comparison emboss_getorf.xml @ 10:9b98d3d903c6 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
author devteam
date Fri, 12 Aug 2016 19:17:10 -0400
parents
children 0e2484b6829b
comparison
equal deleted inserted replaced
9:18a63c800a4d 10:9b98d3d903c6
1 <tool id="EMBOSS: getorf42" name="getorf" version="5.0.0">
2 <description>Finds and extracts open reading frames (ORFs)</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4 <command>getorf -sequence $input1 -outseq $out_file1 -table $table -minsize $minsize -maxsize $maxsize -find $find -methionine $methionine -circular $circular -reverse $reverse -flanking $flanking
5 -osformat2 $out_format1 -auto</command>
6 <inputs>
7 <param format="fasta" name="input1" type="data">
8 <label>Sequences</label>
9 </param>
10 <param name="table" type="select">
11 <label>Code to use</label>
12 <option value="0">Standard</option>
13 <option value="1">Standard (with alternative initiation codons)</option>
14 <option value="2">Vertebrate Mitochondrial</option>
15 <option value="3">Yeast Mitochondrial</option>
16 <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
17 <option value="5">Invertebrate Mitochondrial</option>
18 <option value="6">Ciliate Macronuclear and Dasycladacean</option>
19 <option value="9">Echinoderm Mitochondrial</option>
20 <option value="10">Euplotid Nuclear</option>
21 <option value="11">Bacterial</option>
22 <option value="12">Alternative Yeast Nuclear</option>
23 <option value="13">Ascidian Mitochondrial</option>
24 <option value="14">Flatworm Mitochondrial</option>
25 <option value="15">Blepharisma Macronuclear</option>
26 <option value="16">Chlorophycean Mitochondrial</option>
27 <option value="21">Trematode Mitochondrial</option>
28 <option value="22">Scenedesmus obliquus</option>
29 <option value="23">Thraustochytrium Mitochondrial</option>
30 </param>
31 <param name="minsize" type="text" value="30">
32 <label>Minimum nucleotide size of ORF to report</label>
33 </param>
34 <param name="maxsize" type="text" value="1000000">
35 <label>Maximum nucleotide size of ORF to report</label>
36 </param>
37 <param name="find" type="select">
38 <label>What to output</label>
39 <option value="0">Translation of regions between STOP codons</option>
40 <option value="1">Translation of regions between START and STOP codons</option>
41 <option value="2">Nucleic sequences between STOP codons</option>
42 <option value="3">Nucleic sequences between START and STOP codons</option>
43 <option value="4">Nucleotides flanking START codons</option>
44 <option value="5">Nucleotides flanking initial STOP codons</option>
45 <option value="6">Nucleotides flanking ending STOP codons</option>
46 </param>
47 <param name="methionine" type="select">
48 <label>All START codons to code for Methionine</label>
49 <option value="yes">Yes</option>
50 <option value="no">No</option>
51 </param>
52 <param name="circular" type="select">
53 <label>Circular sequence</label>
54 <option value="no">No</option>
55 <option value="yes">Yes</option>
56 </param>
57 <param name="reverse" type="select">
58 <label>Find ORFs in the reverse complement</label>
59 <option value="yes">Yes</option>
60 <option value="no">No</option>
61 </param>
62 <param name="flanking" type="text" value="100">
63 <label>Number of flanking nucleotides to output</label>
64 </param>
65 <param name="out_format1" type="select">
66 <label>Output Sequence File Format</label>
67 <option value="fasta">FASTA (m)</option>
68 <option value="acedb">ACeDB (m)</option>
69 <option value="asn1">ASN.1 (m)</option>
70 <option value="clustal">Clustal (m)</option>
71 <option value="codata">CODATA (m)</option>
72 <option value="embl">EMBL (m)</option>
73 <option value="fitch">Fitch (m)</option>
74 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
75 <option value="genbank">GENBANK (m)</option>
76 <!-- <option value="gff">GFF (m)</option> -->
77 <option value="hennig86">Hennig86 (m)</option>
78 <option value="ig">Intelligenetics (m)</option>
79 <option value="jackknifer">Jackknifer (m)</option>
80 <option value="jackknifernon">Jackknifernon (m)</option>
81 <option value="mega">Mega (m)</option>
82 <option value="meganon">Meganon (m)</option>
83 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
84 <option value="pir">NBRF (PIR) (m)</option>
85 <option value="ncbi">NCBI style FASTA (m)</option>
86 <option value="nexus">Nexus/PAUP (m)</option>
87 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
88 <option value="phylip">PHYLIP interleaved (m)</option>
89 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
90 <option value="selex">SELEX (m)</option>
91 <option value="staden">Staden (s)</option>
92 <option value="strider">DNA strider (m)</option>
93 <option value="swiss">SwisProt entry (m)</option>
94 <option value="text">Plain sequence (s)</option>
95 <option value="treecon">Treecon (m)</option>
96 </param>
97 </inputs>
98 <outputs>
99 <data format="fasta" name="out_file1" />
100 </outputs>
101 <tests>
102 <test>
103 <param name="input1" value="2.fasta"/>
104 <param name="minsize" value="30"/>
105 <param name="maxsize" value="1000000"/>
106 <param name="find" value="0"/>
107 <param name="methionine" value="yes"/>
108 <param name="circular" value="no"/>
109 <param name="reverse" value="yes"/>
110 <param name="table" value="0"/>
111 <param name="flanking" value="100"/>
112 <param name="out_format1" value="fasta"/>
113 <output name="out_file1" file="emboss_getorf_out.fasta"/>
114 </test>
115 </tests>
116 <code file="emboss_format_corrector.py" />
117 <help>
118
119 .. class:: warningmark
120
121 The input dataset needs to be sequences.
122
123 -----
124
125 You can view the original documentation here_.
126
127 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/getorf.html
128
129 ------
130
131 **Citation**
132
133 For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
134
135 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
136 </help>
137 </tool>