gffread: gffread.xml annotate

annotate gffread.xml @ 5:f312cff50fda draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 35e5b87300fb4e64d6d4eab376012ca9c524a432"

author	iuc
date	Mon, 11 Nov 2019 18:27:24 -0500
parents	0cf496c45054
children	bba49324f2fa

rev	line source
5 f312cff50fda "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 35e5b87300fb4e64d6d4eab376012ca9c524a432" iuc parents: 4 diff changeset	1 <tool id="gffread" name="gffread" version="@VERSION@.0">
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	2 <description>Filters and/or converts GFF3/GTF2 records</description>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	3 <macros>
5 f312cff50fda "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 35e5b87300fb4e64d6d4eab376012ca9c524a432" iuc parents: 4 diff changeset	4 <token name="@VERSION@">0.11.6</token>
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	5 <xml name="fasta_output_select">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	6 <param name="fa_outputs" type="select" display="checkboxes" multiple="true" label="Select fasta outputs">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	7 <option value="-w exons.fa">fasta file with spliced exons for each GFF transcript (-w exons.fa)</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	8 <option value="-x cds.fa">fasta file with spliced CDS for each GFF transcript (-x cds.fa)</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	9 <option value="-y pep.fa">protein fasta file with the translation of CDS for each record (-y pep.fa)</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	10 <option value="-W">for each fasta: record the exon coordinates projected onto the spliced sequence (-W)</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	11 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	12 </xml>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	13 <xml name="ref_filtering_select">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	14 <param name="ref_filtering" type="select" display="checkboxes" multiple="true" label="reference based filters">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	15 <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>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	16 <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>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	17 <option value="-V">discard any mRNAs with CDS having in-frame stop codons (-V)</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	18 <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>
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	19 <!-- gffread bug: B not in missing from param to the arg parser
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	20 <option value="-B">single-exon transcripts are also checked on the opposite strand (-B with -V)</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	21 -->
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	22 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	23 </xml>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	24 <xml name="trackname">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	25 <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}">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	26 <validator type="regex">\w+</validator>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	27 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	28 </xml>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	29 <xml name="merge_opts">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	30 <option value="-K">also collapse shorter, fully contained transcripts with fewer introns than the container (-K)</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	31 <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>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	32 <option value="-d dupinfo">output collapsing info (-d dupinfo)</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	33 </xml>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	34 <xml name="cluster_opts">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	35 <option value="--force-exons"> make sure that the lowest level GFF features are printed as 'exon' features (--force-exons)</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	36 <option value="-Z">merge close exons into a single exon (for intron size < 4) (-Z)</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	37 </xml>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	38 <xml name="merge_opt_sel">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	39 <param name="merge_options" type="select" display="checkboxes" multiple="true" label="Merge options">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	40 <expand macro="cluster_opts" />
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	41 <expand macro="merge_opts" />
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	42 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	43 </xml>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	44 <xml name="cluster_opt_sel">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	45 <param name="merge_options" type="select" display="checkboxes" multiple="true" label="Cluster options">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	46 <expand macro="cluster_opts" />
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	47 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	48 </xml>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	49 </macros>
4 0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	50 <requirements>
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	51 <requirement type="package" version="@VERSION@">gffread</requirement>
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	52 </requirements>
2 6562753c6bdc planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5 devteam parents: 1 diff changeset	53 <command detect_errors="aggressive">
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	54 <![CDATA[
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	55 #if $reference_genome.source == 'history':
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	56 ln -s '$reference_genome.genome_fasta' genomeref.fa &&
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	57 #end if
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	58 gffread '$input'
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	59 #if $reference_genome.source == 'cached':
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	60 -g '${reference_genome.fasta_indexes.fields.path}'
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	61 #if $reference_genome.ref_filtering and str($reference_genome.ref_filtering) != '':
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	62 #echo ' '.join(str($reference_genome.ref_filtering).split(','))
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	63 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	64 #elif $reference_genome.source == 'history':
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	65 -g genomeref.fa
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	66 #if $reference_genome.ref_filtering and str($reference_genome.ref_filtering) != '':
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	67 #echo ' '.join(str($reference_genome.ref_filtering).split(','))
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	68 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	69 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	70 #if $filtering and str($filtering) != '':
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	71 #echo " "
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	72 #echo ' '.join(str($filtering).split(','))
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	73 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	74 #if $maxintron and $maxintron > 0:
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	75 -i $maxintron
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	76 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	77 #if $region.region_filter == 'filter':
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	78 -r '$region.range' $region.discard_partial
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	79 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	80 #if $merging.merge_sel != 'none':
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	81 $merging.merge_cmd
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	82 #if $merging.merge_options:
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	83 #echo ' '.join(str($merging.merge_options).split(','))
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	84 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	85 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	86 #if $chr_replace:
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	87 -m '$chr_replace'
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	88 #end if
3 29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad" devteam parents: 2 diff changeset	89
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad" devteam parents: 2 diff changeset	90 $full_gff_attribute_preservation
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad" devteam parents: 2 diff changeset	91 $decode_url
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad" devteam parents: 2 diff changeset	92 $expose
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad" devteam parents: 2 diff changeset	93
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	94 ##
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	95 ## Although documented, does not appear to be used in the gffread code
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	96 ## #if $seq_info:
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	97 ## -A -s "$seq_info"
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	98 ## #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	99 ##
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	100 ## outputs
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	101 #if $reference_genome.source != 'none':
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	102 #if $reference_genome.fa_outputs and str($reference_genome.fa_outputs) != '':
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	103 #echo ' ' + ' '.join(str($reference_genome.fa_outputs).split(','))
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	104 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	105 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	106 #if $gffs.gff_fmt != 'none':
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	107 #if $gffs.tname:
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	108 -t '$gffs.tname'
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	109 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	110 #if $gffs.gff_fmt == 'gff':
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	111 #if $input.datatype.file_ext == 'gft':
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	112 $gffs.ensembl
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	113 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	114 $gffs.output_cmd
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	115 #elif $gffs.gff_fmt == 'gtf':
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	116 $gffs.output_cmd
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	117 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	118 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	119 ]]>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	120 </command>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	121 <inputs>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	122 <param name="input" type="data" format="gff3,gtf" label="Input GFF3 or GTF feature file"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	123 <!-- filtering -->
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	124 <param name="filtering" type="select" display="checkboxes" multiple="true" label="filters">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	125 <option value="-U">discard single-exon transcripts (-U)</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	126 <option value="-C">coding only: discard mRNAs that have no CDS feature (-C)</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	127 <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>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	128 <option value="-O">process also non-transcript GFF records (by default non-transcript records are ignored) (-O)</option>
5 f312cff50fda "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 35e5b87300fb4e64d6d4eab376012ca9c524a432" iuc parents: 4 diff changeset	129 <option value="--no-pseudo">filter out records matching the 'pseudo' keyword (--no-pseudo)</option>
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	130 </param>
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	131 <conditional name="region">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	132 <param name="region_filter" type="select" label="Filter by genome region">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	133 <option value="none">No</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	134 <option value="filter">Yes</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	135 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	136 <when value="none"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	137 <when value="filter">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	138 <param name="range" type="text" value="" label="Only show transcripts overlapping coordinate range">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	139 <help><![CDATA[
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	140 (-r [['strand']'chr':]'start'..'end') <br>
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	141 examples: <br>
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	142 1000..500000 <br>
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	143 chr1:1000..500000 <br>
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	144 +chr1:1000..500000 <br>
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	145 -chr1:1000..500000
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	146 ]]>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	147 </help>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	148 <validator type="regex">(([+-])?(\w+:))?\d+\.\.\d+</validator>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	149 </param>
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	150 <param name="discard_partial" type="boolean" truevalue="-R" falsevalue="" checked="false"
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	151 label="Discard all transcripts that are not fully contained within the given range" help="(-R)"/>
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	152 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	153 </conditional>
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	154 <param name="maxintron" type="integer" value="" optional="true" min="0" label="Filter out transcipts with large introns"
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	155 help="If set, discard transcripts having an intron larger (-i max_intron)"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	156 <param name="chr_replace" type="data" format="tabular" optional="true" label="Replace reference sequence names" >
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	157 <help><![CDATA[(-m chr_replace) <br>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	158 chr_replace is a reference sequence replacement table consisting of 2 columns: "original_ref_ID" "new_ref_ID"<br>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	159 It is useful for switching between Ensembl and UCSC naming conventions <br>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	160 NOTE: GFF records on reference sequences that are not found among the "original_ref_ID" entries in this file will be filtered out
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	161 ]]>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	162 </help>
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	163 </param>
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	164
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	165 <!-- Although documented, does not appear to be used in the gffread code
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	166 <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">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	167 <help>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	168 (-s seq_info.fsize -A) useful with mRNA/EST/protein mappings <br>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	169 seq_info input file is a 3 column tab-delimited file providing this info for each of the mapped sequences: <br>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	170 "seq-name" "seq-length" "seq-description" <br>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	171 </help>
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	172 </param>
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	173 -->
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	174
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	175 <!-- merging -->
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	176 <conditional name="merging">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	177 <param name="merge_sel" type="select" label="Transcript merging" help="(-M/--merge or --cluster-only)">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	178 <option value="none">none</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	179 <option value="merge">merge: cluster the input transcripts into loci, collapsing matching transcripts</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	180 <option value="cluster">cluster-only: merge but without collapsing matching transcripts</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	181 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	182 <when value="none"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	183 <when value="merge">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	184 <param name="merge_cmd" type="hidden" value="--merge"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	185 <expand macro="merge_opt_sel" />
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	186 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	187 <when value="cluster">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	188 <param name="merge_cmd" type="hidden" value="--cluster-only"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	189 <expand macro="cluster_opt_sel" />
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	190 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	191 </conditional>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	192 <!-- reference sequence file -->
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	193 <!-- Error: -g option is required for options -w, -x, -y, -V, -N, -M -->
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	194 <conditional name="reference_genome">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	195 <param name="source" type="select" label="Reference Genome" help="(-g genome.fasta) NOTE: Required for fasta outputs">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	196 <option value="none">none</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	197 <option value="cached"></option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	198 <option value="history">From your history</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	199 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	200 <when value="none">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	201 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	202 <when value="cached">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	203 <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	204 <options from_data_table="all_fasta"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	205 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	206 <expand macro="ref_filtering_select" />
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	207 <expand macro="fasta_output_select" />
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	208 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	209 <when value="history">
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	210 <param name="genome_fasta" type="data" format="fasta" label="Genome Reference Fasta"/>
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	211 <expand macro="ref_filtering_select" />
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	212 <expand macro="fasta_output_select" />
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	213 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	214 </conditional>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	215
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	216 <!-- outputs -->
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	217 <conditional name="gffs">
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	218 <param name="gff_fmt" type="select" label="Feature File Output" help="(-o output.gff3\|output.gtf)">
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	219 <option value="none">none</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	220 <option value="gff">GFF</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	221 <option value="gtf">GTF</option>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	222 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	223 <when value="none">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	224 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	225 <when value="gff">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	226 <param name="output_cmd" type="hidden" value="-o output.gff3"/>
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	227 <param name="ensembl" type="boolean" truevalue="-L" falsevalue="" checked="false" label="Ensembl GTF to GFF3 conversion" help="(-L)"/>
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	228 <expand macro="trackname" />
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	229 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	230 <when value="gtf">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	231 <param name="output_cmd" type="hidden" value="-T -o output.gtf"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	232 <expand macro="trackname" />
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	233 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	234 </conditional>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	235
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	236 <param name="full_gff_attribute_preservation" type="boolean" truevalue="-F" falsevalue="" checked="false"
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	237 label="full GFF attribute preservation (all attributes are shown)" help="(-F)"/>
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	238 <param name="decode_url" type="boolean" truevalue="-D" falsevalue="" checked="false"
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	239 label="decode url encoded characters within attributes" help="(-D)"/>
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	240 <param name="expose" type="boolean" truevalue="-E" falsevalue="" checked="false"
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	241 label="warn about duplicate transcript IDs and other potential problems with the given GFF/GTF records" help="(-E)"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	242
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	243 </inputs>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	244 <outputs>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	245 <data name="output_gff" format="gff3" metadata_source="input" label="${tool.name} on ${on_string}: gff3" from_work_dir="output.gff3">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	246 <filter>gffs['gff_fmt'] == 'gff'</filter>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	247 </data>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	248 <data name="output_gtf" format="gtf" metadata_source="input" label="${tool.name} on ${on_string}: gtf" from_work_dir="output.gtf">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	249 <filter>gffs['gff_fmt'] == 'gtf'</filter>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	250 </data>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	251 <data name="output_exons" format="fasta" label="${tool.name} on ${on_string}: exons.fa" from_work_dir="exons.fa">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	252 <filter>'fa_outputs' in reference_genome and str(reference_genome['fa_outputs']).find('exons.fa') > 0 </filter>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	253 </data>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	254 <data name="output_cds" format="fasta" label="${tool.name} on ${on_string}: cds.fa" from_work_dir="cds.fa">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	255 <filter>'fa_outputs' in reference_genome and str(reference_genome['fa_outputs']).find('cds.fa') > 0</filter>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	256 </data>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	257 <data name="output_pep" format="fasta" label="${tool.name} on ${on_string}: pep.fa" from_work_dir="pep.fa">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	258 <filter>'fa_outputs' in reference_genome and str(reference_genome['fa_outputs']).find('pep.fa') > 0</filter>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	259 </data>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	260 <data name="output_dupinfo" format="txt" label="${tool.name} on ${on_string}: dupinfo" from_work_dir="dupinfo">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	261 <filter>'merge_options' in merging and merging['merge_options'].find('dupinfo') > 0</filter>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	262 </data>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	263 </outputs>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	264 <tests>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	265 <test>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	266 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	267 <param name="gff_fmt" value="gff"/>
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	268 <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="2" />
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	269 </test>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	270 <test>
3 29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad" devteam parents: 2 diff changeset	271 <param name="input" ftype="gtf" value="ecoli-k12.gff3"/>
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad" devteam parents: 2 diff changeset	272 <param name="gff_fmt" value="gff"/>
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad" devteam parents: 2 diff changeset	273 <param name="full_gff_attribute_preservation" value="-F"/>
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad" devteam parents: 2 diff changeset	274 <output name="output_gff" file="ecoli-k12.processed.gff3" ftype="gff3" lines_diff="2" />
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad" devteam parents: 2 diff changeset	275 </test>
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad" devteam parents: 2 diff changeset	276 <test>
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	277 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
5 f312cff50fda "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 35e5b87300fb4e64d6d4eab376012ca9c524a432" iuc parents: 4 diff changeset	278 <param name="filtering" value="--no-pseudo"/>
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	279 <param name="gff_fmt" value="gtf"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	280 <output name="output_gtf">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	281 <assert_contents>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	282 <not_has_text text="pseudo" />
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	283 </assert_contents>
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	284 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	285 </test>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	286 <test>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	287 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	288 <param name="region_filter" value="filter"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	289 <param name="range" value="19:496500..504965"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	290 <param name="gff_fmt" value="gtf"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	291 <output name="output_gtf">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	292 <assert_contents>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	293 <has_text text="ENST00000587541" />
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	294 <has_text text="ENST00000382683" />
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	295 </assert_contents>
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	296 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	297 </test>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	298 <test>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	299 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	300 <param name="region_filter" value="filter"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	301 <param name="range" value="19:496500..504965"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	302 <param name="discard_partial" value="true"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	303 <param name="gff_fmt" value="gtf"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	304 <output name="output_gtf">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	305 <assert_contents>
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	306 <not_has_text text="ENST00000587541" />
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	307 <has_text text="ENST00000382683" />
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	308 </assert_contents>
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	309 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	310 </test>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	311 <test>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	312 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	313 <param name="filtering" value="-C"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	314 <param name="region_filter" value="filter"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	315 <param name="range" value="19:496500..504965"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	316 <param name="gff_fmt" value="gtf"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	317 <output name="output_gtf">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	318 <assert_contents>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	319 <not_has_text text="ENST00000587541" />
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	320 <has_text text="ENST00000382683" />
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	321 </assert_contents>
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	322 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	323 </test>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	324 <test>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	325 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	326 <param name="source" value="history"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	327 <param name="genome_fasta" ftype="fasta" value="Homo_sapiens.GRCh37.71.dna.chromosome.19.fa"/>
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	328 <param name="fa_outputs" value="-w exons.fa,-x cds.fa,-y pep.fa"/>
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	329 <param name="region_filter" value="filter"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	330 <param name="range" value="19:496500..504965"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	331 <param name="gff_fmt" value="gtf"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	332 <output name="output_gtf">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	333 <assert_contents>
4 0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	334 <has_text text="ENST00000587541" />
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	335 <has_text text="ENST00000382683" />
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	336 </assert_contents>
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	337 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	338 <output name="output_exons">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	339 <assert_contents>
4 0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	340 <has_text text="ENST00000346144 CDS=47-934" />
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	341 <has_text text="CTATTTAAGCGGCTTCCCCGCGGCCTCGGGACAGAGGGGACTGAGCATGGATTTCGGACTGGCCCTCCTG" />
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	342 </assert_contents>
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	343 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	344 <output name="output_cds">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	345 <assert_contents>
4 0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	346 <has_text text="ENST00000346144" />
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	347 <has_text text="ATGGATTTCGGACTGGCCCTCCTGCTGGCGGGGCTTCTGGGGCTCCTCCTCGGCCAGTCCCTCCAGGTGA" />
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	348 </assert_contents>
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	349 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	350 <output name="output_pep">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	351 <assert_contents>
4 0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	352 <has_text text="ENST00000346144" />
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	353 <has_text text="MDFGLALLLAGLLGLLLGQSLQVKPLQVEPPEPVVAVALGASRQLTCRLACADRGASVQWRGLDTSLGAV" />
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	354 </assert_contents>
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	355 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	356 </test>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	357
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	358 </tests>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	359 <help>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	360 <![CDATA[
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	361 gffread Filters and/or converts GFF3/GTF2 records
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	362
4 0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	363 The gffread command is documented with the stringtie_ package.
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	364
4 0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	365 .. _stringtie: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	366
4 0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	367
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	368 gffread v0.11.4. Usage: ::
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	369
4 0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	370 gffread <input_gff> [-g <genomic_seqs_fasta> \| <dir>][-s <seq_info.fsize>]
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	371 [-o <outfile>] [-t <trackname>] [-r [[<strand>]<chr>:]<start>..<end> [-R]]
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	372 [-CTVNJMKQAFPGUBHZWTOLE] [-w <exons.fa>] [-x <cds.fa>] [-y <tr_cds.fa>]
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	373 [-i <maxintron>] [--bed] [--table <attrlist>] [--sort-by <refseq_list.txt>]
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	374
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	375 Filter, convert or cluster GFF/GTF/BED records, extract the sequence of
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	376 transcripts (exon or CDS) and more.
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	377 By default (i.e. without -O) only transcripts are processed, discarding any
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	378 other non-transcript features. Default output is a simplified GFF3 with only
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	379 the basic attributes.
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	380
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	381 <input_gff> is a GFF file, use '-' for stdin
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	382
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	383 Options:
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	384
4 0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	385 -i discard transcripts having an intron larger than <maxintron>
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	386 -l discard transcripts shorter than <minlen> bases
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	387 -r only show transcripts overlapping coordinate range <start>..<end>
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	388 (on chromosome/contig <chr>, strand <strand> if provided)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	389 -R for -r option, discard all transcripts that are not fully
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	390 contained within the given range
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	391 -U discard single-exon transcripts
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	392 -C coding only: discard mRNAs that have no CDS features
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	393 --nc non-coding only: discard mRNAs that have CDS features
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	394 --ignore-locus : discard locus features and attributes found in the input
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	395 -A use the description field from <seq_info.fsize> and add it
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	396 as the value for a 'descr' attribute to the GFF record
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	397 -s <seq_info.fsize> is a tab-delimited file providing this info
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	398 for each of the mapped sequences:
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	399 <seq-name> <seq-length> <seq-description>
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	400 (useful for -A option with mRNA/EST/protein mappings)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	401
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	402 Sorting: (by default, chromosomes are kept in the order they were found)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	403 --sort-alpha : chromosomes (reference sequences) are sorted alphabetically
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	404 --sort-by : sort the reference sequences by the order in which their
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	405 names are given in the <refseq.lst> file
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	406
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	407 Misc options:
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	408 -F preserve all GFF attributes (for non-exon features)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	409 --keep-exon-attrs : for -F option, do not attempt to reduce redundant
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	410 exon/CDS attributes
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	411 -G do not keep exon attributes, move them to the transcript feature
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	412 (for GFF3 output)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	413 --keep-genes : in transcript-only mode (default), also preserve gene records
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	414 --keep-comments: for GFF3 input/output, try to preserve comments
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	415 -O process other non-transcript GFF records (by default non-transcript
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	416 records are ignored)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	417 -V discard any mRNAs with CDS having in-frame stop codons (requires -g)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	418 -H for -V option, check and adjust the starting CDS phase
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	419 if the original phase leads to a translation with an
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	420 in-frame stop codon
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	421 -B for -V option, single-exon transcripts are also checked on the
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	422 opposite strand (requires -g)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	423 -P add transcript level GFF attributes about the coding status of each
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	424 transcript, including partialness or in-frame stop codons (requires -g)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	425 --add-hasCDS : add a "hasCDS" attribute with value "true" for transcripts
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	426 that have CDS features
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	427 --adj-stop stop codon adjustment: enables -P and performs automatic
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	428 adjustment of the CDS stop coordinate if premature or downstream
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	429 -N discard multi-exon mRNAs that have any intron with a non-canonical
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	430 splice site consensus (i.e. not GT-AG, GC-AG or AT-AC)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	431 -J discard any mRNAs that either lack initial START codon
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	432 or the terminal STOP codon, or have an in-frame stop codon
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	433 (i.e. only print mRNAs with a complete CDS)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	434 --no-pseudo: filter out records matching the 'pseudo' keyword
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	435 --in-bed: input should be parsed as BED format (automatic if the input
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	436 filename ends with .bed*)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	437 --in-tlf: input GFF-like one-line-per-transcript format without exon/CDS
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	438 features (see --tlf option below); automatic if the input
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	439 filename ends with .tlf)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	440
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	441 Clustering:
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	442 -M/--merge : cluster the input transcripts into loci, discarding
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	443 "duplicated" transcripts (those with the same exact introns
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	444 and fully contained or equal boundaries)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	445 -d <dupinfo> : for -M option, write duplication info to file <dupinfo>
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	446 --cluster-only: same as -M/--merge but without discarding any of the
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	447 "duplicate" transcripts, only create "locus" features
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	448 -K for -M option: also discard as redundant the shorter, fully contained
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	449 transcripts (intron chains matching a part of the container)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	450 -Q for -M option, no longer require boundary containment when assessing
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	451 redundancy (can be combined with -K); only introns have to match for
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	452 multi-exon transcripts, and >=80% overlap for single-exon transcripts
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	453 -Y for -M option, enforce -Q but also discard overlapping single-exon
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	454 transcripts, even on the opposite strand (can be combined with -K)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	455
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	456 Output options:
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	457 --force-exons: make sure that the lowest level GFF features are considered
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	458 "exon" features
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	459 --gene2exon: for single-line genes not parenting any transcripts, add an
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	460 exon feature spanning the entire gene (treat it as a transcript)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	461 --t-adopt: try to find a parent gene overlapping/containing a transcript
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	462 that does not have any explicit gene Parent
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	463 -D decode url encoded characters within attributes
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	464 -Z merge very close exons into a single exon (when intron size<4)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	465 -g full path to a multi-fasta file with the genomic sequences
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	466 for all input mappings, OR a directory with single-fasta files
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	467 (one per genomic sequence, with file names matching sequence names)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	468 -w write a fasta file with spliced exons for each GFF transcript
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	469 -x write a fasta file with spliced CDS for each GFF transcript
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	470 -y write a protein fasta file with the translation of CDS for each record
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	471 -W for -w and -x options, write in the FASTA defline the exon
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	472 coordinates projected onto the spliced sequence;
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	473 for -y option, write transcript attributes in the FASTA defline
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	474 -S for -y option, use '*' instead of '.' as stop codon translation
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	475 -L Ensembl GTF to GFF3 conversion (implies -F; should be used with -m)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	476 -m <chr_replace> is a name mapping table for converting reference
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	477 sequence names, having this 2-column format:
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	478 <original_ref_ID> <new_ref_ID>
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	479 WARNING: all GFF records on reference sequences whose original IDs
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	480 are not found in the 1st column of this table will be discarded!
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	481 -t use <trackname> in the 2nd column of each GFF/GTF output line
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	482 -o write the records into <outfile> instead of stdout
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	483 -T main output will be GTF instead of GFF3
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	484 --bed output records in BED format instead of default GFF3
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	485 --tlf output "transcript line format" which is like GFF
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	486 but exons, CDS features and related data are stored as GFF
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	487 attributes in the transcript feature line, like this:
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	488 exoncount=N;exons=<exons>;CDSphase=<N>;CDS=<CDScoords>
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	489 <exons> is a comma-delimited list of exon_start-exon_end coordinates;
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	490 <CDScoords> is CDS_start:CDS_end coordinates or a list like <exons>
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	491 --table output a simple tab delimited format instead of GFF, with columns
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	492 having the values of GFF attributes given in <attrlist>; special
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	493 pseudo-attributes (prefixed by @) are recognized:
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	494 @chr, @start, @end, @strand, @numexons, @exons, @cds, @covlen, @cdslen
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	495 -v,-E expose (warn about) duplicate transcript IDs and other potential
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4" iuc parents: 3 diff changeset	496 problems with the given GFF/GTF records
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	497 ]]>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	498 </help>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	499 <citations>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	500 <citation type="doi">10.1038/nbt.1621</citation>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	501 </citations>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	502 </tool>

Mercurial > repos > devteam > gffread

annotate gffread.xml @ 5:f312cff50fda draft