comparison gffread.xml @ 6:6ea09f60dee9 draft

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

5:69e0806b63a4

<tool id="gffread" name="gffread" version="@VERSION@.2">
    <description>Filters and/or converts GFF3/GTF2 records</description>
    <macros>
        <import>cuff_macros.xml</import>
        <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" />
    <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>
        </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>

        <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="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>
            <output name="output_exons">
                <assert_contents>
                    <has_text text="ENST00000346144 gene=MADCAM1 CDS=47-932" />
                    <has_text text="CTATTTAAGCGGCTTCCCCGCGGCCTCGGGACAGAGGGGACTGAGCATGGATTTCGGACTGGCCCTCCTG" />
                </assert_contents>
            </output>
            <output name="output_cds">
                <assert_contents>
                    <has_text text="ENST00000346144 gene=MADCAM1" />
                    <has_text text="ATGGATTTCGGACTGGCCCTCCTGCTGGCGGGGCTTCTGGGGCTCCTCCTCGGCCAGTCCCTCCAGGTGA" />
                </assert_contents>
            </output>
            <output name="output_pep">
                <assert_contents>
                    <has_text text="ENST00000346144 gene=MADCAM1" />
                    <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.

.. _cufflinks: http://cole-trapnell-lab.github.io/cufflinks/

Usage: ::

 gffread "input_gff" [-g "genomic_seqs_fasta" | "dir"][-s "seq_info.fsize"]
   [-o "outfile.gff"] [-t "tname"] [-r [["strand"]"chr":]"start".."end" [-R]]
   [-CTVNJMKQAFGUBHZWTOLE] [-w "exons.fa"] [-x "cds.fa"] [-y "tr_cds.fa"]
   [-i "maxintron"]

Options: ::

  -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)
  -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)
  -i  discard transcripts having an intron larger than <maxintron>
  -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 feature
  -F  full GFF attribute preservation (all attributes are shown)
  -G  only parse additional exon attributes from the first exon
      and move them to the mRNA level (useful for GTF input)
  -A  use the description field from <seq_info.fsize> and add it
      as the value for a 'descr' attribute to the GFF record

  -O  process also non-transcript GFF records (by default non-transcript
      records are ignored)
  -V  discard any mRNAs with CDS having in-frame stop codons
  -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
  -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
      (only print mRNAs with a fulll, valid CDS)
  --no-pseudo: filter out records matching the 'pseudo' keyword

  -M/--merge : cluster the input transcripts into loci, collapsing matching
       transcripts (those with the same exact introns and fully contained)
  -d <dupinfo> : for -M option, write collapsing info to file <dupinfo>
  --cluster-only: same as --merge but without collapsing matching transcripts
  -K  for -M option: also collapse shorter, fully contained transcripts
      with fewer introns than the container
  -Q  for -M option, remove the containment restriction:
      (multi-exon transcripts will be collapsed if just their introns match,
      while single-exon transcripts can partially overlap (80%))

  --force-exons: make sure that the lowest level GFF features are printed as
      "exon" features
  -E  expose (warn about) duplicate transcript IDs and other potential
      problems with the given GFF/GTF records
  -D  decode url encoded characters within attributes
  -Z  merge close exons into a single exon (for intron size<4)
  -w  write a fasta file with spliced exons for each GFF transcript
  -x  write a fasta file with spliced CDS for each GFF transcript
  -W  for -w and -x options, also write for each fasta record the exon
      coordinates projected onto the spliced sequence
  -y  write a protein fasta file with the translation of CDS for each record
  -L  Ensembl GTF to GFF3 conversion (implies -F; should be used with -m)
  -m  <chr_replace> is a reference (genomic) sequence replacement table with
      this format:
      <original_ref_ID> <new_ref_ID>
      For example from UCSC naming to Ensembl naming:
      chr1	1
      chr2	2
      GFF records on reference sequences that are not found among the
      <original_ref_ID> entries in this file will be filtered out
  -o  the "filtered" GFF records will be written to <outfile.gff>
      (use -o- for printing to stdout)
  -t  use <trackname> in the second column of each GFF output line
  -T  -o option will output GTF format instead of GFF3

]]>
    </help>
    <citations>
        <citation type="doi">10.1038/nbt.1621</citation>
    </citations>

6:6ea09f60dee9

<tool id="gffread" name="gffread" version="@VERSION@.1">
    <description>Filters and/or converts GFF3/GTF2 records</description>
    <macros>
        <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>
    <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>
            <!-- 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"/> # 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>
                    <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>