gffread: gffread.xml comparison

comparison gffread.xml @ 4:0cf496c45054 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"

author	iuc
date	Fri, 01 Nov 2019 12:54:23 -0400
parents	29769f789b8f
children	f312cff50fda

comparison

equal deleted inserted replaced

-:29769f789b8f
+:0cf496c45054
-<tool id="gffread" name="gffread" version="@VERSION@.2">
+<tool id="gffread" name="gffread" version="@VERSION@.1">
 <description>Filters and/or converts GFF3/GTF2 records</description>
 <macros>
-<import>cuff_macros.xml</import>
+<token name="@VERSION@">0.11.4</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>
 <param name="merge_options" type="select" display="checkboxes" multiple="true" label="Cluster options">
 <expand macro="cluster_opts" />
 </param>
 </xml>
 </macros>
-<expand macro="requirements" />
+<requirements>
+<requirement type="package" version="@VERSION@">gffread</requirement>
+</requirements>
 <command detect_errors="aggressive">
 <![CDATA[
 #if $reference_genome.source == 'history':
 ln -s '$reference_genome.genome_fasta' genomeref.fa &&
 #end if
 <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>
+<!-- The no-pseudo option is broken in 0.11.4 of gffread.
+See https://github.com/gpertea/gffread/issues/43 -->
+<!-- <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 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>
+<!-- The no-pseudo option is broken in 0.11.4 of gffread.
+See https://github.com/gpertea/gffread/issues/43 -->
+<!--
 <test>
 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
-<param name="filtering" value="--no-pseudo"/>
+<param name="filtering" value="/-/-no-pseudo"/> # Fix dashes when uncommenting
 <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="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="ENST00000587541" />
 <has_text text="ENST00000382683" />
 </assert_contents>
 </output>
 <output name="output_exons">
 <assert_contents>
-<has_text text="ENST00000346144 gene=MADCAM1 CDS=47-932" />
+<has_text text="ENST00000346144 CDS=47-934" />
 <has_text text="CTATTTAAGCGGCTTCCCCGCGGCCTCGGGACAGAGGGGACTGAGCATGGATTTCGGACTGGCCCTCCTG" />
 </assert_contents>
 </output>
 <output name="output_cds">
 <assert_contents>
-<has_text text="ENST00000346144 gene=MADCAM1" />
+<has_text text="ENST00000346144" />
 <has_text text="ATGGATTTCGGACTGGCCCTCCTGCTGGCGGGGCTTCTGGGGCTCCTCCTCGGCCAGTCCCTCCAGGTGA" />
 </assert_contents>
 </output>
 <output name="output_pep">
 <assert_contents>
-<has_text text="ENST00000346144 gene=MADCAM1" />
+<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 distributed with the cufflinks_ package.
+The gffread command is documented with the stringtie_ package.
-.. _cufflinks: http://cole-trapnell-lab.github.io/cufflinks/
+.. _stringtie: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread
-Usage: ::
+gffread v0.11.4. Usage: ::
-gffread "input_gff" [-g "genomic_seqs_fasta" | "dir"][-s "seq_info.fsize"]
-[-o "outfile.gff"] [-t "tname"] [-r [["strand"]"chr":]"start".."end" [-R]]
+gffread <input_gff> [-g <genomic_seqs_fasta> | <dir>][-s <seq_info.fsize>]
-[-CTVNJMKQAFGUBHZWTOLE] [-w "exons.fa"] [-x "cds.fa"] [-y "tr_cds.fa"]
+[-o <outfile>] [-t <trackname>] [-r [[<strand>]<chr>:]<start>..<end> [-R]]
-[-i "maxintron"]
+[-CTVNJMKQAFPGUBHZWTOLE] [-w <exons.fa>] [-x <cds.fa>] [-y <tr_cds.fa>]
+[-i <maxintron>] [--bed] [--table <attrlist>] [--sort-by <refseq_list.txt>]
-Options: ::
+Filter, convert or cluster GFF/GTF/BED records, extract the sequence of
--g  full path to a multi-fasta file with the genomic sequences
+transcripts (exon or CDS) and more.
-for all input mappings, OR a directory with single-fasta files
+By default (i.e. without -O) only transcripts are processed, discarding any
-(one per genomic sequence, with file names matching sequence names)
+other non-transcript features. Default output is a simplified GFF3 with only
--s  <seq_info.fsize> is a tab-delimited file providing this info
+the basic attributes.
-for each of the mapped sequences:
-<seq-name> <seq-length> <seq-description>
+<input_gff> is a GFF file, use '-' for stdin
-(useful for -A option with mRNA/EST/protein mappings)
--i  discard transcripts having an intron larger than <maxintron>
+Options:
--r  only show transcripts overlapping coordinate range <start>..<end>
-(on chromosome/contig <chr>, strand <strand> if provided)
+-i   discard transcripts having an intron larger than <maxintron>
--R  for -r option, discard all transcripts that are not fully
+-l   discard transcripts shorter than <minlen> bases
-contained within the given range
+-r   only show transcripts overlapping coordinate range <start>..<end>
--U  discard single-exon transcripts
+(on chromosome/contig <chr>, strand <strand> if provided)
--C  coding only: discard mRNAs that have no CDS feature
+-R   for -r option, discard all transcripts that are not fully
--F  full GFF attribute preservation (all attributes are shown)
+contained within the given range
--G  only parse additional exon attributes from the first exon
+-U   discard single-exon transcripts
-and move them to the mRNA level (useful for GTF input)
+-C   coding only: discard mRNAs that have no CDS features
--A  use the description field from <seq_info.fsize> and add it
+--nc non-coding only: discard mRNAs that have CDS features
-as the value for a 'descr' attribute to the GFF record
+--ignore-locus : discard locus features and attributes found in the input
+-A   use the description field from <seq_info.fsize> and add it
--O  process also non-transcript GFF records (by default non-transcript
+as the value for a 'descr' attribute to the GFF record
-records are ignored)
+-s   <seq_info.fsize> is a tab-delimited file providing this info
--V  discard any mRNAs with CDS having in-frame stop codons
+for each of the mapped sequences:
--H  for -V option, check and adjust the starting CDS phase
+<seq-name> <seq-length> <seq-description>
-if the original phase leads to a translation with an
+(useful for -A option with mRNA/EST/protein mappings)
-in-frame stop codon
--B  for -V option, single-exon transcripts are also checked on the
+Sorting: (by default, chromosomes are kept in the order they were found)
-opposite strand
+--sort-alpha : chromosomes (reference sequences) are sorted alphabetically
--N  discard multi-exon mRNAs that have any intron with a non-canonical
+--sort-by : sort the reference sequences by the order in which their
-splice site consensus (i.e. not GT-AG, GC-AG or AT-AC)
+names are given in the <refseq.lst> file
--J  discard any mRNAs that either lack initial START codon
-or the terminal STOP codon, or have an in-frame stop codon
+Misc options:
-(only print mRNAs with a fulll, valid CDS)
+-F   preserve all GFF attributes (for non-exon features)
---no-pseudo: filter out records matching the 'pseudo' keyword
+--keep-exon-attrs : for -F option, do not attempt to reduce redundant
+exon/CDS attributes
--M/--merge : cluster the input transcripts into loci, collapsing matching
+-G   do not keep exon attributes, move them to the transcript feature
-transcripts (those with the same exact introns and fully contained)
+(for GFF3 output)
--d <dupinfo> : for -M option, write collapsing info to file <dupinfo>
+--keep-genes : in transcript-only mode (default), also preserve gene records
---cluster-only: same as --merge but without collapsing matching transcripts
+--keep-comments: for GFF3 input/output, try to preserve comments
--K  for -M option: also collapse shorter, fully contained transcripts
+-O   process other non-transcript GFF records (by default non-transcript
-with fewer introns than the container
+records are ignored)
--Q  for -M option, remove the containment restriction:
+-V   discard any mRNAs with CDS having in-frame stop codons (requires -g)
-(multi-exon transcripts will be collapsed if just their introns match,
+-H   for -V option, check and adjust the starting CDS phase
-while single-exon transcripts can partially overlap (80%))
+if the original phase leads to a translation with an
+in-frame stop codon
---force-exons: make sure that the lowest level GFF features are printed as
+-B   for -V option, single-exon transcripts are also checked on the
-"exon" features
+opposite strand (requires -g)
--E  expose (warn about) duplicate transcript IDs and other potential
+-P   add transcript level GFF attributes about the coding status of each
-problems with the given GFF/GTF records
+transcript, including partialness or in-frame stop codons (requires -g)
--D  decode url encoded characters within attributes
+--add-hasCDS : add a "hasCDS" attribute with value "true" for transcripts
--Z  merge close exons into a single exon (for intron size<4)
+that have CDS features
--w  write a fasta file with spliced exons for each GFF transcript
+--adj-stop stop codon adjustment: enables -P and performs automatic
--x  write a fasta file with spliced CDS for each GFF transcript
+adjustment of the CDS stop coordinate if premature or downstream
--W  for -w and -x options, also write for each fasta record the exon
+-N   discard multi-exon mRNAs that have any intron with a non-canonical
-coordinates projected onto the spliced sequence
+splice site consensus (i.e. not GT-AG, GC-AG or AT-AC)
--y  write a protein fasta file with the translation of CDS for each record
+-J   discard any mRNAs that either lack initial START codon
--L  Ensembl GTF to GFF3 conversion (implies -F; should be used with -m)
+or the terminal STOP codon, or have an in-frame stop codon
--m  <chr_replace> is a reference (genomic) sequence replacement table with
+(i.e. only print mRNAs with a complete CDS)
-this format:
+--no-pseudo: filter out records matching the 'pseudo' keyword
-<original_ref_ID> <new_ref_ID>
+--in-bed: input should be parsed as BED format (automatic if the input
-For example from UCSC naming to Ensembl naming:
+filename ends with .bed*)
-chr1	1
+--in-tlf: input GFF-like one-line-per-transcript format without exon/CDS
-chr2	2
+features (see --tlf option below); automatic if the input
-GFF records on reference sequences that are not found among the
+filename ends with .tlf)
-<original_ref_ID> entries in this file will be filtered out
--o  the "filtered" GFF records will be written to <outfile.gff>
+Clustering:
-(use -o- for printing to stdout)
+-M/--merge : cluster the input transcripts into loci, discarding
--t  use <trackname> in the second column of each GFF output line
+"duplicated" transcripts (those with the same exact introns
--T  -o option will output GTF format instead of GFF3
+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>

Mercurial > repos > devteam > gffread

comparison gffread.xml @ 4:0cf496c45054 draft