Mercurial > repos > jjohnson > arriba
changeset 0:5ebf2354cc9b draft
"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
| author | jjohnson |
|---|---|
| date | Thu, 07 Oct 2021 11:47:02 +0000 |
| parents | |
| children | 9f2665b32c45 |
| files | arriba.help arriba.xml macros.xml |
| diffstat | 3 files changed, 453 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/arriba.help Thu Oct 07 11:47:02 2021 +0000 @@ -0,0 +1,191 @@ +% arriba -h +[2021-10-06T19:04:33] Launching Arriba 2.1.0 + +Arriba gene fusion detector +--------------------------- +Version: 2.1.0 + +Arriba is a fast tool to search for aberrant transcripts such as gene fusions. +It is based on chimeric alignments found by the STAR RNA-Seq aligner. + +Usage: arriba [-c Chimeric.out.sam] -x Aligned.out.bam \ + -g annotation.gtf -a assembly.fa [-b blacklists.tsv] [-k known_fusions.tsv] \ + [-t tags.tsv] [-p protein_domains.gff3] [-d structural_variants_from_WGS.tsv] \ + -o fusions.tsv [-O fusions.discarded.tsv] \ + [OPTIONS] + + -c FILE File in SAM/BAM/CRAM format with chimeric alignments as generated by STAR + (Chimeric.out.sam). This parameter is only required, if STAR was run with the + parameter '--chimOutType SeparateSAMold'. When STAR was run with the parameter + '--chimOutType WithinBAM', it suffices to pass the parameter -x to Arriba and -c + can be omitted. + + -x FILE File in SAM/BAM/CRAM format with main alignments as generated by STAR + (Aligned.out.sam). Arriba extracts candidate reads from this file. + + -g FILE GTF file with gene annotation. The file may be gzip-compressed. + + -G GTF_FEATURES Comma-/space-separated list of names of GTF features. + Default: gene_name=gene_name|gene_id gene_id=gene_id + transcript_id=transcript_id feature_exon=exon feature_CDS=CDS + + -a FILE FastA file with genome sequence (assembly). The file may be gzip-compressed. An + index with the file extension .fai must exist only if CRAM files are processed. + + -b FILE File containing blacklisted events (recurrent artifacts and transcripts + observed in healthy tissue). + + -k FILE File containing known/recurrent fusions. Some cancer entities are often + characterized by fusions between the same pair of genes. In order to boost + sensitivity, a list of known fusions can be supplied using this parameter. The list + must contain two columns with the names of the fused genes, separated by tabs. + + -o FILE Output file with fusions that have passed all filters. + + -O FILE Output file with fusions that were discarded due to filtering. + + -t FILE Tab-separated file containing fusions to annotate with tags in the 'tags' column. + The first two columns specify the genes; the third column specifies the tag. The + file may be gzip-compressed. + + -p FILE File in GFF3 format containing coordinates of the protein domains of genes. The + protein domains retained in a fusion are listed in the column + 'retained_protein_domains'. The file may be gzip-compressed. + + -d FILE Tab-separated file with coordinates of structural variants found using + whole-genome sequencing data. These coordinates serve to increase sensitivity + towards weakly expressed fusions and to eliminate fusions with low evidence. + + -D MAX_GENOMIC_BREAKPOINT_DISTANCE When a file with genomic breakpoints obtained via + whole-genome sequencing is supplied via the -d + parameter, this parameter determines how far a + genomic breakpoint may be away from a + transcriptomic breakpoint to consider it as a + related event. For events inside genes, the + distance is added to the end of the gene; for + intergenic events, the distance threshold is + applied as is. Default: 100000 + + -s STRANDEDNESS Whether a strand-specific protocol was used for library preparation, + and if so, the type of strandedness (auto/yes/no/reverse). When + unstranded data is processed, the strand can sometimes be inferred from + splice-patterns. But in unclear situations, stranded data helps + resolve ambiguities. Default: auto + + -i CONTIGS Comma-/space-separated list of interesting contigs. Fusions between genes + on other contigs are ignored. Contigs can be specified with or without the + prefix "chr". Asterisks (*) are treated as wild-cards. + Default: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_* + + -v CONTIGS Comma-/space-separated list of viral contigs. Asterisks (*) are treated as + wild-cards. + Default: AC_* NC_* + + -f FILTERS Comma-/space-separated list of filters to disable. By default all filters are + enabled. Valid values: homologs, low_entropy, isoforms, + top_expressed_viral_contigs, viral_contigs, non_coding_neighbors, + mismatches, duplicates, no_genomic_support, genomic_support, intronic, + end_to_end, relative_support, low_coverage_viral_contigs, + merge_adjacent, mismappers, multimappers, same_gene, long_gap, + internal_tandem_duplication, small_insert_size, read_through, + inconsistently_clipped, uninteresting_contigs, intragenic_exonic, + spliced, hairpin, blacklist, min_support, select_best, in_vitro, + short_anchor, known_fusions, no_coverage, homopolymer, many_spliced + + -E MAX_E-VALUE 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 + of fusions (e-value) is higher than this threshold, the fusion is + discarded by the 'relative_support' filter. Note: Increasing this + threshold can dramatically increase the number of false positives and may + increase the runtime of resource-intensive steps. Fractional values are + possible. Default: 0.300000 + + -S MIN_SUPPORTING_READS The 'min_support' filter discards all fusions with fewer than + this many supporting reads (split reads and discordant mates + combined). Default: 2 + + -m MAX_MISMAPPERS When more than this fraction of supporting reads turns out to be + mismappers, the 'mismappers' filter discards the fusion. Default: + 0.800000 + + -L MAX_HOMOLOG_IDENTITY Genes with more than the given fraction of sequence identity are + considered homologs and removed by the 'homologs' filter. + Default: 0.300000 + + -H HOMOPOLYMER_LENGTH The 'homopolymer' filter removes breakpoints adjacent to + homopolymers of the given length or more. Default: 6 + + -R READ_THROUGH_DISTANCE The 'read_through' filter removes read-through fusions + where the breakpoints are less than the given distance away + from each other. Default: 10000 + + -A MIN_ANCHOR_LENGTH Alignment artifacts are often characterized by split reads coming + from only one gene and no discordant mates. Moreover, the split + reads only align to a short stretch in one of the genes. The + 'short_anchor' filter removes these fusions. This parameter sets + the threshold in bp for what the filter considers short. Default: 23 + + -M MANY_SPLICED_EVENTS The 'many_spliced' filter recovers fusions between genes that + have at least this many spliced breakpoints. Default: 4 + + -K MAX_KMER_CONTENT The 'low_entropy' filter removes reads with repetitive 3-mers. If + the 3-mers make up more than the given fraction of the sequence, then + the read is discarded. Default: 0.600000 + + -V MAX_MISMATCH_PVALUE The 'mismatches' filter uses a binomial model to calculate a + p-value for observing a given number of mismatches in a read. If + the number of mismatches is too high, the read is discarded. + Default: 0.010000 + + -F FRAGMENT_LENGTH When paired-end data is given, the fragment length is estimated + automatically and this parameter has no effect. But when single-end + data is given, the mean fragment length should be specified to + effectively filter fusions that arise from hairpin structures. + Default: 200 + + -U MAX_READS Subsample fusions with more than the given number of supporting reads. This + improves performance without compromising sensitivity, as long as the + threshold is high. Counting of supporting reads beyond the threshold is + inaccurate, obviously. Default: 300 + + -Q QUANTILE Highly expressed genes are prone to produce artifacts during library + preparation. Genes with an expression above the given quantile are eligible + for filtering by the 'in_vitro' filter. Default: 0.998000 + + -e EXONIC_FRACTION The breakpoints of false-positive predictions of intragenic events + are often both in exons. True predictions are more likely to have at + least one breakpoint in an intron, because introns are larger. If the + fraction of exonic sequence between two breakpoints is smaller than + the given fraction, the 'intragenic_exonic' filter discards the + event. Default: 0.330000 + + -T TOP_N Only report viral integration sites of the top N most highly expressed viral + contigs. Default: 5 + + -C COVERED_FRACTION Ignore virally associated events if the virus is not fully + expressed, i.e., less than the given fraction of the viral contig is + transcribed. Default: 0.150000 + + -l MAX_ITD_LENGTH Maximum length of internal tandem duplications. Note: Increasing + this value beyond the default can impair performance and lead to many + false positives. Default: 100 + + -u Instead of performing duplicate marking itself, Arriba relies on duplicate marking by a + preceding program using the BAM_FDUP flag. This makes sense when unique molecular + identifiers (UMI) are used. + + -X To reduce the runtime and file size, by default, the columns 'fusion_transcript', + 'peptide_sequence', and 'read_identifiers' are left empty in the file containing + discarded fusion candidates (see parameter -O). When this flag is set, this extra + information is reported in the discarded fusions file. + + -I If assembly of the fusion transcript sequence from the supporting reads is incomplete + (denoted as '...'), fill the gaps using the assembly sequence wherever possible. + + -h Print help and exit. + + Code repository: https://github.com/suhrig/arriba + Get help/report bugs: https://github.com/suhrig/arriba/issues + User manual: https://arriba.readthedocs.io/ + Please cite: https://doi.org/10.1101/gr.257246.119 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/arriba.xml Thu Oct 07 11:47:02 2021 +0000 @@ -0,0 +1,242 @@ +<tool id="arriba" name="Arriba" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5"> + <description>detect gene fusions from STAR aligned RNA-Seq data</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command detect_errors="exit_code"><![CDATA[ + arriba + -x '$input' + #if $chimeric + -c '$chimeric' + #endif + -a '$genome_assembly' + -g '$gtf' + -b '$blacklist' + #if '$protein_domains' + -p '$protein_domains' + #endif + #if '$known_fusions' + -k '$known_fusions' + #endif + #if '$tags' + -t '$tags' + #endif + -o fusions.tsv + -O fusions.discarded.tsv + ]]></command> + <inputs> + <param name="input" argument="-x" type="data" format="sam,bam,cram" label="STAR Aligned.out.sam"/> + <param name="chimeric" argument="-c" type="data" format="sam,bam,cram" optional="true" label="STAR Chimeric.out.sam"> + <help><![CDATA[ only required, if STAR was run with the parameter '--chimOutType SeparateSAMold' ]]></help> + </param> + <param name="genome_assembly" argument="-a" type="data" format="fasta" label="genome assembly fasta"/> + <param name="gtf" argument="-g" type="data" format="gtf" label="GTF file with gene annotation"/> + <param name="blacklist" argument="-b" type="data" format="tabular" label="File containing blacklisted ranges."/> + <param name="protein_domains" argument="-p" type="data" format="gff3" optional="true" label="File containing blacklisted ranges."/> + <param name="known_fusions" argument="-k" type="data" format="tabular" optional="true" label="File containing known fusions"> + <help><![CDATA[ file two TAB separated columns: five-prime region three-prime region ]]></help> + </param> + <param name="tags" argument="-t" type="data" format="tabular" optional="true" label="File containing tag names for a fusion."/> + </inputs> + <outputs> + <data name="fusions" format="tabular" label="${tool.name} on ${on_string}: fusions.tsv" from_work_dir="fusions.tsv"/> + <data name="discarded" format="tabular" label="${tool.name} on ${on_string}: fusions.discarded.tsv" from_work_dir="fusions.discarded.tsv"/> + </outputs> + <help><![CDATA[ + +arriba -h +[2021-10-06T19:04:33] Launching Arriba 2.1.0 + +Arriba gene fusion detector +--------------------------- +Version: 2.1.0 + +Arriba is a fast tool to search for aberrant transcripts such as gene fusions. +It is based on chimeric alignments found by the STAR RNA-Seq aligner. + +Usage: arriba [-c Chimeric.out.sam] -x Aligned.out.bam \ + -g annotation.gtf -a assembly.fa [-b blacklists.tsv] [-k known_fusions.tsv] \ + [-t tags.tsv] [-p protein_domains.gff3] [-d structural_variants_from_WGS.tsv] \ + -o fusions.tsv [-O fusions.discarded.tsv] \ + [OPTIONS] + + -c FILE File in SAM/BAM/CRAM format with chimeric alignments as generated by STAR + (Chimeric.out.sam). This parameter is only required, if STAR was run with the + parameter '--chimOutType SeparateSAMold'. When STAR was run with the parameter + '--chimOutType WithinBAM', it suffices to pass the parameter -x to Arriba and -c + can be omitted. + + -x FILE File in SAM/BAM/CRAM format with main alignments as generated by STAR + (Aligned.out.sam). Arriba extracts candidate reads from this file. + + -g FILE GTF file with gene annotation. The file may be gzip-compressed. + + -G GTF_FEATURES Comma-/space-separated list of names of GTF features. + Default: gene_name=gene_name|gene_id gene_id=gene_id + transcript_id=transcript_id feature_exon=exon feature_CDS=CDS + + -a FILE FastA file with genome sequence (assembly). The file may be gzip-compressed. An + index with the file extension .fai must exist only if CRAM files are processed. + + -b FILE File containing blacklisted events (recurrent artifacts and transcripts + observed in healthy tissue). + + -k FILE File containing known/recurrent fusions. Some cancer entities are often + characterized by fusions between the same pair of genes. In order to boost + sensitivity, a list of known fusions can be supplied using this parameter. The list + must contain two columns with the names of the fused genes, separated by tabs. + + -o FILE Output file with fusions that have passed all filters. + + -O FILE Output file with fusions that were discarded due to filtering. + + -t FILE Tab-separated file containing fusions to annotate with tags in the 'tags' column. + The first two columns specify the genes; the third column specifies the tag. The + file may be gzip-compressed. + + -p FILE File in GFF3 format containing coordinates of the protein domains of genes. The + protein domains retained in a fusion are listed in the column + 'retained_protein_domains'. The file may be gzip-compressed. + + -d FILE Tab-separated file with coordinates of structural variants found using + whole-genome sequencing data. These coordinates serve to increase sensitivity + towards weakly expressed fusions and to eliminate fusions with low evidence. + + -D MAX_GENOMIC_BREAKPOINT_DISTANCE When a file with genomic breakpoints obtained via + whole-genome sequencing is supplied via the -d + parameter, this parameter determines how far a + genomic breakpoint may be away from a + transcriptomic breakpoint to consider it as a + related event. For events inside genes, the + distance is added to the end of the gene; for + intergenic events, the distance threshold is + applied as is. Default: 100000 + + -s STRANDEDNESS Whether a strand-specific protocol was used for library preparation, + and if so, the type of strandedness (auto/yes/no/reverse). When + unstranded data is processed, the strand can sometimes be inferred from + splice-patterns. But in unclear situations, stranded data helps + resolve ambiguities. Default: auto + + -i CONTIGS Comma-/space-separated list of interesting contigs. Fusions between genes + on other contigs are ignored. Contigs can be specified with or without the + prefix "chr". Asterisks (*) are treated as wild-cards. + Default: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_* + + -v CONTIGS Comma-/space-separated list of viral contigs. Asterisks (*) are treated as + wild-cards. + Default: AC_* NC_* + + -f FILTERS Comma-/space-separated list of filters to disable. By default all filters are + enabled. Valid values: homologs, low_entropy, isoforms, + top_expressed_viral_contigs, viral_contigs, non_coding_neighbors, + mismatches, duplicates, no_genomic_support, genomic_support, intronic, + end_to_end, relative_support, low_coverage_viral_contigs, + merge_adjacent, mismappers, multimappers, same_gene, long_gap, + internal_tandem_duplication, small_insert_size, read_through, + inconsistently_clipped, uninteresting_contigs, intragenic_exonic, + spliced, hairpin, blacklist, min_support, select_best, in_vitro, + short_anchor, known_fusions, no_coverage, homopolymer, many_spliced + + -E MAX_E-VALUE 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 + of fusions (e-value) is higher than this threshold, the fusion is + discarded by the 'relative_support' filter. Note: Increasing this + threshold can dramatically increase the number of false positives and may + increase the runtime of resource-intensive steps. Fractional values are + possible. Default: 0.300000 + + -S MIN_SUPPORTING_READS The 'min_support' filter discards all fusions with fewer than + this many supporting reads (split reads and discordant mates + combined). Default: 2 + + -m MAX_MISMAPPERS When more than this fraction of supporting reads turns out to be + mismappers, the 'mismappers' filter discards the fusion. Default: + 0.800000 + + -L MAX_HOMOLOG_IDENTITY Genes with more than the given fraction of sequence identity are + considered homologs and removed by the 'homologs' filter. + Default: 0.300000 + + -H HOMOPOLYMER_LENGTH The 'homopolymer' filter removes breakpoints adjacent to + homopolymers of the given length or more. Default: 6 + + -R READ_THROUGH_DISTANCE The 'read_through' filter removes read-through fusions + where the breakpoints are less than the given distance away + from each other. Default: 10000 + + -A MIN_ANCHOR_LENGTH Alignment artifacts are often characterized by split reads coming + from only one gene and no discordant mates. Moreover, the split + reads only align to a short stretch in one of the genes. The + 'short_anchor' filter removes these fusions. This parameter sets + the threshold in bp for what the filter considers short. Default: 23 + + -M MANY_SPLICED_EVENTS The 'many_spliced' filter recovers fusions between genes that + have at least this many spliced breakpoints. Default: 4 + + -K MAX_KMER_CONTENT The 'low_entropy' filter removes reads with repetitive 3-mers. If + the 3-mers make up more than the given fraction of the sequence, then + the read is discarded. Default: 0.600000 + + -V MAX_MISMATCH_PVALUE The 'mismatches' filter uses a binomial model to calculate a + p-value for observing a given number of mismatches in a read. If + the number of mismatches is too high, the read is discarded. + Default: 0.010000 + + -F FRAGMENT_LENGTH When paired-end data is given, the fragment length is estimated + automatically and this parameter has no effect. But when single-end + data is given, the mean fragment length should be specified to + effectively filter fusions that arise from hairpin structures. + Default: 200 + + -U MAX_READS Subsample fusions with more than the given number of supporting reads. This + improves performance without compromising sensitivity, as long as the + threshold is high. Counting of supporting reads beyond the threshold is + inaccurate, obviously. Default: 300 + + -Q QUANTILE Highly expressed genes are prone to produce artifacts during library + preparation. Genes with an expression above the given quantile are eligible + for filtering by the 'in_vitro' filter. Default: 0.998000 + + -e EXONIC_FRACTION The breakpoints of false-positive predictions of intragenic events + are often both in exons. True predictions are more likely to have at + least one breakpoint in an intron, because introns are larger. If the + fraction of exonic sequence between two breakpoints is smaller than + the given fraction, the 'intragenic_exonic' filter discards the + event. Default: 0.330000 + + -T TOP_N Only report viral integration sites of the top N most highly expressed viral + contigs. Default: 5 + + -C COVERED_FRACTION Ignore virally associated events if the virus is not fully + expressed, i.e., less than the given fraction of the viral contig is + transcribed. Default: 0.150000 + + -l MAX_ITD_LENGTH Maximum length of internal tandem duplications. Note: Increasing + this value beyond the default can impair performance and lead to many + false positives. Default: 100 + + -u Instead of performing duplicate marking itself, Arriba relies on duplicate marking by a + preceding program using the BAM_FDUP flag. This makes sense when unique molecular + identifiers (UMI) are used. + + -X To reduce the runtime and file size, by default, the columns 'fusion_transcript', + 'peptide_sequence', and 'read_identifiers' are left empty in the file containing + discarded fusion candidates (see parameter -O). When this flag is set, this extra + information is reported in the discarded fusions file. + + -I If assembly of the fusion transcript sequence from the supporting reads is incomplete + (denoted as '...'), fill the gaps using the assembly sequence wherever possible. + + -h Print help and exit. + + Code repository: https://github.com/suhrig/arriba + Get help/report bugs: https://github.com/suhrig/arriba/issues + User manual: https://arriba.readthedocs.io/ + Please cite: https://doi.org/10.1101/gr.257246.119 + + ]]></help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Oct 07 11:47:02 2021 +0000 @@ -0,0 +1,20 @@ +<macros> + <token name="@TOOL_VERSION@">2.1.0</token> + <token name="@VERSION_SUFFIX@">0</token> +dd + <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> +</macros>