+ #if $options.homopolymer_length\n+ -H $options.homopolymer_length\n+ #end if\n+ #if $options.read_through_distance\n+ -R $options.read_through_distance\n+ #end if\n+ #if $options.min_anchor_length\n+ -A $options.min_anchor_length\n+ #end if\n+ #if $options.many_spliced_events\n+ -M $options.many_spliced_events\n+ #end if\n+ #if $options.max_kmer_content\n+ -m $options.max_kmer_content\n+ #end if\n+ #if $options.max_mismatch_pvalue\n+ -V $options.max_mismatch_pvalue\n+ #end if\n+ #if $options.fragment_length\n+ -F $options.fragment_length\n+ #end if\n+ #if $options.max_reads\n+ -U $options.max_reads\n+ #end if\n+ #if $options.quantile\n+ -Q $options.quantile\n+ #end if\n+ #if $options.exonic_fraction\n+ -e $options.exonic_fraction\n+ #end if\n+ #if $options.top_n\n+ -T $options.top_n\n+ #end if\n+ #if $options.covered_fraction\n+ -C $options.covered_fraction\n+ #end if\n+ #if $options.max_itd_length\n+ -l $options.max_itd_length\n+ #end if\n+ $options.duplicate_marking\n+ $options.fill_discarded_columns\n+ $options.fill_the_gaps\n #if str($input_params.input_source) == "use_fastq"\n && samtools sort -@ \\${GALAXY_SLOTS:-1} -m 4G -T tmp -O bam Aligned.out.bam > Aligned.sortedByCoord.out.bam\n && samtools index Aligned.sortedByCoord.out.bam\n@@ -85,16 +158,55 @@\n && draw_fusions.R \n --fusions=fusions.tsv \n --alignments=Aligned.sortedByCoord.out.bam \n+ --annotation=\'$gtf\'\n --output=fusions.pdf \n- --annotation=\'$gtf\'\n #if $visualization.cytobands\n --cytobands=\'$visualization.cytobands\'\n #end if\n #if $protein_domains\n --proteinDomains=\'$protein_domains\'\n #end if\n+ ## Visualization Options\n+ #if $visualization.options.transcriptSelection\n+ --transcriptSelection=$visualization.options.transcriptSelection\n+ #end if\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+ #end if\n+ #if $visualization.options.mergeDomainsOverlappingBy\n+ --mergeDomainsOverlappingBy=$visualization.options.mergeDomainsOverlappingBy\n+ #end if\n+ #if $visualization.options.printExonLabels\n+ --printExonLabels=$visualization.options.printExonLabels\n+ #end if\n+ #if $visualization.options.render3dEffect\n+ --render3dEffect=$visualization.options.render3dEffect\n+ #end if\n+ #if $visualization.options.optimizeDomainColors\n+ --optimizeDomainColors=$visualization.options.optimizeDomainColors\n+ #end if\n+ #if $visualization.options.color1\n+ --co'..b', the colors are recomputed for each fusion separately. \n+ This ensures that the colors have the maximum distance for each individual fusion, \n+ but they are no longer consistent across different fusions. \n+ Default: FALSE\n+ </help>\n+ <option value="TRUE">True</option>\n+ <option value="FALSE">False</option>\n+ </param>\n+ <param argument="--color1" type="color" value="" optional="true" label="Color of the 5\' end of the fusion."/>\n+ <param argument="--color2" type="color" value="" optional="true" label="Color of the 3\' end of the fusion."/>\n+ <param argument="--pdfWidth" type="float" value="" min="1." optional="true" label="Width of PDF output file in inches"\n+ help="Default: 11.692"/>\n+ <param argument="--pdfHeight" type="float" value="" min="1." optional="true" label="Height of PDF output file in inches"\n+ help="Default: 8.267"/>\n+ <param argument="--fontSize" type="float" value="" min="0." optional="true" label="Scale the size of text"\n+ help="Default: 1.0"/>\n+ </section>\n+\n </when>\n <when value="no"/>\n </conditional>\n+\n </inputs>\n <outputs>\n <data name="fusions" format="tabular" label="${tool.name} on ${on_string}: fusions.tsv" from_work_dir="fusions.tsv"/>\n@@ -203,15 +596,16 @@\n \n </tests>\n <help><![CDATA[\n-** Arriba **\n+**Arriba**\n \n \n Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions.\n It is based on chimeric alignments found by the STAR RNA-Seq aligner.\n \n \n-** INPUTS_ **\n+**INPUTS**\n \n+See: https://arriba.readthedocs.io/en/latest/input-files/\n \n - Alignments\n \n@@ -352,7 +746,9 @@\n NOTE: Arriba was designed for alignments from RNA-Seq data. It should not be run on WGS data directly. Many assumptions made by Arriba about the data (statistical models, blacklist, etc.) only apply to RNA-Seq data and are not valid for DNA-Seq data. For such data, a structural variant calling algorithm should be used and the results should be passed to Arriba.\n \n \n-** OUTPUTS_ **\n+**OUTPUTS**\n+\n+See: https://arriba.readthedocs.io/en/latest/output-files/\n \n - fusions.tsv\n \n@@ -403,22 +799,27 @@\n The file fusions.discarded.tsv (as specified by the parameter -O) contains all events that Arriba classified as an artifact or that are also observed in healthy tissue. It has the same format as the file fusions.tsv. \n \n \n-** VISUALIZATION_ **\n+**VISUALIZATION**\n+\n+See: https://arriba.readthedocs.io/en/latest/visualization/\n+\n - fusions.pdf\n \n A PDF file with one page for each predicted fusion. Each page depicts the fusion partners, their orientation, the retained exons in the fusion transcript, statistics about the number of supporting reads, and if the column fusion_transcript has a value an excerpt of the sequence around the breakpoint.\n \n \n-Code repository: https://github.com/suhrig/arriba\n-Get help/report bugs: https://github.com/suhrig/arriba/issues\n-User manual: https://arriba.readthedocs.io/\n-Please cite: https://doi.org/10.1101/gr.257246.119\n+**OPTIONS**\n+\n+ - Arriba: https://arriba.readthedocs.io/en/latest/command-line-options/#arriba\n+ - Visualization: https://arriba.readthedocs.io/en/latest/command-line-options/#draw_fusionsr\n+ - RNA STAR: https://arriba.readthedocs.io/en/latest/workflow/\n \n \n .. _Arriba: https://arriba.readthedocs.io/en/latest/\n .. _INPUTS: https://arriba.readthedocs.io/en/latest/input-files/\n .. _OUTPUTS: https://arriba.readthedocs.io/en/latest/output-files/\n .. _VISUALIZATION: https://arriba.readthedocs.io/en/latest/visualization/\n+.. _OPTIONS: https://arriba.readthedocs.io/en/latest/command-line-options/\n \n ]]></help>\n <expand macro="citations" />\n' |