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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
author | devteam |
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date | Tue, 07 Feb 2017 18:39:51 -0500 |
parents | baeea9c2ff0f |
children | 6562753c6bdc |
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<tool id="gffread" name="gffread" version="@VERSION@.0"> <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> <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> <expand macro="requirements" /> <expand macro="stdio" /> <command> <![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 ## ## 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="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> <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> </tool>