Mercurial > repos > enios > nc_rna
diff gffread.xml @ 19:d928c656a8f3 draft
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| author | enios |
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| date | Sat, 22 May 2021 07:35:58 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gffread.xml Sat May 22 07:35:58 2021 +0000 @@ -0,0 +1,503 @@ +<tool id="gffread" name="gffreadB" version="@VERSION@.0"> + <description>Filters and/or converts GFF3/GTF2 records</description> + <requirements> + <container type="docker">343307676715.dkr.ecr.eu-central-1.amazonaws.com/galaxy:gffread</container> + </requirements> + <macros> + <token name="@VERSION@">0.11.6</token> + <xml name="fasta_output_select"> + <param name="fa_outputs" type="select" display="checkboxes" multiple="true" label="Select fasta outputs"> + <option value="-w exons.fa">fasta file with spliced exons for each GFF transcript (-w exons.fa)</option> + <option value="-x cds.fa">fasta file with spliced CDS for each GFF transcript (-x cds.fa)</option> + <option value="-y pep.fa">protein fasta file with the translation of CDS for each record (-y pep.fa)</option> + <option value="-W">for each fasta: record the exon coordinates projected onto the spliced sequence (-W)</option> + </param> + </xml> + <xml name="ref_filtering_select"> + <param name="ref_filtering" type="select" display="checkboxes" multiple="true" label="reference based filters"> + <option value="-N">discard multi-exon mRNAs that have any intron with a non-canonical splice site consensus, i.e. not GT-AG, GC-AG or AT-AC (-N)</option> + <option value="-J">discard any mRNAs that either lack initial START codon or the terminal STOP codon, or have an in-frame stop codon (-J)</option> + <option value="-V">discard any mRNAs with CDS having in-frame stop codons (-V)</option> + <option value="-H">check and adjust the starting CDS phase if the original phase leads to a translation with an in-frame stop codon (-H with -V)</option> + <!-- gffread bug: B not in missing from param to the arg parser + <option value="-B">single-exon transcripts are also checked on the opposite strand (-B with -V)</option> + --> + </param> + </xml> + <xml name="trackname"> + <param name="tname" type="text" value="" optional="true" label="Trackname to use in the second column of each GFF output line" help="(-t track_name}"> + <validator type="regex">\w+</validator> + </param> + </xml> + <xml name="merge_opts"> + <option value="-K">also collapse shorter, fully contained transcripts with fewer introns than the container (-K)</option> + <option value="-Q">remove the containment restriction: multi-exon transcripts will be collapsed if just their introns match, while single-exon transcripts can partially overlap 80% (-Q)</option> + <option value="-d dupinfo">output collapsing info (-d dupinfo)</option> + </xml> + <xml name="cluster_opts"> + <option value="--force-exons"> make sure that the lowest level GFF features are printed as 'exon' features (--force-exons)</option> + <option value="-Z">merge close exons into a single exon (for intron size < 4) (-Z)</option> + </xml> + <xml name="merge_opt_sel"> + <param name="merge_options" type="select" display="checkboxes" multiple="true" label="Merge options"> + <expand macro="cluster_opts" /> + <expand macro="merge_opts" /> + </param> + </xml> + <xml name="cluster_opt_sel"> + <param name="merge_options" type="select" display="checkboxes" multiple="true" label="Cluster options"> + <expand macro="cluster_opts" /> + </param> + </xml> + </macros> + <command detect_errors="aggressive"> +<![CDATA[ + #if $reference_genome.source == 'history': + ln -s '$reference_genome.genome_fasta' genomeref.fa && + #end if + gffread '$input' + #if $reference_genome.source == 'cached': + -g '${reference_genome.fasta_indexes.fields.path}' + #if $reference_genome.ref_filtering and str($reference_genome.ref_filtering) != '': + #echo ' '.join(str($reference_genome.ref_filtering).split(',')) + #end if + #elif $reference_genome.source == 'history': + -g genomeref.fa + #if $reference_genome.ref_filtering and str($reference_genome.ref_filtering) != '': + #echo ' '.join(str($reference_genome.ref_filtering).split(',')) + #end if + #end if + #if $filtering and str($filtering) != '': + #echo " " + #echo ' '.join(str($filtering).split(',')) + #end if + #if $maxintron and $maxintron > 0: + -i $maxintron + #end if + #if $region.region_filter == 'filter': + -r '$region.range' $region.discard_partial + #end if + #if $merging.merge_sel != 'none': + $merging.merge_cmd + #if $merging.merge_options: + #echo ' '.join(str($merging.merge_options).split(',')) + #end if + #end if + #if $chr_replace: + -m '$chr_replace' + #end if + + $full_gff_attribute_preservation + $decode_url + $expose + + ## + ## Although documented, does not appear to be used in the gffread code + ## #if $seq_info: + ## -A -s "$seq_info" + ## #end if + ## + ## outputs + #if $reference_genome.source != 'none': + #if $reference_genome.fa_outputs and str($reference_genome.fa_outputs) != '': + #echo ' ' + ' '.join(str($reference_genome.fa_outputs).split(',')) + #end if + #end if + #if $gffs.gff_fmt != 'none': + #if $gffs.tname: + -t '$gffs.tname' + #end if + #if $gffs.gff_fmt == 'gff': + #if $input.datatype.file_ext == 'gft': + $gffs.ensembl + #end if + $gffs.output_cmd + #elif $gffs.gff_fmt == 'gtf': + $gffs.output_cmd + #end if + #end if +]]> + </command> + <inputs> + <param name="input" type="data" format="gff3,gtf" label="Input GFF3 or GTF feature file"/> + <!-- filtering --> + <param name="filtering" type="select" display="checkboxes" multiple="true" label="filters"> + <option value="-U">discard single-exon transcripts (-U)</option> + <option value="-C">coding only: discard mRNAs that have no CDS feature (-C)</option> + <option value="-G">only parse additional exon attributes from the first exon and move them to the mRNA level (useful for GTF input) (-G)</option> + <option value="-O">process also non-transcript GFF records (by default non-transcript records are ignored) (-O)</option> + <option value="--no-pseudo">filter out records matching the 'pseudo' keyword (--no-pseudo)</option> + </param> + <conditional name="region"> + <param name="region_filter" type="select" label="Filter by genome region"> + <option value="none">No</option> + <option value="filter">Yes</option> + </param> + <when value="none"/> + <when value="filter"> + <param name="range" type="text" value="" label="Only show transcripts overlapping coordinate range"> + <help><![CDATA[ + (-r [['strand']'chr':]'start'..'end') <br> + examples: <br> + 1000..500000 <br> + chr1:1000..500000 <br> + +chr1:1000..500000 <br> + -chr1:1000..500000 + ]]> + </help> + <validator type="regex">(([+-])?(\w+:))?\d+\.\.\d+</validator> + </param> + <param name="discard_partial" type="boolean" truevalue="-R" falsevalue="" checked="false" + label="Discard all transcripts that are not fully contained within the given range" help="(-R)"/> + </when> + </conditional> + <param name="maxintron" type="integer" value="" optional="true" min="0" label="Filter out transcipts with large introns" + help="If set, discard transcripts having an intron larger (-i max_intron)"/> + <param name="chr_replace" type="data" format="tabular" optional="true" label="Replace reference sequence names" > + <help><![CDATA[(-m chr_replace) <br> + chr_replace is a reference sequence replacement table consisting of 2 columns: "original_ref_ID" "new_ref_ID"<br> + It is useful for switching between Ensembl and UCSC naming conventions <br> + NOTE: GFF records on reference sequences that are not found among the "original_ref_ID" entries in this file will be filtered out + ]]> + </help> + </param> + + <!-- Although documented, does not appear to be used in the gffread code + <param name="seq_info" type="data" format="tabular" optional="true" label="Use the description field as the value for a 'descr' attribute to the GFF record"> + <help> + (-s seq_info.fsize -A) useful with mRNA/EST/protein mappings <br> + seq_info input file is a 3 column tab-delimited file providing this info for each of the mapped sequences: <br> + "seq-name" "seq-length" "seq-description" <br> + </help> + </param> + --> + + <!-- merging --> + <conditional name="merging"> + <param name="merge_sel" type="select" label="Transcript merging" help="(-M/--merge or --cluster-only)"> + <option value="none">none</option> + <option value="merge">merge: cluster the input transcripts into loci, collapsing matching transcripts</option> + <option value="cluster">cluster-only: merge but without collapsing matching transcripts</option> + </param> + <when value="none"/> + <when value="merge"> + <param name="merge_cmd" type="hidden" value="--merge"/> + <expand macro="merge_opt_sel" /> + </when> + <when value="cluster"> + <param name="merge_cmd" type="hidden" value="--cluster-only"/> + <expand macro="cluster_opt_sel" /> + </when> + </conditional> + <!-- reference sequence file --> + <!-- Error: -g option is required for options -w, -x, -y, -V, -N, -M --> + <conditional name="reference_genome"> + <param name="source" type="select" label="Reference Genome" help="(-g genome.fasta) NOTE: Required for fasta outputs"> + <option value="none">none</option> + <option value="cached"></option> + <option value="history">From your history</option> + </param> + <when value="none"> + </when> + <when value="cached"> + <param name="fasta_indexes" type="select" label="Source FASTA Sequence"> + <options from_data_table="all_fasta"/> + </param> + <expand macro="ref_filtering_select" /> + <expand macro="fasta_output_select" /> + </when> + <when value="history"> + <param name="genome_fasta" type="data" format="fasta" label="Genome Reference Fasta"/> + <expand macro="ref_filtering_select" /> + <expand macro="fasta_output_select" /> + </when> + </conditional> + + <!-- outputs --> + <conditional name="gffs"> + <param name="gff_fmt" type="select" label="Feature File Output" help="(-o output.gff3|output.gtf)"> + <option value="none">none</option> + <option value="gff">GFF</option> + <option value="gtf">GTF</option> + </param> + <when value="none"> + </when> + <when value="gff"> + <param name="output_cmd" type="hidden" value="-o output.gff3"/> + <param name="ensembl" type="boolean" truevalue="-L" falsevalue="" checked="false" label="Ensembl GTF to GFF3 conversion" help="(-L)"/> + <expand macro="trackname" /> + </when> + <when value="gtf"> + <param name="output_cmd" type="hidden" value="-T -o output.gtf"/> + <expand macro="trackname" /> + </when> + </conditional> + + <param name="full_gff_attribute_preservation" type="boolean" truevalue="-F" falsevalue="" checked="false" + label="full GFF attribute preservation (all attributes are shown)" help="(-F)"/> + <param name="decode_url" type="boolean" truevalue="-D" falsevalue="" checked="false" + label="decode url encoded characters within attributes" help="(-D)"/> + <param name="expose" type="boolean" truevalue="-E" falsevalue="" checked="false" + label="warn about duplicate transcript IDs and other potential problems with the given GFF/GTF records" help="(-E)"/> + + </inputs> + <outputs> + <data name="output_gff" format="gff3" metadata_source="input" label="${tool.name} on ${on_string}: gff3" from_work_dir="output.gff3"> + <filter>gffs['gff_fmt'] == 'gff'</filter> + </data> + <data name="output_gtf" format="gtf" metadata_source="input" label="${tool.name} on ${on_string}: gtf" from_work_dir="output.gtf"> + <filter>gffs['gff_fmt'] == 'gtf'</filter> + </data> + <data name="output_exons" format="fasta" label="${tool.name} on ${on_string}: exons.fa" from_work_dir="exons.fa"> + <filter>'fa_outputs' in reference_genome and str(reference_genome['fa_outputs']).find('exons.fa') > 0 </filter> + </data> + <data name="output_cds" format="fasta" label="${tool.name} on ${on_string}: cds.fa" from_work_dir="cds.fa"> + <filter>'fa_outputs' in reference_genome and str(reference_genome['fa_outputs']).find('cds.fa') > 0</filter> + </data> + <data name="output_pep" format="fasta" label="${tool.name} on ${on_string}: pep.fa" from_work_dir="pep.fa"> + <filter>'fa_outputs' in reference_genome and str(reference_genome['fa_outputs']).find('pep.fa') > 0</filter> + </data> + <data name="output_dupinfo" format="txt" label="${tool.name} on ${on_string}: dupinfo" from_work_dir="dupinfo"> + <filter>'merge_options' in merging and merging['merge_options'].find('dupinfo') > 0</filter> + </data> + </outputs> + <tests> + <test> + <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> + <param name="gff_fmt" value="gff"/> + <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="2" /> + </test> + <test> + <param name="input" ftype="gtf" value="ecoli-k12.gff3"/> + <param name="gff_fmt" value="gff"/> + <param name="full_gff_attribute_preservation" value="-F"/> + <output name="output_gff" file="ecoli-k12.processed.gff3" ftype="gff3" lines_diff="2" /> + </test> + <test> + <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> + <param name="filtering" value="--no-pseudo"/> + <param name="gff_fmt" value="gtf"/> + <output name="output_gtf"> + <assert_contents> + <not_has_text text="pseudo" /> + </assert_contents> + </output> + </test> + <test> + <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> + <param name="region_filter" value="filter"/> + <param name="range" value="19:496500..504965"/> + <param name="gff_fmt" value="gtf"/> + <output name="output_gtf"> + <assert_contents> + <has_text text="ENST00000587541" /> + <has_text text="ENST00000382683" /> + </assert_contents> + </output> + </test> + <test> + <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> + <param name="region_filter" value="filter"/> + <param name="range" value="19:496500..504965"/> + <param name="discard_partial" value="true"/> + <param name="gff_fmt" value="gtf"/> + <output name="output_gtf"> + <assert_contents> + <not_has_text text="ENST00000587541" /> + <has_text text="ENST00000382683" /> + </assert_contents> + </output> + </test> + <test> + <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> + <param name="filtering" value="-C"/> + <param name="region_filter" value="filter"/> + <param name="range" value="19:496500..504965"/> + <param name="gff_fmt" value="gtf"/> + <output name="output_gtf"> + <assert_contents> + <not_has_text text="ENST00000587541" /> + <has_text text="ENST00000382683" /> + </assert_contents> + </output> + </test> + <test> + <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> + <param name="source" value="history"/> + <param name="genome_fasta" ftype="fasta" value="Homo_sapiens.GRCh37.71.dna.chromosome.19.fa"/> + <param name="fa_outputs" value="-w exons.fa,-x cds.fa,-y pep.fa"/> + <param name="region_filter" value="filter"/> + <param name="range" value="19:496500..504965"/> + <param name="gff_fmt" value="gtf"/> + <output name="output_gtf"> + <assert_contents> + <has_text text="ENST00000587541" /> + <has_text text="ENST00000382683" /> + </assert_contents> + </output> + <output name="output_exons"> + <assert_contents> + <has_text text="ENST00000346144 CDS=47-934" /> + <has_text text="CTATTTAAGCGGCTTCCCCGCGGCCTCGGGACAGAGGGGACTGAGCATGGATTTCGGACTGGCCCTCCTG" /> + </assert_contents> + </output> + <output name="output_cds"> + <assert_contents> + <has_text text="ENST00000346144" /> + <has_text text="ATGGATTTCGGACTGGCCCTCCTGCTGGCGGGGCTTCTGGGGCTCCTCCTCGGCCAGTCCCTCCAGGTGA" /> + </assert_contents> + </output> + <output name="output_pep"> + <assert_contents> + <has_text text="ENST00000346144" /> + <has_text text="MDFGLALLLAGLLGLLLGQSLQVKPLQVEPPEPVVAVALGASRQLTCRLACADRGASVQWRGLDTSLGAV" /> + </assert_contents> + </output> + </test> + + </tests> + <help> +<![CDATA[ +**gffread Filters and/or converts GFF3/GTF2 records** + +The gffread command is documented with the stringtie_ package. + +.. _stringtie: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread + + +gffread v0.11.4. Usage: :: + + gffread <input_gff> [-g <genomic_seqs_fasta> | <dir>][-s <seq_info.fsize>] + [-o <outfile>] [-t <trackname>] [-r [[<strand>]<chr>:]<start>..<end> [-R]] + [-CTVNJMKQAFPGUBHZWTOLE] [-w <exons.fa>] [-x <cds.fa>] [-y <tr_cds.fa>] + [-i <maxintron>] [--bed] [--table <attrlist>] [--sort-by <refseq_list.txt>] + + Filter, convert or cluster GFF/GTF/BED records, extract the sequence of + transcripts (exon or CDS) and more. + By default (i.e. without -O) only transcripts are processed, discarding any + other non-transcript features. Default output is a simplified GFF3 with only + the basic attributes. + + <input_gff> is a GFF file, use '-' for stdin + + Options: + + -i discard transcripts having an intron larger than <maxintron> + -l discard transcripts shorter than <minlen> bases + -r only show transcripts overlapping coordinate range <start>..<end> + (on chromosome/contig <chr>, strand <strand> if provided) + -R for -r option, discard all transcripts that are not fully + contained within the given range + -U discard single-exon transcripts + -C coding only: discard mRNAs that have no CDS features + --nc non-coding only: discard mRNAs that have CDS features + --ignore-locus : discard locus features and attributes found in the input + -A use the description field from <seq_info.fsize> and add it + as the value for a 'descr' attribute to the GFF record + -s <seq_info.fsize> is a tab-delimited file providing this info + for each of the mapped sequences: + <seq-name> <seq-length> <seq-description> + (useful for -A option with mRNA/EST/protein mappings) + + Sorting: (by default, chromosomes are kept in the order they were found) + --sort-alpha : chromosomes (reference sequences) are sorted alphabetically + --sort-by : sort the reference sequences by the order in which their + names are given in the <refseq.lst> file + + Misc options: + -F preserve all GFF attributes (for non-exon features) + --keep-exon-attrs : for -F option, do not attempt to reduce redundant + exon/CDS attributes + -G do not keep exon attributes, move them to the transcript feature + (for GFF3 output) + --keep-genes : in transcript-only mode (default), also preserve gene records + --keep-comments: for GFF3 input/output, try to preserve comments + -O process other non-transcript GFF records (by default non-transcript + records are ignored) + -V discard any mRNAs with CDS having in-frame stop codons (requires -g) + -H for -V option, check and adjust the starting CDS phase + if the original phase leads to a translation with an + in-frame stop codon + -B for -V option, single-exon transcripts are also checked on the + opposite strand (requires -g) + -P add transcript level GFF attributes about the coding status of each + transcript, including partialness or in-frame stop codons (requires -g) + --add-hasCDS : add a "hasCDS" attribute with value "true" for transcripts + that have CDS features + --adj-stop stop codon adjustment: enables -P and performs automatic + adjustment of the CDS stop coordinate if premature or downstream + -N discard multi-exon mRNAs that have any intron with a non-canonical + splice site consensus (i.e. not GT-AG, GC-AG or AT-AC) + -J discard any mRNAs that either lack initial START codon + or the terminal STOP codon, or have an in-frame stop codon + (i.e. only print mRNAs with a complete CDS) + --no-pseudo: filter out records matching the 'pseudo' keyword + --in-bed: input should be parsed as BED format (automatic if the input + filename ends with .bed*) + --in-tlf: input GFF-like one-line-per-transcript format without exon/CDS + features (see --tlf option below); automatic if the input + filename ends with .tlf) + + Clustering: + -M/--merge : cluster the input transcripts into loci, discarding + "duplicated" transcripts (those with the same exact introns + and fully contained or equal boundaries) + -d <dupinfo> : for -M option, write duplication info to file <dupinfo> + --cluster-only: same as -M/--merge but without discarding any of the + "duplicate" transcripts, only create "locus" features + -K for -M option: also discard as redundant the shorter, fully contained + transcripts (intron chains matching a part of the container) + -Q for -M option, no longer require boundary containment when assessing + redundancy (can be combined with -K); only introns have to match for + multi-exon transcripts, and >=80% overlap for single-exon transcripts + -Y for -M option, enforce -Q but also discard overlapping single-exon + transcripts, even on the opposite strand (can be combined with -K) + + Output options: + --force-exons: make sure that the lowest level GFF features are considered + "exon" features + --gene2exon: for single-line genes not parenting any transcripts, add an + exon feature spanning the entire gene (treat it as a transcript) + --t-adopt: try to find a parent gene overlapping/containing a transcript + that does not have any explicit gene Parent + -D decode url encoded characters within attributes + -Z merge very close exons into a single exon (when intron size<4) + -g full path to a multi-fasta file with the genomic sequences + for all input mappings, OR a directory with single-fasta files + (one per genomic sequence, with file names matching sequence names) + -w write a fasta file with spliced exons for each GFF transcript + -x write a fasta file with spliced CDS for each GFF transcript + -y write a protein fasta file with the translation of CDS for each record + -W for -w and -x options, write in the FASTA defline the exon + coordinates projected onto the spliced sequence; + for -y option, write transcript attributes in the FASTA defline + -S for -y option, use '*' instead of '.' as stop codon translation + -L Ensembl GTF to GFF3 conversion (implies -F; should be used with -m) + -m <chr_replace> is a name mapping table for converting reference + sequence names, having this 2-column format: + <original_ref_ID> <new_ref_ID> + WARNING: all GFF records on reference sequences whose original IDs + are not found in the 1st column of this table will be discarded! + -t use <trackname> in the 2nd column of each GFF/GTF output line + -o write the records into <outfile> instead of stdout + -T main output will be GTF instead of GFF3 + --bed output records in BED format instead of default GFF3 + --tlf output "transcript line format" which is like GFF + but exons, CDS features and related data are stored as GFF + attributes in the transcript feature line, like this: + exoncount=N;exons=<exons>;CDSphase=<N>;CDS=<CDScoords> + <exons> is a comma-delimited list of exon_start-exon_end coordinates; + <CDScoords> is CDS_start:CDS_end coordinates or a list like <exons> + --table output a simple tab delimited format instead of GFF, with columns + having the values of GFF attributes given in <attrlist>; special + pseudo-attributes (prefixed by @) are recognized: + @chr, @start, @end, @strand, @numexons, @exons, @cds, @covlen, @cdslen + -v,-E expose (warn about) duplicate transcript IDs and other potential + problems with the given GFF/GTF records +]]> + </help> + <citations> + <citation type="doi">10.1038/nbt.1621</citation> + </citations> +</tool> +