Mercurial > repos > devteam > gffread

annotate gffread.xml @ 7:9c298cab341d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
author iuc
date Sat, 25 Sep 2021 15:38:01 +0000
parents bba49324f2fa
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
1 <tool id="gffread" name="gffread" version="@GALAXY_TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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>
6
bba49324f2fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 5
diff changeset
3 <xrefs>
bba49324f2fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 5
diff changeset
4 <xref type="bio.tools">gffread</xref>
bba49324f2fa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 5
diff changeset
5 </xrefs>
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
6 <macros>
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
7 <!-- the version of this tool must not be lowered since in the past 2.x was used
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
8 lets use small increments and hope that gffread catches up one day -->
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
9 <token name="@GALAXY_TOOL_VERSION@">2.2.1.3</token>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
10 <token name="@TOOL_VERSION@">0.12.7</token>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
11 <token name="@VERSION_SUFFIX@">0</token>
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
12 <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
13 <param name="fa_outputs" type="select" display="checkboxes" multiple="true" label="Select fasta outputs">
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
14 <option value="-w exons.fa">fasta file with spliced exons for each GFF transcript (-w)</option>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
15 <option value="-x cds.fa">fasta file with spliced CDS for each GFF transcript (-x)</option>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
16 <option value="-y pep.fa">protein fasta file with the translation of CDS for each record (-y)</option>
0
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="-W">for each fasta: record the exon coordinates projected onto the spliced sequence (-W)</option>
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
18 <option value="-S">for protein fasta: use '*' instead of '.' as stop codon translation (-S)</option>
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
19 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
20 </xml>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
21 <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
22 <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
23 <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
24 <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
25 <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
26 <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
27 <!-- 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
28 <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
29 -->
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
30 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
31 </xml>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
32 <xml name="trackname">
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
33 <param argument="-t" name="tname" type="text" value="" optional="true" label="Trackname to use in the second column of each GFF output line" help="">
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
34 <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
35 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
36 </xml>
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 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
38 <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
39 <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>
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
40 <option value="-d dupinfo">output collapsing info (-d)</option>
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
41 </xml>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
42 <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
43 <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
44 <option value="-Z">merge close exons into a single exon (for intron size &lt; 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
45 </xml>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
46 <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
47 <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
48 <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
49 <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
50 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
51 </xml>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
52 <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
53 <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
54 <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
55 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
56 </xml>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
57 </macros>
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
58 <requirements>
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
59 <requirement type="package" version="@TOOL_VERSION@">gffread</requirement>
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
60 </requirements>
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
61 <version_command>gffread --version</version_command>
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
62 <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
63 <![CDATA[
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 $reference_genome.source == 'history':
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 0
diff changeset
65 ln -s '$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
66 #end if
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
67
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
68 gffread '$input'
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
69 #if $input.ext.startswith("bed")
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
70 --in-bed
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
71 #end if
0
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 $reference_genome.source == 'cached':
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 0
diff changeset
73 -g '${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
74 #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
75 #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
76 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
77 #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
78 -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
79 #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
80 #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
81 #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
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 #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
84 #echo " "
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
85 #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
86 #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
87 #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
88 -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
89 #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
90 #if $region.region_filter == 'filter':
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 0
diff changeset
91 -r '$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
92 #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
93 #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
94 $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
95 #if $merging.merge_options:
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
96 #echo ' '.join(str($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
97 #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
98 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
99 #if $chr_replace:
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 0
diff changeset
100 -m '$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
101 #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
102
29769f789b8f "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 1203e3cccd40108df09ab2286d25aa7e638e9cad"
devteam
parents: 2
diff changeset
103 $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
104 $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
105 $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
106
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 ##
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
108 ## 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
109 ## #if $seq_info:
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
110 ## -A -s "$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
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 ##
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
113 ## outputs
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
114 #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
115 #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
116 #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
117 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
118 #end if
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
119 #if $gffs.gff_fmt != 'none':
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
120 #if $gffs.gff_fmt != 'bed' and $gffs.tname:
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 0
diff changeset
121 -t '$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
122 #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
123 #if $gffs.gff_fmt == 'gff':
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
124 ## TODO bug 'gft' -> '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
125 #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
126 $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
127 #end if
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
128 #end if
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
129 #if $gffs.gff_fmt == 'gtf'
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
130 -T
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
131 #elif $gffs.gff_fmt == 'bed'
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
132 --bed
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
133 #end if
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
134 -o output.$gffs.gff_fmt
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
135 #end if
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
136
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
137 ## Missing options
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
138 ##
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
139 ## --ids
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
140 ## --nids
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
141 ## -l
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
142 ## --jmatch
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
143 ## --nc
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
144 ## --ignore-locus
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
145 ## -A -s (see above)
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
146 ## --sort-alpha : chromosomes (reference sequences) are sorted alphabetically
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
147 ## --sort-by : sort the reference sequences by the order in which their
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
148 ## names are given in the <refseq.lst> file
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
149 ## Misc
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
150 ## --keep-exon-attrs : for -F option, do not attempt to reduce redundant
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
151 ## --attrs
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
152 ## --keep-genes : in transcript-only mode (default), also preserve gene records
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
153 ## --keep-comments: for GFF3 input/output, try to preserve comments
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
154 ## -B (see above)
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
155 ## -P
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
156 ## --add-hasCDS : add a "hasCDS" attribute with value "true" for transcripts
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
157 ## that have CDS features
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
158 ## --adj-stop stop codon adjustment: enables -P and performs automatic
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
159 ## adjustment of the CDS stop coordinate if premature or downstream
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
160
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
161 ## --in-tlf: input GFF-like one-line-per-transcript format without exon/CDS
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
162 ## features (see --tlf option below); automatic if the input
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
163 ## filename ends with .tlf)
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
164 ## --stream: fast processing of input GFF/BED transcripts as they are received
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
165 ## ((no sorting, exons must be grouped by transcript in the input data)
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
166
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
167 ## Clustering
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
168
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
169 ## -Y
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
170
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
171 ## Output
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
172
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
173 ## --gene2exon
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
174 ## --t-adopt
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
175 ## -j
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
176 ## --w-add
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
177 ## --w-nocds
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
178 ]]>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
179 </command>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
180 <inputs>
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
181 <param name="input" type="data" format="bed,gff3,gtf" label="Input BED, GFF3 or GTF feature file"/>
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
182 <!-- filtering -->
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
183 <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
184 <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
185 <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
186 <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
187 <option value="-O">process also non-transcript GFF records (by default non-transcript records are ignored) (-O)</option>
5
f312cff50fda "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 35e5b87300fb4e64d6d4eab376012ca9c524a432"
iuc
parents: 4
diff changeset
188 <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
189 </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
190 <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
191 <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
192 <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
193 <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
194 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
195 <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
196 <when value="filter">
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
197 <param argument="-r" name="range" type="text" value="" label="Only show transcripts overlapping coordinate range">
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
198 <help><![CDATA[
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
199 [['strand']'chr':]'start'..'end' <br>
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
200 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
201 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
202 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
203 +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
204 -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
205 ]]>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
206 </help>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
207 <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
208 </param>
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
209 <param argument="-R" name="discard_partial" type="boolean" truevalue="-R" falsevalue="" checked="false"
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
210 label="Discard all transcripts that are not fully contained within the given range" help=""/>
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
211 </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>
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
213 <param argument="-i" name="maxintron" type="integer" value="" optional="true" min="0" label="Filter out transcipts with large introns"
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
214 help="If set, discard transcripts having an intron larger"/>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
215 <param argument="-m" name="chr_replace" type="data" format="tabular" optional="true" label="Replace reference sequence names" >
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
216 <help><![CDATA[
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 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
218 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
219 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
220 ]]>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
221 </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
222 </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
223
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
224 <!-- 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
225 <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
226 <help>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
227 (-s seq_info.fsize -A) useful with mRNA/EST/protein mappings &lt;br&gt;
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
228 seq_info input file is a 3 column tab-delimited file providing this info for each of the mapped sequences: &lt;br&gt;
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
229 "seq-name" "seq-length" "seq-description" &lt;br&gt;
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
230 </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
231 </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
232 -->
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
233
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
234 <!-- merging -->
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
235 <conditional name="merging">
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
236 <param name="merge_sel" type="select" label="Transcript merging" help="">
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 <option value="none">none</option>
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
238 <option value="merge">merge: cluster the input transcripts into loci, collapsing matching transcripts (--merge)</option>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
239 <option value="cluster">cluster-only: merge but without collapsing matching transcripts (--cluster-only)</option>
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
240 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
241 <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
242 <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
243 <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
244 <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
245 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
246 <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
247 <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
248 <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
249 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
250 </conditional>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
251 <!-- 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
252 <!-- 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
253 <conditional name="reference_genome">
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
254 <param name="source" type="select" label="Reference Genome" help="NOTE: Required for fasta outputs">
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
255 <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
256 <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
257 <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
258 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
259 <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
260 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
261 <when value="cached">
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
262 <param argument="-g" name="fasta_indexes" type="select" label="Source FASTA Sequence">
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
263 <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
264 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
265 <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
266 <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
267 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
268 <when value="history">
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
269 <param argument="-g" 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
270 <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
271 <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
272 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
273 </conditional>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
274
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
275 <!-- outputs -->
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
276 <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
277 <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
278 <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
279 <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
280 <option value="gtf">GTF</option>
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
281 <option value="bed">BED</option>
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
282 </param>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
283 <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
284 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
285 <when value="gff">
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
286 <param argument="-L" name="ensembl" type="boolean" truevalue="-L" falsevalue="" checked="false" label="Ensembl GTF to GFF3 conversion" help=""/>
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
287 <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
288 </when>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
289 <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
290 <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
291 </when>
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
292 <when value="bed">
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
293 </when>
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
294 </conditional>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
295
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
296 <param argument="-F" name="full_gff_attribute_preservation" type="boolean" truevalue="-F" falsevalue="" checked="false"
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
297 label="full GFF attribute preservation (all attributes are shown)" help=""/>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
298 <param argument="-D" name="decode_url" type="boolean" truevalue="-D" falsevalue="" checked="false"
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
299 label="decode url encoded characters within attributes" help=""/>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
300 <param argument="-E" name="expose" type="boolean" truevalue="-E" falsevalue="" checked="false"
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
301 label="warn about duplicate transcript IDs and other potential problems with the given GFF/GTF records" help=""/>
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
302
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
303 </inputs>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
304 <outputs>
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
305 <data name="output_gff" format="gff3" metadata_source="input" label="${tool.name} on ${on_string}: gff3" from_work_dir="output.gff">
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
306 <filter>gffs['gff_fmt'] == 'gff'</filter>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
307 </data>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
308 <data name="output_gtf" format="gtf" metadata_source="input" label="${tool.name} on ${on_string}: gtf" from_work_dir="output.gtf">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
309 <filter>gffs['gff_fmt'] == 'gtf'</filter>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
310 </data>
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
311 <data name="output_bed" format="bed" metadata_source="input" label="${tool.name} on ${on_string}: bed" from_work_dir="output.bed">
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
312 <filter>gffs['gff_fmt'] == 'bed'</filter>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
313 </data>
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
314 <data name="output_exons" format="fasta" label="${tool.name} on ${on_string}: exons.fa" from_work_dir="exons.fa">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
315 <filter>'fa_outputs' in reference_genome and str(reference_genome['fa_outputs']).find('exons.fa') > 0 </filter>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
316 </data>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
317 <data name="output_cds" format="fasta" label="${tool.name} on ${on_string}: cds.fa" from_work_dir="cds.fa">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
318 <filter>'fa_outputs' in reference_genome and str(reference_genome['fa_outputs']).find('cds.fa') > 0</filter>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
319 </data>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
320 <data name="output_pep" format="fasta" label="${tool.name} on ${on_string}: pep.fa" from_work_dir="pep.fa">
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
321 <filter>'fa_outputs' in reference_genome and str(reference_genome['fa_outputs']).find('pep.fa') > 0</filter>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
322 </data>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
323 <data name="output_dupinfo" format="txt" label="${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
324 <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
325 </data>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
326 </outputs>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
327 <tests>
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
328 <test expect_num_outputs="1">
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
329 <param name="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="gff_fmt" value="gff"/>
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
331 <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="4" />
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
332 </test>
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
333 <test expect_num_outputs="1">
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
334 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
335 <param name="gff_fmt" value="gff"/>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
336 <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="4" />
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
337 </test>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
338 <test expect_num_outputs="1">
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
339 <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
340 <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
341 <param name="full_gff_attribute_preservation" value="-F"/>
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
342 <output name="output_gff" file="ecoli-k12.processed.gff3" ftype="gff3" lines_diff="4" />
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
343 </test>
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
344 <!-- bed output -->
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
345 <test expect_num_outputs="1">
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
346 <param name="input" ftype="gff3" value="Homo_sapiens.GRCh37_19.71.gff3"/>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
347 <param name="gff_fmt" value="bed"/>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
348 <output name="output_bed" ftype="bed">
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
349 <assert_contents>
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
350 <has_n_lines n="42"/>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
351 <has_n_columns n="13"/>
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 </test>
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
355 <!-- bed input and test tname -->
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
356 <test expect_num_outputs="1">
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
357 <param name="input" ftype="bed" value="Homo_sapiens.GRCh37_19.71.bed"/>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
358 <param name="gff_fmt" value="gff"/>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
359 <param name="tname" value="track name"/>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
360 <output name="output_bed" ftype="gff3">
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
361 <assert_contents>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
362 <has_n_lines n="388"/>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
363 <!-- this will work with https://github.com/galaxyproject/galaxy/pull/12528 -->
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
364 <!-- <has_n_columns n="9" comment="#"/> -->
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
365 <has_text text="track name"/>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
366 </assert_contents>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
367 </output>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
368 </test>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
369 <test expect_num_outputs="1">
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
370 <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
371 <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
372 <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
373 <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
374 <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
375 <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
376 <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
377 <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
378 </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
379 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
380 </test>
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
381 <test expect_num_outputs="1">
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
382 <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
383 <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
384 <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
385 <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
386 <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
387 <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
388 <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
389 <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
390 <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
391 </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
392 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
393 </test>
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
394 <test expect_num_outputs="1">
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
395 <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
396 <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
397 <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
398 <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
399 <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
400 <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
401 <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
402 <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
403 <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
404 </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
405 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
406 </test>
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
407 <test expect_num_outputs="4">
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
408 <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
409 <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
410 <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
411 <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
412 <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
413 <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
414 <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
415 <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
416 <assert_contents>
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
417 <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
418 <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
419 </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
420 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
421 <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
422 <assert_contents>
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
423 <has_text text="ENST00000346144 CDS=47-934" />
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
424 <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
425 </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
426 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
427 <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
428 <assert_contents>
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
429 <has_text text="ENST00000346144" />
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
430 <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
431 </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
432 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
433 <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
434 <assert_contents>
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
435 <has_text text="ENST00000346144" />
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
436 <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
437 </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
438 </output>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
439 </test>
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
440 <test expect_num_outputs="1">
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
441 <param name="input" ftype="gtf" value="stop_codons.gtf"/>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
442 <param name="source" value="history"/>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
443 <param name="genome_fasta" ftype="fasta" value="Homo_sapiens.GRCh37.71.dna.chromosome.19.fa"/>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
444 <param name="fa_outputs" value="-y pep.fa,-S"/>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
445 <output name="output_pep">
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
446 <assert_contents>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
447 <has_text text="ENST00000269812" />
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
448 <has_text text="PLRGLHPRV*LQTPLERCPCWPPAGGTGGCPHCLLHLRLLQSPTPTALSEGGGAGTEAQPVTDVDPGRG*" />
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
449 </assert_contents>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
450 </output>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
451 </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
452 </tests>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
453 <help>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
454 <![CDATA[
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
455 **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
456
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
457 The gffread command is documented with the stringtie_ package.
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
458
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
459 .. _stringtie: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread
1
96c4d0e18546 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
devteam
parents: 0
diff changeset
460
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
461 gffread v0.12.7. Usage: ::
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
462
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
463 gffread [-g <genomic_seqs_fasta> | <dir>] [-s <seq_info.fsize>]
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
464 [-o <outfile>] [-t <trackname>] [-r [<strand>]<chr>:<start>-<end> [-R]]
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
465 [--jmatch <chr>:<start>-<end>] [--no-pseudo]
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
466 [-CTVNJMKQAFPGUBHZWTOLE] [-w <exons.fa>] [-x <cds.fa>] [-y <tr_cds.fa>]
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
467 [-j ][--ids <IDs.lst> | --nids <IDs.lst>] [--attrs <attr-list>] [-i <maxintron>]
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
468 [--stream] [--bed | --gtf | --tlf] [--table <attrlist>] [--sort-by <ref.lst>]
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
469 [<input_gff>]
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
470
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
471 Filter, convert or cluster GFF/GTF/BED records, extract the sequence of
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
472 transcripts (exon or CDS) and more.
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
473 By default (i.e. without -O) only transcripts are processed, discarding any
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
474 other non-transcript features. Default output is a simplified GFF3 with only
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
475 the basic attributes.
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
476
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
477 Options:
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
478 --ids discard records/transcripts if their IDs are not listed in <IDs.lst>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
479 --nids discard records/transcripts if their IDs are listed in <IDs.lst>
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
480 -i discard transcripts having an intron larger than <maxintron>
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
481 -l discard transcripts shorter than <minlen> bases
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
482 -r only show transcripts overlapping coordinate range <start>..<end>
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
483 (on chromosome/contig <chr>, strand <strand> if provided)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
484 -R for -r option, discard all transcripts that are not fully
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
485 contained within the given range
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
486 --jmatch only output transcripts matching the given junction
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
487 -U discard single-exon transcripts
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
488 -C coding only: discard mRNAs that have no CDS features
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
489 --nc non-coding only: discard mRNAs that have CDS features
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
490 --ignore-locus : discard locus features and attributes found in the input
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
491 -A use the description field from <seq_info.fsize> and add it
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
492 as the value for a 'descr' attribute to the GFF record
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
493 -s <seq_info.fsize> is a tab-delimited file providing this info
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
494 for each of the mapped sequences:
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
495 <seq-name> <seq-length> <seq-description>
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
496 (useful for -A option with mRNA/EST/protein mappings)
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
497 Sorting: (by default, chromosomes are kept in the order they were found)
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
498 --sort-alpha : chromosomes (reference sequences) are sorted alphabetically
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
499 --sort-by : sort the reference sequences by the order in which their
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
500 names are given in the <refseq.lst> file
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
501 Misc options:
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
502 -F keep all GFF attributes (for non-exon features)
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
503 --keep-exon-attrs : for -F option, do not attempt to reduce redundant
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
504 exon/CDS attributes
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
505 -G do not keep exon attributes, move them to the transcript feature
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
506 (for GFF3 output)
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
507 --attrs <attr-list> only output the GTF/GFF attributes listed in <attr-list>
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
508 which is a comma delimited list of attribute names to
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
509 --keep-genes : in transcript-only mode (default), also preserve gene records
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
510 --keep-comments: for GFF3 input/output, try to preserve comments
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
511 -O process other non-transcript GFF records (by default non-transcript
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
512 records are ignored)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
513 -V discard any mRNAs with CDS having in-frame stop codons (requires -g)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
514 -H for -V option, check and adjust the starting CDS phase
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
515 if the original phase leads to a translation with an
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
516 in-frame stop codon
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
517 -B for -V option, single-exon transcripts are also checked on the
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
518 opposite strand (requires -g)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
519 -P add transcript level GFF attributes about the coding status of each
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
520 transcript, including partialness or in-frame stop codons (requires -g)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
521 --add-hasCDS : add a "hasCDS" attribute with value "true" for transcripts
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
522 that have CDS features
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
523 --adj-stop stop codon adjustment: enables -P and performs automatic
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
524 adjustment of the CDS stop coordinate if premature or downstream
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
525 -N discard multi-exon mRNAs that have any intron with a non-canonical
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
526 splice site consensus (i.e. not GT-AG, GC-AG or AT-AC)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
527 -J discard any mRNAs that either lack initial START codon
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
528 or the terminal STOP codon, or have an in-frame stop codon
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
529 (i.e. only print mRNAs with a complete CDS)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
530 --no-pseudo: filter out records matching the 'pseudo' keyword
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
531 --in-bed: input should be parsed as BED format (automatic if the input
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
532 filename ends with .bed*)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
533 --in-tlf: input GFF-like one-line-per-transcript format without exon/CDS
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
534 features (see --tlf option below); automatic if the input
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
535 filename ends with .tlf)
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
536 --stream: fast processing of input GFF/BED transcripts as they are received
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
537 ((no sorting, exons must be grouped by transcript in the input data)
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
538 Clustering:
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
539 -M/--merge : cluster the input transcripts into loci, discarding
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
540 "redundant" transcripts (those with the same exact introns
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
541 and fully contained or equal boundaries)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
542 -d <dupinfo> : for -M option, write duplication info to file <dupinfo>
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
543 --cluster-only: same as -M/--merge but without discarding any of the
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
544 "duplicate" transcripts, only create "locus" features
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
545 -K for -M option: also discard as redundant the shorter, fully contained
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
546 transcripts (intron chains matching a part of the container)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
547 -Q for -M option, no longer require boundary containment when assessing
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
548 redundancy (can be combined with -K); only introns have to match for
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
549 multi-exon transcripts, and >=80% overlap for single-exon transcripts
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
550 -Y for -M option, enforce -Q but also discard overlapping single-exon
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
551 transcripts, even on the opposite strand (can be combined with -K)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
552 Output options:
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
553 --force-exons: make sure that the lowest level GFF features are considered
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
554 "exon" features
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
555 --gene2exon: for single-line genes not parenting any transcripts, add an
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
556 exon feature spanning the entire gene (treat it as a transcript)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
557 --t-adopt: try to find a parent gene overlapping/containing a transcript
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
558 that does not have any explicit gene Parent
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
559 -D decode url encoded characters within attributes
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
560 -Z merge very close exons into a single exon (when intron size<4)
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
561 -g full path to a multi-fasta file with the genomic sequences
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
562 for all input mappings, OR a directory with single-fasta files
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
563 (one per genomic sequence, with file names matching sequence names)
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
564 -j output the junctions and the corresponding transcripts
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
565 -w write a fasta file with spliced exons for each transcript
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
566 --w-add <N> for the -w option, extract additional <N> bases
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
567 both upstream and downstream of the transcript boundaries
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
568 --w-nocds for -w, disable the output of CDS info in the FASTA file
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
569 -x write a fasta file with spliced CDS for each GFF transcript
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
570 -y write a protein fasta file with the translation of CDS for each record
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
571 -W for -w, -x and -y options, write in the FASTA defline all the exon
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
572 coordinates projected onto the spliced sequence;
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
573 -S for -y option, use '*' instead of '.' as stop codon translation
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
574 -L Ensembl GTF to GFF3 conversion, adds version to IDs
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
575 -m <chr_replace> is a name mapping table for converting reference
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
576 sequence names, having this 2-column format:
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
577 <original_ref_ID> <new_ref_ID>
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
578 -t use <trackname> in the 2nd column of each GFF/GTF output line
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
579 -o write the output records into <outfile> instead of stdout
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
580 -T main output will be GTF instead of GFF3
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
581 --bed output records in BED format instead of default GFF3
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
582 --tlf output "transcript line format" which is like GFF
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
583 but with exons and CDS related features stored as GFF
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
584 attributes in the transcript feature line, like this:
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
585 exoncount=N;exons=<exons>;CDSphase=<N>;CDS=<CDScoords>
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
586 <exons> is a comma-delimited list of exon_start-exon_end coordinates;
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
587 <CDScoords> is CDS_start:CDS_end coordinates or a list like <exons>
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
588 --table output a simple tab delimited format instead of GFF, with columns
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
589 having the values of GFF attributes given in <attrlist>; special
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
590 pseudo-attributes (prefixed by @) are recognized:
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
591 @id, @geneid, @chr, @start, @end, @strand, @numexons, @exons,
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
592 @cds, @covlen, @cdslen
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
593 If any of -w/-y/-x FASTA output files are enabled, the same fields
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
594 (excluding @id) are appended to the definition line of corresponding
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
595 FASTA records
4
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
596 -v,-E expose (warn about) duplicate transcript IDs and other potential
0cf496c45054 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
iuc
parents: 3
diff changeset
597 problems with the given GFF/GTF records
7
9c298cab341d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit f40643d8b80299ebb84faebe92579321ac459746"
iuc
parents: 6
diff changeset
598
0
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
599 ]]>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
600 </help>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
601 <citations>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
602 <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
603 </citations>
baeea9c2ff0f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
604 </tool>