| Previous changeset 1:48fe74f391ab (2015-11-11) Next changeset 3:9f243677c4c6 (2017-02-07) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 3bc5271145f939d85bb709fc95197be66b348328 |
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modified:
cuff_macros.xml gffread.xml |
| b |
| diff -r 48fe74f391ab -r 12aeae6d8587 cuff_macros.xml --- a/cuff_macros.xml Wed Nov 11 12:36:04 2015 -0500 +++ b/cuff_macros.xml Tue Jun 07 17:58:15 2016 -0400 |
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| @@ -1,11 +1,13 @@ <macros> <token name="@VERSION@">2.2.1</token> + <xml name="requirements"> <requirements> <requirement type="package" version="2.2.1">cufflinks</requirement> <yield /> </requirements> </xml> + <xml name="stdio"> <stdio> <exit_code range="1:" /> |
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| diff -r 48fe74f391ab -r 12aeae6d8587 gffread.xml --- a/gffread.xml Wed Nov 11 12:36:04 2015 -0500 +++ b/gffread.xml Tue Jun 07 17:58:15 2016 -0400 |
| [ |
| b'@@ -18,7 +18,7 @@\n <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>\n <option value="-V">discard any mRNAs with CDS having in-frame stop codons (-V)</option>\n <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>\n- <!-- gffread bug: B not in missing from param to the arg parser \n+ <!-- gffread bug: B not in missing from param to the arg parser\n <option value="-B">single-exon transcripts are also checked on the opposite strand (-B with -V)</option>\n -->\n </param>\n@@ -54,7 +54,7 @@\n #if $reference_genome.source == \'history\':\n ln -s $reference_genome.genome_fasta genomeref.fa &&\n #end if\n- gffread $input \n+ gffread $input\n #if $reference_genome.source == \'cached\':\n -g "${reference_genome.fasta_indexes.fields.path}"\n #if $reference_genome.ref_filtering and str($reference_genome.ref_filtering) != \'\':\n@@ -121,7 +121,7 @@\n <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>\n <option value="-O">process also non-transcript GFF records (by default non-transcript records are ignored) (-O)</option>\n <option value="--no-pseudo">filter out records matching the \'pseudo\' keyword (--no-pseudo)</option>\n- </param> \n+ </param>\n <conditional name="region">\n <param name="region_filter" type="select" label="Filter by genome region">\n <option value="none">No</option>\n@@ -131,21 +131,21 @@\n <when value="filter">\n <param name="range" type="text" value="" label="Only show transcripts overlapping coordinate range">\n <help><![CDATA[\n- (-r [[\'strand\']\'chr\':]\'start\'..\'end\') <br> \n- examples: <br> \n- 1000..500000 <br> \n- chr1:1000..500000 <br> \n- +chr1:1000..500000 <br> \n+ (-r [[\'strand\']\'chr\':]\'start\'..\'end\') <br>\n+ examples: <br>\n+ 1000..500000 <br>\n+ chr1:1000..500000 <br>\n+ +chr1:1000..500000 <br>\n -chr1:1000..500000\n ]]>\n </help>\n <validator type="regex">(([+-])?(\\w+:))?\\d+\\.\\.\\d+</validator>\n </param>\n- <param name="discard_partial" type="boolean" truevalue="-R" falsevalue="" check="false" \n+ <param name="discard_partial" type="boolean" truevalue="-R" falsevalue="" check="false"\n label="discard all transcripts that are not fully contained within the given range" help="(-R)"/>\n </when>\n </conditional>\n- <param name="maxintron" type="integer" value="" optional="true" min="0" label="Filter out transcipts with large introns" \n+ <param name="maxintron" type="integer" value="" optional="true" min="0" label="Filter out transcipts with large introns"\n help="If set, discard transcripts having an intron larger (-i max_intron)"/>\n <param name="chr_replace" type="data" format="tabular" optional="true" label="Replace reference sequence names" >\n <help><![CDATA[(-m chr_replace) <br>\n@@ -154,7 +154,7 @@\n NOTE: GFF records on reference sequences that are not found among the "original_ref_ID" entries in this file will be filtered out\n ]]>\n </help>\n- </param> \n+ </param>\n \n <!-- Although documented, does not appear to be used in the gffread code\n <param name="seq_info" type="data" format="tabular" optional="true" la'..b'tput.gff3|output.gtf)">\n <option value="none">none</option>\n <option value="gff">GFF</option>\n <option value="gtf">GTF</option>\n@@ -227,11 +227,11 @@\n </when>\n </conditional>\n \n- <param name="full_gff_attribute_preservation" type="boolean" truevalue="-F" falsevalue="" check="false" \n+ <param name="full_gff_attribute_preservation" type="boolean" truevalue="-F" falsevalue="" check="false"\n label="full GFF attribute preservation (all attributes are shown)" help="(-F)"/>\n- <param name="decode_url" type="boolean" truevalue="-D" falsevalue="" check="false" \n+ <param name="decode_url" type="boolean" truevalue="-D" falsevalue="" check="false"\n label="decode url encoded characters within attributes" help="(-D)"/>\n- <param name="expose" type="boolean" truevalue="-E" falsevalue="" check="false" \n+ <param name="expose" type="boolean" truevalue="-E" falsevalue="" check="false"\n label="warn about duplicate transcript IDs and other potential problems with the given GFF/GTF records" help="(-E)"/>\n \n </inputs>\n@@ -359,11 +359,11 @@\n \n Usage: ::\n \n- gffread "input_gff" [-g "genomic_seqs_fasta" | "dir"][-s "seq_info.fsize"] \n+ gffread "input_gff" [-g "genomic_seqs_fasta" | "dir"][-s "seq_info.fsize"]\n [-o "outfile.gff"] [-t "tname"] [-r [["strand"]"chr":]"start".."end" [-R]]\n [-CTVNJMKQAFGUBHZWTOLE] [-w "exons.fa"] [-x "cds.fa"] [-y "tr_cds.fa"]\n- [-i "maxintron"] \n- \n+ [-i "maxintron"]\n+\n Options: ::\n \n -g full path to a multi-fasta file with the genomic sequences\n@@ -376,7 +376,7 @@\n -i discard transcripts having an intron larger than <maxintron>\n -r only show transcripts overlapping coordinate range <start>..<end>\n (on chromosome/contig <chr>, strand <strand> if provided)\n- -R for -r option, discard all transcripts that are not fully \n+ -R for -r option, discard all transcripts that are not fully\n contained within the given range\n -U discard single-exon transcripts\n -C coding only: discard mRNAs that have no CDS feature\n@@ -385,12 +385,12 @@\n and move them to the mRNA level (useful for GTF input)\n -A use the description field from <seq_info.fsize> and add it\n as the value for a \'descr\' attribute to the GFF record\n- \n+\n -O process also non-transcript GFF records (by default non-transcript\n records are ignored)\n -V discard any mRNAs with CDS having in-frame stop codons\n -H for -V option, check and adjust the starting CDS phase\n- if the original phase leads to a translation with an \n+ if the original phase leads to a translation with an\n in-frame stop codon\n -B for -V option, single-exon transcripts are also checked on the\n opposite strand\n@@ -400,7 +400,7 @@\n or the terminal STOP codon, or have an in-frame stop codon\n (only print mRNAs with a fulll, valid CDS)\n --no-pseudo: filter out records matching the \'pseudo\' keyword\n- \n+\n -M/--merge : cluster the input transcripts into loci, collapsing matching\n transcripts (those with the same exact introns and fully contained)\n -d <dupinfo> : for -M option, write collapsing info to file <dupinfo>\n@@ -410,10 +410,10 @@\n -Q for -M option, remove the containment restriction:\n (multi-exon transcripts will be collapsed if just their introns match,\n while single-exon transcripts can partially overlap (80%))\n- \n- --force-exons: make sure that the lowest level GFF features are printed as \n+\n+ --force-exons: make sure that the lowest level GFF features are printed as\n "exon" features\n- -E expose (warn about) duplicate transcript IDs and other potential \n+ -E expose (warn about) duplicate transcript IDs and other potential\n problems with the given GFF/GTF records\n -D decode url encoded characters within attributes\n -Z merge close exons into a single exon (for intron size<4)\n' |