Mercurial > repos > iuc > orfipy

annotate orfipy.xml @ 2:f5114c60dc95 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/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
author iuc
date Tue, 04 Jun 2024 10:56:16 +0000
parents 45d4d26e01b5
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
45d4d26e01b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 472277ff42e1d7018e0d2921bd51a018572793c5
iuc
parents: 0
diff changeset
1 <tool id="orfipy" name="ORFipy" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
0
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
2 <description>a versatile ORF finder</description>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
3 <macros>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
4 <import>macros.xml</import>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
5 </macros>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
6 <expand macro="xrefs"/>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
7 <requirements>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
8 <requirement type="package" version="@TOOL_VERSION@">orfipy</requirement>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
9 </requirements>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
11 orfipy
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
12 --procs "\${GALAXY_SLOTS:-1}"
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
13 --outdir ./
2
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
14 #if 'BED' in $out_files or $longest:
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
15 --bed '$out_bed'
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
16 #end if
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
17 #if 'BED12' in $out_files:
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
18 --bed12 '$out_bed12'
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
19 #end if
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
20 #if 'DNA' in $out_files:
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
21 --dna '$out_dna'
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
22 #end if
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
23 #if 'RNA' in $out_files:
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
24 --rna '$out_rna'
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
25 #end if
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
26 #if 'PEP' in $out_files:
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
27 --pep '$out_pep'
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
28 #end if
0
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
29 --strand $strand
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
30 #if $min:
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
31 --min $min
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
32 #end if
1
45d4d26e01b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 472277ff42e1d7018e0d2921bd51a018572793c5
iuc
parents: 0
diff changeset
33 #if $max:
45d4d26e01b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 472277ff42e1d7018e0d2921bd51a018572793c5
iuc
parents: 0
diff changeset
34 --max $max
45d4d26e01b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 472277ff42e1d7018e0d2921bd51a018572793c5
iuc
parents: 0
diff changeset
35 #end if
0
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
36 --table $table
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
37 #if $start:
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
38 --start '$start'
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
39 #end if
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
40 #if $stop:
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
41 --stop '$stop'
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
42 #end if
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
43 $ignore_case
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
44 $partial_3
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
45 $partial_5
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
46 $between_stops
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
47 $include_stop
2
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
48 $longest
0
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
49 '$input1'
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
50 ]]></command>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
51 <inputs>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
52 <param name="input1" type="data" format="fasta,fasta.gz" label="Find ORFs in:" help="ORFs will be detected in this sequence"/>
2
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
53 <param argument="--table" type="select" label="Specify genetic code">
0
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
54 <option value="1" selected="true">1 Standard</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
55 <option value="2">2 Vertebrate mitochondrial</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
56 <option value="3">3 Yeast mitochondrial</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
57 <option value="4">4 Mold, Protozoan, Coelenterate, Mycoplasma, Spiroplasma mitochondrial</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
58 <option value="5">5 Invertebrate Mitochondrial</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
59 <option value="6">6 Ciliate, Dasycladacean, Hexamita Nuclear</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
60 <option value="7">7 Echinoderm and Flatworm Mitochondrial</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
61 <option value="8">8 Euplotid Nuclear</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
62 <option value="9">9 Bacterial, Archaeal and Plant Plastid</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
63 <option value="10">10 Alternative Yeast nuclear</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
64 <option value="11">11 Ascidian mitochondrial</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
65 <option value="12">12 Alternative Flatworm mitochondrial</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
66 <option value="13">13 Chlorophycean mitochondrial</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
67 <option value="14">14 Trematode mitochondrial</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
68 <option value="15">15 Scenedesmus obliquus mitochondrial</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
69 <option value="16">16 Thraustochytrium mitochondrial code</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
70 <option value="17">17 Pterobranchia mitochondrial</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
71 <option value="18">18 Candidate Division SR1 and Gracilibacteria</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
72 <option value="19">19 Pachysolen tannophilus Nuclear Code</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
73 <option value="20">20 Karyorelict nuclear</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
74 <option value="21">21 Condylostoma nuclear</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
75 <option value="22">22 Mesodinium nuclear</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
76 <option value="23">23 Peritrich nuclear</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
77 </param>
2
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
78 <param name="out_files" type="select" label="Select outputs" help="DNA, RNA, and Peptide options will produce FASTA outputs" multiple="true" display="checkboxes">
0
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
79 <option value="BED" selected="true">BED</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
80 <option value="BED12">BED12</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
81 <option value="DNA">DNA</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
82 <option value="RNA">RNA</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
83 <option value="PEP">Peptides</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
84 </param>
2
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
85 <param argument="--strand" type="select" label="Select strand" help="Identify ORFs on which strand" display="radio">
0
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
86 <option value="b" selected="true">Both</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
87 <option value="f">Forward</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
88 <option value="r">Reverse</option>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
89 </param>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
90 <param argument="--min" type="integer" min="0" optional="true" label="Minimum length of ORFs"
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
91 help="No ORFs below this value will be reported. All ORFs will be reported if this parameter is not set. Default is 30"/>
1
45d4d26e01b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 472277ff42e1d7018e0d2921bd51a018572793c5
iuc
parents: 0
diff changeset
92 <param argument="--max" type="integer" min="0" optional="true" label="Maximum length of ORFs"
45d4d26e01b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 472277ff42e1d7018e0d2921bd51a018572793c5
iuc
parents: 0
diff changeset
93 help="This value doesn't take in account the STOP codon. No ORFs over this value will be reported. Default is 1.000.000.000."/>
0
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
94 <param argument="--start" type="text" optional="true" label="Start codon(s) to use"
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
95 help="A comma-separated list without spaces. Only ATCG and comma are allowed">
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
96 <validator type="regex" message="Only 'ATCGatcg' and ',' are allowed in this field">^[ATGCatcg,]*$</validator>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
97 </param>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
98 <param argument="--stop" type="text" optional="true" label="Stop codon(s) to use"
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
99 help="A commma separated list without spaces. Only ATCG and comma are allowed">
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
100 <validator type="regex" message="Only 'ATCGatcg' and ',' are allowed in this field">^[ATGCatcg,]*$</validator>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
101 </param>
2
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
102 <param argument="--ignore-case" type="boolean" truevalue="--ignore-case" falsevalue="" label="Ignore case?" help="Ignore case and find ORFs in lower case sequences too. NO = do not ignore (use upper case only). YES = ignore" display="radio"/>
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
103 <param argument="--partial-3" type="boolean" truevalue="--partial-3" falsevalue="" label="Output ORFs with Start but no Stop?" help="Output ORFs with a start codon but lacking an inframe stop codon. NO = do not output. YES = do output" display="radio"/>
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
104 <param argument="--partial-5" type="boolean" truevalue="--partial-5" falsevalue="" label="Output ORFs with Stop but no Start?" help="Output ORFs with an inframe stop codon lacking an inframe start codon. NO = do not output. YES = do output" display="radio"/>
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
105 <param argument="--between-stops" type="boolean" truevalue="--between-stops" falsevalue="" label="Output ORFs bound by Stop codons?" help="Output ORFs defined as regions between stop codons (regions free of stop codon). This will set --partial-3 and --partial-5 true" display="radio"/>
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
106 <param argument="--include-stop" type="boolean" truevalue="--include-stop" falsevalue="" label="Include stop codon in the results?" help="Output ORFs with an inframe stop codon lacking an inframe start codon. NO = do not include. YES = include" display="radio"/>
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
107 <param argument="--longest" type="boolean" truevalue="--longest" falsevalue="" label="Output separate BED file with longest ORFs per sequence" help="Setting this option will automatically enable the BED option."/>
0
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
108 </inputs>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
109 <outputs>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
110 <data name="out_bed" format="bed6" label="ORFs on ${on_string} (BED format)">
2
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
111 <filter>"BED" in out_files or longest</filter>
0
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
112 </data>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
113 <data name="out_bed12" format="bed12" label="ORFs on ${on_string} (BED12 format)">
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
114 <filter>"BED12" in out_files</filter>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
115 </data>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
116 <data name="out_dna" format="fasta" label="ORFs on ${on_string} (FASTA DNA)">
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
117 <filter>"DNA" in out_files</filter>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
118 </data>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
119 <data name="out_rna" format="fasta" label="ORFs on ${on_string} (FASTA RNA)">
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
120 <filter>"RNA" in out_files</filter>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
121 </data>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
122 <data name="out_pep" format="fasta" label="ORFs on ${on_string} (FASTA Protein)">
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
123 <filter>"PEP" in out_files</filter>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
124 </data>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
125 </outputs>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
126 <tests>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
127 <test expect_num_outputs="1">
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
128 <param name="input1" value="orfipy.fa"/>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
129 <param name="out_files" value="BED"/>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
130 <output name="out_bed" file="test1.bed"/>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
131 </test>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
132 <test expect_num_outputs="1">
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
133 <param name="input1" value="orfipy.fa"/>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
134 <param name="out_files" value="DNA"/>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
135 <param name="min" value="100"/>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
136 <param name="partial_5" value="true"/>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
137 <output name="out_dna" file="test2.fa"/>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
138 </test>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
139 <test expect_num_outputs="1">
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
140 <param name="input1" value="orfipy.fa.gz"/>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
141 <param name="out_files" value="DNA"/>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
142 <param name="min" value="100"/>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
143 <param name="partial_5" value="true"/>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
144 <output name="out_dna" file="test2.fa"/>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
145 </test>
1
45d4d26e01b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 472277ff42e1d7018e0d2921bd51a018572793c5
iuc
parents: 0
diff changeset
146 <test expect_num_outputs="1">
45d4d26e01b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 472277ff42e1d7018e0d2921bd51a018572793c5
iuc
parents: 0
diff changeset
147 <param name="input1" value="orfipy.fa.gz"/>
45d4d26e01b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 472277ff42e1d7018e0d2921bd51a018572793c5
iuc
parents: 0
diff changeset
148 <param name="out_files" value="DNA"/>
45d4d26e01b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 472277ff42e1d7018e0d2921bd51a018572793c5
iuc
parents: 0
diff changeset
149 <param name="max" value="100000000"/>
45d4d26e01b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 472277ff42e1d7018e0d2921bd51a018572793c5
iuc
parents: 0
diff changeset
150 <output name="out_dna" file="test3.fa"/>
45d4d26e01b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 472277ff42e1d7018e0d2921bd51a018572793c5
iuc
parents: 0
diff changeset
151 </test>
2
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
152 <test expect_num_outputs="2">
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
153 <param name="input1" value="orfipy.fa.gz"/>
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
154 <param name="out_files" value="DNA"/>
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
155 <param name="max" value="100000000"/>
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
156 <param name="longest" value="true"/>
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
157 <output name="out_dna" file="test3.fa"/>
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
158 <output name="out_bed" file="test1.bed"/>
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
159 </test>
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
160 <test expect_num_outputs="1">
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
161 <param name="input1" value="orfipy.fa"/>
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
162 <param name="out_files" value="BED"/>
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
163 <param name="longest" value="true"/>
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
164 <output name="out_bed" file="test1.bed"/>
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
165 </test>
0
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
166 </tests>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
167 <help><![CDATA[
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
168 **What it does**
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
169
2
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
170 Orfipy is a tool for finding open reading frames (ORFs) in sequences (FASTA files).
0
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
171
2
f5114c60dc95 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 02b217857afbabac1f86b825a902a5cc20fcf5ed
iuc
parents: 1
diff changeset
172
0
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
173 ]]></help>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
174 <citations>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
175 <citation type="doi">10.1093/bioinformatics/btab090</citation>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
176 </citations>
c147914c9f02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13
iuc
parents:
diff changeset
177 </tool>