Mercurial > repos > jjohnson > arriba
changeset 11:8ed8af5836d1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit e0aa03add09ecc4ad5a5d41c439b8af9551fc53c"
| author | jjohnson |
|---|---|
| date | Tue, 26 Apr 2022 20:21:29 +0000 |
| parents | c58d1774c762 |
| children | 73fd7703a743 |
| files | arriba.xml |
| diffstat | 1 files changed, 82 insertions(+), 9 deletions(-) [+] |
line wrap: on
line diff
--- a/arriba.xml Fri Feb 11 19:04:06 2022 +0000 +++ b/arriba.xml Tue Apr 26 20:21:29 2022 +0000 @@ -2,6 +2,12 @@ <description>detect gene fusions from STAR aligned RNA-Seq data</description> <macros> <import>macros.xml</import> + <xml name="fusion_actions"> + <actions> + <action name="comment_lines" type="metadata" default="1" /> + <action name="column_names" type="metadata" default="gene1,gene2,strand1(gene/fusion),strand2(gene/fusion),breakpoint1,breakpoint2,site1,site2,type,split_reads1,split_reads2,discordant_mates,coverage1,coverage2,confidence,reading_frame,tags,retained_protein_domains,closest_genomic_breakpoint1,closest_genomic_breakpoint2,gene_id1,gene_id2,transcript_id1,transcript_id2,direction1,direction2,filters,fusion_transcript,peptide_sequence,read_identifiers" /> + </actions> + </xml> </macros> <expand macro="requirements" /> <expand macro="version_command" /> @@ -39,6 +45,31 @@ #else #set $star_index_dir = $input_params.index.arriba_ref.fields.star_index #end if + #if $blacklist + #if $blacklist.is_of_type('tabular.gz') + #set $blacklist_file = 'blacklist.tsv.gz' + ln -sf '$blacklist' $blacklist_file && + #else + #set $blacklist_file = $blacklist + #end if + #end if + #if $known_fusions + #if $known_fusions.is_of_type('tabular.gz') + #set $known_fusions_file = 'known_fusions.tsv.gz' + ln -sf '$known_fusions' $known_fusions_file && + #else + #set $known_fusions_file = $known_fusions + #end if + #end if + #if $tags + #if $tags.is_of_type('tabular.gz') + #set $tags_file = 'tags.tsv.gz' + ln -sf '$tags' $tags_file && + #else + #set $tags_file = $tags + #end if + #end if + STAR --runThreadN \${GALAXY_SLOTS:-1} --genomeDir $star_index_dir @@ -74,7 +105,7 @@ -a '$genome_assembly' -g '$genome_annotation' #if $blacklist - -b '$blacklist' + -b '$blacklist_file' #else -f 'blacklist' #end if @@ -82,10 +113,10 @@ -p '$protein_domains' #end if #if $known_fusions - -k '$known_fusions' + -k '$known_fusions_file' #end if #if $tags - -t '$tags' + -t '$tags_file' #end if #if str($wgs.use_wgs) == "yes" -d '$wgs.wgs' @@ -177,9 +208,16 @@ && samtools sort -@ \${GALAXY_SLOTS:-1} -m 4G -T tmp -O bam '$input_params.input' > Aligned.sortedByCoord.out.bam && samtools index Aligned.sortedByCoord.out.bam #end if +#if $output_fusions_vcf + && convert_fusions_to_vcf.sh '$genome_assembly' fusions.tsv fusions.vcf +#end if +#if $output_fusion_bams + && mkdir fusion_bams + && extract_fusion-supporting_alignments.sh fusions.tsv Aligned.sortedByCoord.out.bam 'fusion_bams/fusion' +#end if #if str($visualization.do_viz) == "yes" -#set $fusions = 'fusions.tsv' -&& @DRAW_FUSIONS@ + #set $fusions = 'fusions.tsv' + && @DRAW_FUSIONS@ #end if ]]></command> <inputs> @@ -189,7 +227,9 @@ <option value="use_fastq">Let Arriba control running STAR</option> </param> <when value="use_star"> - <param name="input" argument="-x" type="data" format="sam,bam,cram" label="STAR Aligned.out.sam"/> + <param name="input" argument="-x" type="data" format="sam,bam,cram" label="STAR Aligned.out.sam"> + <help><![CDATA[ recommended STAR options: --chimSegmentMin 10 --chimOutType WithinBAM ]]></help> + </param> <param name="chimeric" argument="-c" type="data" format="sam,bam,cram" optional="true" label="STAR Chimeric.out.sam"> <help><![CDATA[ only required, if STAR was run with the parameter '--chimOutType SeparateSAMold' ]]></help> </param> @@ -423,6 +463,8 @@ </param> </section> <param name="output_fusions_discarded" argument="-O" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Output fusions.discarded.tsv"/> + <param name="output_fusions_vcf" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Output fusions.vcf"/> + <param name="output_fusion_bams" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output fusion BAMs"/> <conditional name="visualization"> <param name="do_viz" type="select" label="Generate visualization"> <option value="yes">Yes</option> @@ -433,13 +475,23 @@ </when> <when value="no"/> </conditional> - </inputs> <outputs> - <data name="fusions_tsv" format="tabular" label="${tool.name} on ${on_string}: fusions.tsv" from_work_dir="fusions.tsv"/> + <data name="fusions_tsv" format="tabular" label="${tool.name} on ${on_string}: fusions.tsv" from_work_dir="fusions.tsv"> + <expand macro="fusion_actions" /> + </data> + <data name="discarded_fusions_tsv" format="tabular" label="${tool.name} on ${on_string}: fusions.discarded.tsv" from_work_dir="fusions.discarded.tsv"> <filter> output_fusions_discarded == True</filter> + <expand macro="fusion_actions" /> </data> + <data name="fusions_vcf" format="vcf" label="${tool.name} on ${on_string}: fusions.vcf" from_work_dir="fusions.vcf"> + <filter> output_fusions_vcf == True</filter> + </data> + <collection name="fusion_bams" type="list" label="${tool.name} on ${on_string}: Fusion Alignments"> + <discover_datasets pattern="(?P<name>fusion_\d+\.bam)$" format="bam" directory="fusion_bams" visible="false"/> + <filter>output_fusion_bams == True</filter> + </collection> <data name="aligned_bam" format="bam" label="${tool.name} on ${on_string}: Aligned.bam" from_work_dir="Aligned.sortedByCoord.out.bam"> <filter>input_params['input_source'] == "use_fastq"</filter> </data> @@ -471,7 +523,6 @@ </output> </test> <!-- Test 2 - From exisitng BAM with protein_domains and visualization --> - <test> <conditional name="input_params"> <param name="input_source" value="use_star"/> @@ -537,6 +588,28 @@ Arriba takes the main output file of STAR (Aligned.out.bam) as input (parameter -x). If STAR was run with the parameter --chimOutType WithinBAM, then this file contains all the information needed by Arriba to find fusions. When STAR was run with the parameter --chimOutType SeparateSAMold, the main output file lacks chimeric alignments. Instead, STAR writes them to a separate output file named Chimeric.out.sam. In this case, the file needs to be passed to Arriba via the parameter -c in addition to the main output file Aligned.out.bam. + STAR index create recommended parameter value: + + * --sjdbOverhang 250 + + + STAR recommended parameter values :: + + * --outSAMunmapped Within + * --outFilterMultimapNmax 50 + * --peOverlapNbasesMin 10 + * --alignSplicedMateMapLminOverLmate 0.5 + * --alignSJstitchMismatchNmax 5 -1 5 5 + * --chimSegmentMin 10 + * --chimOutType WithinBAM HardClip + * --chimJunctionOverhangMin 10 + * --chimScoreDropMax 30 + * --chimScoreJunctionNonGTAG 0 + * --chimScoreSeparation 1 + * --chimSegmentReadGapMax 3 + * --chimMultimapNmax 50 + + Arriba extracts three types of reads from the alignment file(s): * Split-reads, i.e., reads composed of segments which map in a non-linear way. STAR stores such reads as supplementary alignments.