Mercurial > repos > devteam > gffread
diff gffread.xml @ 1:96c4d0e18546 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
| author | devteam |
|---|---|
| date | Tue, 07 Feb 2017 18:39:51 -0500 |
| parents | baeea9c2ff0f |
| children | 6562753c6bdc |
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--- a/gffread.xml Mon Nov 09 12:06:36 2015 -0500 +++ b/gffread.xml Tue Feb 07 18:39:51 2017 -0500 @@ -1,7 +1,5 @@ <tool id="gffread" name="gffread" version="@VERSION@.0"> <description>Filters and/or converts GFF3/GTF2 records</description> - <expand macro="requirements" /> - <expand macro="stdio" /> <macros> <import>cuff_macros.xml</import> <xml name="fasta_output_select"> @@ -18,7 +16,7 @@ <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 + <!-- 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> @@ -49,14 +47,16 @@ </param> </xml> </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> <command> <![CDATA[ #if $reference_genome.source == 'history': - ln -s $reference_genome.genome_fasta genomeref.fa && + ln -s '$reference_genome.genome_fasta' genomeref.fa && #end if - gffread $input + gffread '$input' #if $reference_genome.source == 'cached': - -g "${reference_genome.fasta_indexes.fields.path}" + -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 @@ -74,7 +74,7 @@ -i $maxintron #end if #if $region.region_filter == 'filter': - -r $region.range $region.discard_partial + -r '$region.range' $region.discard_partial #end if #if $merging.merge_sel != 'none': $merging.merge_cmd @@ -83,7 +83,7 @@ #end if #end if #if $chr_replace: - -m "$chr_replace" + -m '$chr_replace' #end if ## ## Although documented, does not appear to be used in the gffread code @@ -99,7 +99,7 @@ #end if #if $gffs.gff_fmt != 'none': #if $gffs.tname: - -t "$gffs.tname" + -t '$gffs.tname' #end if #if $gffs.gff_fmt == 'gff': #if $input.datatype.file_ext == 'gft': @@ -121,7 +121,7 @@ <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> + </param> <conditional name="region"> <param name="region_filter" type="select" label="Filter by genome region"> <option value="none">No</option> @@ -131,21 +131,21 @@ <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> + (-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="" check="false" - label="discard all transcripts that are not fully contained within the given range" help="(-R)"/> + <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" + <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> @@ -154,7 +154,7 @@ 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> + </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"> @@ -163,7 +163,7 @@ 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> + </param> --> <!-- merging --> @@ -201,7 +201,7 @@ <expand macro="fasta_output_select" /> </when> <when value="history"> - <param name="genome_fasta" type="data" format="fasta" label="Genome Reference Fasta"/> + <param name="genome_fasta" type="data" format="fasta" label="Genome Reference Fasta"/> <expand macro="ref_filtering_select" /> <expand macro="fasta_output_select" /> </when> @@ -209,7 +209,7 @@ <!-- outputs --> <conditional name="gffs"> - <param name="gff_fmt" type="select" optional="true" label="Feature File Output" help="(-o output.gff3|output.gtf)"> + <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> @@ -218,7 +218,7 @@ </when> <when value="gff"> <param name="output_cmd" type="hidden" value="-o output.gff3"/> - <param name="ensembl" type="boolean" truevalue="-L" falsevalue="" check="false" label="Ensembl GTF to GFF3 conversion" help="(-L)"/> + <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"> @@ -227,11 +227,11 @@ </when> </conditional> - <param name="full_gff_attribute_preservation" type="boolean" truevalue="-F" falsevalue="" check="false" + <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="" check="false" + <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="" check="false" + <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> @@ -259,7 +259,7 @@ <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" /> + <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="2" /> </test> <test> @@ -269,7 +269,7 @@ <output name="output_gtf"> <assert_contents> <not_has_text text="pseudo" /> - </assert_contents> + </assert_contents> </output> </test> @@ -282,7 +282,7 @@ <assert_contents> <has_text text="ENST00000587541" /> <has_text text="ENST00000382683" /> - </assert_contents> + </assert_contents> </output> </test> @@ -294,9 +294,9 @@ <param name="gff_fmt" value="gtf"/> <output name="output_gtf"> <assert_contents> - <has_text text="ENST00000587541" /> + <not_has_text text="ENST00000587541" /> <has_text text="ENST00000382683" /> - </assert_contents> + </assert_contents> </output> </test> @@ -310,7 +310,7 @@ <assert_contents> <not_has_text text="ENST00000587541" /> <has_text text="ENST00000382683" /> - </assert_contents> + </assert_contents> </output> </test> @@ -318,7 +318,7 @@ <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.f,-x cds.fa,-y pep.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"/> @@ -326,25 +326,25 @@ <assert_contents> <not_has_text text="ENST00000587541" /> <has_text text="ENST00000382683" /> - </assert_contents> + </assert_contents> </output> <output name="output_exons"> <assert_contents> <has_text text="ENST00000346144 gene=MADCAM1 CDS=47-932" /> <has_text text="CTATTTAAGCGGCTTCCCCGCGGCCTCGGGACAGAGGGGACTGAGCATGGATTTCGGACTGGCCCTCCTG" /> - </assert_contents> + </assert_contents> </output> <output name="output_cds"> <assert_contents> <has_text text="ENST00000346144 gene=MADCAM1" /> <has_text text="ATGGATTTCGGACTGGCCCTCCTGCTGGCGGGGCTTCTGGGGCTCCTCCTCGGCCAGTCCCTCCAGGTGA" /> - </assert_contents> + </assert_contents> </output> <output name="output_pep"> <assert_contents> <has_text text="ENST00000346144 gene=MADCAM1" /> <has_text text="MDFGLALLLAGLLGLLLGQSLQVKPLQVEPPEPVVAVALGASRQLTCRLACADRGASVQWRGLDTSLGAV" /> - </assert_contents> + </assert_contents> </output> </test> @@ -359,11 +359,11 @@ Usage: :: - gffread "input_gff" [-g "genomic_seqs_fasta" | "dir"][-s "seq_info.fsize"] + 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"] - + [-i "maxintron"] + Options: :: -g full path to a multi-fasta file with the genomic sequences @@ -376,7 +376,7 @@ -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 + -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 @@ -385,12 +385,12 @@ 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 + 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 @@ -400,7 +400,7 @@ 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> @@ -410,10 +410,10 @@ -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 + + --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 + -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)