gffread: gffread.xml annotate

annotate gffread.xml @ 3:29769f789b8f draft

"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"

author	devteam
date	Tue, 01 Oct 2019 12:19:52 -0400
parents	6562753c6bdc
children	0cf496c45054

rev	line source
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	1 <tool id="gffread" name="gffread" version="@VERSION@.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	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>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	4 <import>cuff_macros.xml</import>
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>
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	50 <expand macro="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	51 <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	52 <![CDATA[
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	53 #if $reference_genome.source == 'history':
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	54 ln -s '$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	55 #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	56 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	57 #if $reference_genome.source == 'cached':
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	58 -g '${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	59 #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	60 #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	61 #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	62 #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	63 -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	64 #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	65 #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	66 #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	67 #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	68 #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	69 #echo " "
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	70 #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	71 #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	72 #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	73 -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	74 #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	75 #if $region.region_filter == 'filter':
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	76 -r '$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	77 #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	78 #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	79 $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	80 #if $merging.merge_options:
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	81 #echo ' '.join(str($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	82 #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	83 #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	84 #if $chr_replace:
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	85 -m '$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	86 #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	87
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad" devteam parents: 2 diff changeset	88 $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	89 $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	90 $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	91
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	92 ##
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	93 ## 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	94 ## #if $seq_info:
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	95 ## -A -s "$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	96 ## #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	97 ##
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	98 ## outputs
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	99 #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	100 #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	101 #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	102 #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	103 #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	104 #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	105 #if $gffs.tname:
1 96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	106 -t '$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	107 #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	108 #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	109 #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	110 $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	111 #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	112 $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	113 #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	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 #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	116 #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	117 ]]>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	118 </command>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	119 <inputs>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	120 <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	121 <!-- filtering -->
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="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	123 <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	124 <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	125 <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	126 <option value="-O">process also non-transcript GFF records (by default non-transcript records are ignored) (-O)</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="--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	128 </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	129 <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	130 <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	131 <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	132 <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	133 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	134 <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	135 <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	136 <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	137 <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	138 (-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	139 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	140 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	141 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	142 +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	143 -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	144 ]]>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	145 </help>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	146 <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	147 </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	148 <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	149 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	150 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	151 </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	152 <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	153 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	154 <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	155 <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	156 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	157 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	158 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	159 ]]>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	160 </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	161 </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	162
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	163 <!-- 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	164 <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	165 <help>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	166 (-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	167 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	168 "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	169 </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	170 </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	171 -->
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	172
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	173 <!-- merging -->
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	174 <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	175 <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	176 <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	177 <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	178 <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	179 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	180 <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	181 <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	182 <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	183 <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	184 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	185 <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	186 <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	187 <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	188 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	189 </conditional>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	190 <!-- 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	191 <!-- 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	192 <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	193 <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	194 <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	195 <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	196 <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	197 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	198 <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	199 </when>
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="cached">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	201 <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	202 <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	203 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	204 <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	205 <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	206 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	207 <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	208 <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	209 <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	210 <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	211 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	212 </conditional>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	213
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	214 <!-- outputs -->
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	215 <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	216 <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	217 <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	218 <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	219 <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	220 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	221 <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	222 </when>
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="gff">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	224 <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	225 <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	226 <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	227 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	228 <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	229 <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	230 <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	231 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	232 </conditional>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	233
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	234 <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	235 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	236 <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	237 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	238 <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	239 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	240
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	241 </inputs>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	242 <outputs>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	243 <data name="output_gff" format="gff3" metadata_source="input" label="${tool.name} on ${on_string}: gff3" from_work_dir="output.gff3">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	244 <filter>gffs['gff_fmt'] == 'gff'</filter>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	245 </data>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	246 <data name="output_gtf" format="gtf" metadata_source="input" label="${tool.name} on ${on_string}: gtf" from_work_dir="output.gtf">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	247 <filter>gffs['gff_fmt'] == 'gtf'</filter>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	248 </data>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	249 <data name="output_exons" format="fasta" label="${tool.name} on ${on_string}: exons.fa" from_work_dir="exons.fa">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	250 <filter>'fa_outputs' in reference_genome and str(reference_genome['fa_outputs']).find('exons.fa') > 0 </filter>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	251 </data>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	252 <data name="output_cds" format="fasta" label="${tool.name} on ${on_string}: cds.fa" from_work_dir="cds.fa">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	253 <filter>'fa_outputs' in reference_genome and str(reference_genome['fa_outputs']).find('cds.fa') > 0</filter>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	254 </data>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	255 <data name="output_pep" format="fasta" label="${tool.name} on ${on_string}: pep.fa" from_work_dir="pep.fa">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	256 <filter>'fa_outputs' in reference_genome and str(reference_genome['fa_outputs']).find('pep.fa') > 0</filter>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	257 </data>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	258 <data name="output_dupinfo" format="txt" label="${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	259 <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	260 </data>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	261 </outputs>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	262 <tests>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	263 <test>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	264 <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	265 <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	266 <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	267 </test>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	268
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>
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	270 <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	271 <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	272 <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	273 <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	274 </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	275
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"/>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	278 <param name="filtering" value="--no-pseudo"/>
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
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	287 <test>
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="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	289 <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	290 <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	291 <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	292 <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	293 <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	294 <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	295 <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	296 </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	297 </output>
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
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	300 <test>
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="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	302 <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	303 <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	304 <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	305 <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	306 <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	307 <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	308 <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	309 <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	310 </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	311 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	312 </test>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	313
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	314 <test>
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="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	316 <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	317 <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	318 <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	319 <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	320 <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	321 <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	322 <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	323 <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	324 </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	325 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	326 </test>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	327
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	328 <test>
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="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	330 <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	331 <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	332 <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	333 <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	334 <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	335 <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	336 <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	337 <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	338 <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	339 <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	340 </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	341 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	342 <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	343 <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	344 <has_text text="ENST00000346144 gene=MADCAM1 CDS=47-932" />
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	345 <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	346 </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	347 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	348 <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	349 <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	350 <has_text text="ENST00000346144 gene=MADCAM1" />
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	351 <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	352 </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	353 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	354 <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	355 <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	356 <has_text text="ENST00000346144 gene=MADCAM1" />
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	357 <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	358 </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	359 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	360 </test>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	361
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	362 </tests>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	363 <help>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	364 <![CDATA[
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	365 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	366
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	367 The gffread command is distributed with the cufflinks_ package.
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	368
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	369 .. _cufflinks: http://cole-trapnell-lab.github.io/cufflinks/
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	370
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	371 Usage: ::
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	372
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	373 gffread "input_gff" [-g "genomic_seqs_fasta" \| "dir"][-s "seq_info.fsize"]
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	374 [-o "outfile.gff"] [-t "tname"] [-r [["strand"]"chr":]"start".."end" [-R]]
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	375 [-CTVNJMKQAFGUBHZWTOLE] [-w "exons.fa"] [-x "cds.fa"] [-y "tr_cds.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	376 [-i "maxintron"]
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	377
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	378 Options: ::
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	379
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	380 -g full path to a multi-fasta file with the genomic sequences
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	381 for all input mappings, OR a directory with single-fasta files
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	382 (one per genomic sequence, with file names matching 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	383 -s <seq_info.fsize> is a tab-delimited file providing this info
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	384 for each of the mapped sequences:
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	385 <seq-name> <seq-length> <seq-description>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	386 (useful for -A option with mRNA/EST/protein mappings)
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	387 -i discard transcripts having an intron larger than <maxintron>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	388 -r only show transcripts overlapping coordinate range <start>..<end>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	389 (on chromosome/contig <chr>, strand <strand> if provided)
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	390 -R for -r option, discard all transcripts that are not fully
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	391 contained within the given range
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	392 -U discard single-exon transcripts
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	393 -C coding only: discard mRNAs that have no CDS feature
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	394 -F full GFF attribute preservation (all attributes are shown)
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	395 -G only parse additional exon attributes from the first exon
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	396 and move them to the mRNA level (useful for GTF input)
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	397 -A use the description field from <seq_info.fsize> and add it
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	398 as the value for a 'descr' attribute to the GFF record
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	399
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	400 -O process also non-transcript GFF records (by default non-transcript
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	401 records are ignored)
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	402 -V discard any mRNAs with CDS having in-frame stop codons
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	403 -H for -V option, check and adjust the starting CDS phase
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	404 if the original phase leads to a translation with an
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	405 in-frame stop codon
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	406 -B for -V option, single-exon transcripts are also checked on the
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	407 opposite strand
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	408 -N discard multi-exon mRNAs that have any intron with a non-canonical
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	409 splice site consensus (i.e. not GT-AG, GC-AG or AT-AC)
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	410 -J discard any mRNAs that either lack initial START codon
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	411 or the terminal STOP codon, or have an in-frame stop codon
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	412 (only print mRNAs with a fulll, valid CDS)
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	413 --no-pseudo: filter out records matching the 'pseudo' keyword
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	414
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	415 -M/--merge : cluster the input transcripts into loci, collapsing matching
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	416 transcripts (those with the same exact introns and fully contained)
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	417 -d <dupinfo> : for -M option, write collapsing info to file <dupinfo>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	418 --cluster-only: same as --merge but without collapsing matching transcripts
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	419 -K for -M option: also collapse shorter, fully contained transcripts
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	420 with fewer introns than the container
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	421 -Q for -M option, remove the containment restriction:
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	422 (multi-exon transcripts will be collapsed if just their introns match,
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	423 while single-exon transcripts can partially overlap (80%))
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	424
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 0 diff changeset	425 --force-exons: make sure that the lowest level GFF features are printed as
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	426 "exon" features
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	427 -E expose (warn about) duplicate transcript IDs and other potential
0 baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	428 problems with the given GFF/GTF records
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	429 -D decode url encoded characters within attributes
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	430 -Z merge close exons into a single exon (for intron size<4)
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	431 -w write a fasta file with spliced exons for each GFF transcript
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	432 -x write a fasta file with spliced CDS for each GFF transcript
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	433 -W for -w and -x options, also write for each fasta record the exon
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	434 coordinates projected onto the spliced sequence
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	435 -y write a protein fasta file with the translation of CDS for each record
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	436 -L Ensembl GTF to GFF3 conversion (implies -F; should be used with -m)
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	437 -m <chr_replace> is a reference (genomic) sequence replacement table with
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	438 this format:
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	439 <original_ref_ID> <new_ref_ID>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	440 For example from UCSC naming to Ensembl naming:
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	441 chr1 1
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	442 chr2 2
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	443 GFF records on reference sequences that are not found among the
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	444 <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	445 -o the "filtered" GFF records will be written to <outfile.gff>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	446 (use -o- for printing to stdout)
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	447 -t use <trackname> in the second column of each GFF output line
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	448 -T -o option will output GTF format instead of GFF3
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	449
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	450 ]]>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	451 </help>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	452 <citations>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	453 <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	454 </citations>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	455 </tool>

Mercurial > repos > devteam > gffread

annotate gffread.xml @ 3:29769f789b8f draft