annotate transdecoder.xml @ 1:1de64ee71145 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 35197ad36518c35aa983181b0e4a7bc178fc403d
author iuc
date Tue, 28 Jun 2016 11:42:04 -0400
parents 8aef9a17faae
children b408e5a8b137
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
1de64ee71145 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 35197ad36518c35aa983181b0e4a7bc178fc403d
iuc
parents: 0
diff changeset
1 <tool id="transdecoder" name="TransDecoder" version="1.1">
0
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
2 <description>Find coding regions within transcripts</description>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
3 <requirements>
1
1de64ee71145 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 35197ad36518c35aa983181b0e4a7bc178fc403d
iuc
parents: 0
diff changeset
4 <requirement type="package" version="2.1.0">transdecoder</requirement>
0
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
5 </requirements>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
6
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
7 <stdio>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
8 <exit_code range="1:" level="fatal" description="Error occurred" />
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
9 </stdio>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
10
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
11 <command><![CDATA[
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
12 TransDecoder.LongOrfs -t "${input}"
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
13
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
14 #if ($min_len):
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
15 -m ${min_len}
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
16 #end if
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
17
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
18 ${adv.stranded}
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
19
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
20 #if ($adv.gen_code):
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
21 -G ${adv.gen_code}
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
22 #end if
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
23
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
24 &&
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
25
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
26 TransDecoder.Predict -t "${input}"
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
27
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
28 #if ($adv.retain_long_orfs):
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
29 --retain_long_orfs ${adv.retain_long_orfs}
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
30 #end if
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
31
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
32 #if str( $training_sect.training.training_selector ) == "training_top":
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
33 #if ($training_sect.training.top_longest):
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
34 -T ${training_sect.training.top_longest}
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
35 #end if
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
36 #else
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
37 #if ($training_sect.training.train):
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
38 --train ${training_sect.training.train}
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
39 #end if
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
40 #end if
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
41
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
42 &&
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
43
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
44 out_prefix=`basename "${input}"`
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
45
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
46 mv `basename "${input}"`.transdecoder.pep transcript.transdecoder.pep &&
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
47 mv `basename "${input}"`.transdecoder.cds transcript.transdecoder.cds &&
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
48 mv `basename "${input}"`.transdecoder.bed transcript.transdecoder.bed &&
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
49 mv `basename "${input}"`.transdecoder.gff3 transcript.transdecoder.gff3 &&
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
50 mv `basename "${input}"`.transdecoder.mRNA transcript.transdecoder.mRNA
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
51 ]]></command>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
52
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
53 <inputs>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
54 <param format="fasta" name="input" type="data" label="Transcripts"/>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
55
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
56 <param name="min_len" size="5" type="integer" optional='true' value="100" label="Minimum protein length (default: 100aa)"/>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
57
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
58 <section name="adv" title="Advanced Options" expanded="False">
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
59 <param name="stranded" type="boolean" checked="false" truevalue="-S" falsevalue="" label="Strand-specific" help="Only analyzes top strand"/>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
60 <param name="gen_code" type="select" label="Genetic code">
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
61 <option value="universal" selected="True">universal</option>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
62 <option value="Euplotes">Euplotes</option>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
63 <option value="Tetrahymena">Tetrahymena</option>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
64 <option value="Candida">Candida</option>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
65 <option value="Acetabularia">Acetabularia</option>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
66 <option value="Mitochondrial-Canonical">Mitochondrial-Canonical</option>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
67 <option value="Mitochondrial-Vertebrates">Mitochondrial-Vertebrates</option>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
68 <option value="Mitochondrial-Arthropods">Mitochondrial-Arthropods</option>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
69 <option value="Mitochondrial-Echinoderms">Mitochondrial-Echinoderms</option>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
70 <option value="Mitochondrial-Molluscs">Mitochondrial-Molluscs</option>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
71 <option value="Mitochondrial-Ascidians">Mitochondrial-Ascidians</option>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
72 <option value="Mitochondrial-Nematodes">Mitochondrial-Nematodes</option>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
73 <option value="Mitochondrial-Platyhelminths">Mitochondrial-Platyhelminths</option>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
74 <option value="Mitochondrial-Yeasts">Mitochondrial-Yeasts</option>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
75 <option value="Mitochondrial-Euascomycetes">Mitochondrial-Euascomycetes</option>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
76 <option value="Mitochondrial-Protozoans">Mitochondrial-Protozoans</option>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
77 </param>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
78
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
79 <param name="retain_long_orfs" type="integer" optional="true" label="Retain long orfs" help="Retain all ORFs found that are equal or longer than these many nucleotides even if no other evidence marks it as coding (default: 900 bp => 300aa)" />
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
80 </section>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
81
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
82 <section name="training_sect" title="Training Options" expanded="False">
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
83 <conditional name="training">
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
84 <param name="training_selector" type="select" label="Select the training method">
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
85 <option value="training_top" selected="True">Train with the top longest ORFs</option>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
86 <option value="training_set">Train with a set of known ORFs</option>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
87 </param>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
88 <when value="training_top">
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
89 <param name="top_longest" type="integer" optional="true" label="Number of top longest ORFs" help="Number of top longest ORFs to train Markov Model (hexamer stats) (default: 500 sequences)" />
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
90 </when>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
91 <when value="training_set">
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
92 <param format="fasta" name="train" type="data" label="Training set of transcripts" optional="true" help="FASTA file with ORFs to train Markov Mod for protein identification" />
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
93 </when>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
94 </conditional>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
95 </section>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
96
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
97 </inputs>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
98
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
99
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
100 <outputs>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
101 <data name='transdecoder_pep' format='fasta' label="${tool.name} on ${on_string}: pep" from_work_dir="transcript.transdecoder.pep"/>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
102 <data name='transdecoder_cds' format='fasta' label="${tool.name} on ${on_string}: cds" from_work_dir="transcript.transdecoder.cds"/>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
103 <data name='transdecoder_bed' format='bed' label="${tool.name} on ${on_string}: bed" from_work_dir="transcript.transdecoder.bed"/>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
104 <data name='transdecoder_gff3' format='gff3' label="${tool.name} on ${on_string}: gff3" from_work_dir="transcript.transdecoder.gff3"/>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
105 <data name='transdecoder_mRNA' format='fasta' label="${tool.name} on ${on_string}: mRNA" from_work_dir="transcript.transdecoder.mRNA"/>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
106 </outputs>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
107
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
108
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
109 <tests>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
110 <test>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
111 <param name="input" value="test.fa"/>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
112 <output name="transdecoder_gff3" file="raw/test.fa.transdecoder.gff3" compare="sim_size" />
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
113 <output name="transdecoder_bed" file="raw/test.fa.transdecoder.bed" compare="sim_size" />
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
114 <output name="transdecoder_cds" file="raw/test.fa.transdecoder.cds" compare="sim_size" />
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
115 <output name="transdecoder_mRNA" file="raw/test.fa.transdecoder.mRNA" compare="sim_size" />
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
116 <output name="transdecoder_pep" file="raw/test.fa.transdecoder.pep" compare="sim_size" />
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
117 </test>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
118 <test>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
119 <param name="input" value="test.fa"/>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
120 <param name="training_selector" value="training_top"/>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
121 <param name="top_longest" value="10"/>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
122 <output name="transdecoder_gff3" file="top/test.fa.transdecoder.gff3" compare="sim_size" />
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
123 <output name="transdecoder_bed" file="top/test.fa.transdecoder.bed" compare="sim_size" />
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
124 <output name="transdecoder_cds" file="top/test.fa.transdecoder.cds" compare="sim_size" />
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
125 <output name="transdecoder_mRNA" file="top/test.fa.transdecoder.mRNA" compare="sim_size" />
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
126 <output name="transdecoder_pep" file="top/test.fa.transdecoder.pep" compare="sim_size" />
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
127 </test>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
128 <test>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
129 <param name="input" value="test.fa"/>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
130 <param name="gen_code" value="Mitochondrial-Arthropods"/>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
131 <output name="transdecoder_gff3" file="gencode/test.fa.transdecoder.gff3" compare="sim_size" />
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
132 <output name="transdecoder_bed" file="gencode/test.fa.transdecoder.bed" compare="sim_size" />
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
133 <output name="transdecoder_cds" file="gencode/test.fa.transdecoder.cds" compare="sim_size" />
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
134 <output name="transdecoder_mRNA" file="gencode/test.fa.transdecoder.mRNA" compare="sim_size" />
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
135 <output name="transdecoder_pep" file="gencode/test.fa.transdecoder.pep" compare="sim_size" />
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
136 </test>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
137 <test>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
138 <param name="input" value="test.fa"/>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
139 <param name="stranded" value="true"/>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
140 <output name="transdecoder_gff3" file="strand/test.fa.transdecoder.gff3" compare="sim_size" />
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
141 <output name="transdecoder_bed" file="strand/test.fa.transdecoder.bed" compare="sim_size" />
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
142 <output name="transdecoder_cds" file="strand/test.fa.transdecoder.cds" compare="sim_size" />
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
143 <output name="transdecoder_mRNA" file="strand/test.fa.transdecoder.mRNA" compare="sim_size" />
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
144 <output name="transdecoder_pep" file="strand/test.fa.transdecoder.pep" compare="sim_size" />
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
145 </test>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
146 </tests>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
147 <help>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
148
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
149 **What it does**
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
150
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
151 TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
152
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
153 TransDecoder identifies likely coding sequences based on the following criteria:
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
154
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
155 - a minimum length open reading frame (ORF) is found in a transcript sequence
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
156
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
157 - a log-likelihood score similar to what is computed by the GeneID software is > 0.
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
158
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
159 - the above coding score is greatest when the ORF is scored in the 1st reading frame as compared to scores in the other 5 reading frames.
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
160
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
161 - if a candidate ORF is found fully encapsulated by the coordinates of another candidate ORF, the longer one is reported. However, a single transcript can report multiple ORFs (allowing for operons, chimeras, etc).
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
162
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
163 - optional the putative peptide has a match to a Pfam domain above the noise cutoff score.
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
164
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
165 The software is primarily maintained by Brian Haas at the Broad Institute and Alexie Papanicolaou at the Commonwealth Scientific and Industrial Research Organisation (CSIRO). It is integrated into other related software such as Trinity, PASA, EVidenceModeler, and Trinotate.
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
166
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
167 </help>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
168 <citations>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
169 <citation type="doi">10.1038/nprot.2013.084</citation>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
170 </citations>
8aef9a17faae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
iuc
parents:
diff changeset
171 </tool>