|
0
|
1 <tool id="EMBOSS: sixpack90" name="sixpack" version="5.0.0">
|
|
|
2 <!-- tool adds file description and timestamp to output data -->
|
|
|
3 <description>Display a DNA sequence with 6-frame translation and ORFs</description>
|
|
|
4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
|
|
5 <command>sixpack -sequence $input1 -outfile $ofile1 -outseq $ofile2 -table $table -firstorf $firstorf -lastorf $lastorf -mstart $mstart -reverse $reverse -orfminsize $orfminsize -uppercase
|
|
|
6 "$uppercase" -number $number -width "$width" -length "$length" -margin "$margin" -name $disp_name -description $description -offset "$offset" -html $html_out1 -osformat $out_format2 -auto</command>
|
|
|
7 <inputs>
|
|
|
8 <param format="fasta" name="input1" type="data">
|
|
|
9 <label>Sequences</label>
|
|
|
10 </param>
|
|
|
11 <param name="table" type="select">
|
|
|
12 <label>Code to use</label>
|
|
|
13 <option value="0">Standard</option>
|
|
|
14 <option value="1">Standard (with alternative initiation codons)</option>
|
|
|
15 <option value="2">Vertebrate Mitochondrial</option>
|
|
|
16 <option value="3">Yeast Mitochondrial</option>
|
|
|
17 <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
|
|
|
18 <option value="5">Invertebrate Mitochondrial</option>
|
|
|
19 <option value="6">Ciliate Macronuclear and Dasycladacean</option>
|
|
|
20 <option value="9">Echinoderm Mitochondrial</option>
|
|
|
21 <option value="10">Euplotid Nuclear</option>
|
|
|
22 <option value="11">Bacterial</option>
|
|
|
23 <option value="12">Alternative Yeast Nuclear</option>
|
|
|
24 <option value="13">Ascidian Mitochondrial</option>
|
|
|
25 <option value="14">Flatworm Mitochondrial</option>
|
|
|
26 <option value="15">Blepharisma Macronuclear</option>
|
|
|
27 <option value="16">Chlorophycean Mitochondrial</option>
|
|
|
28 <option value="21">Trematode Mitochondrial</option>
|
|
|
29 <option value="22">Scenedesmus obliquus</option>
|
|
|
30 <option value="23">Thraustochytrium Mitochondrial</option>
|
|
|
31 </param>
|
|
|
32 <param name="firstorf" type="select">
|
|
|
33 <label>Count the beginning of a sequence as a possible ORF</label>
|
|
|
34 <option value="yes">Yes</option>
|
|
|
35 <option value="no">No</option>
|
|
|
36 </param>
|
|
|
37 <param name="lastorf" type="select">
|
|
|
38 <label>Count the end of a sequence as a possible ORF</label>
|
|
|
39 <option value="yes">Yes</option>
|
|
|
40 <option value="no">No</option>
|
|
|
41 </param>
|
|
|
42 <param name="mstart" type="select">
|
|
|
43 <label>Displays only ORFs starting with an M</label>
|
|
|
44 <option value="no">No</option>
|
|
|
45 <option value="yes">Yes</option>
|
|
|
46 </param>
|
|
|
47 <param name="reverse" type="select">
|
|
|
48 <label>Display the translation of the DNA sequence in the 3 reverse frames</label>
|
|
|
49 <option value="yes">Yes</option>
|
|
|
50 <option value="no">No</option>
|
|
|
51 </param>
|
|
|
52 <param name="orfminsize" size="4" type="text" value="1">
|
|
|
53 <label>Minimum size of Open Reading Frames (ORFs) to display in the translations</label>
|
|
|
54 </param>
|
|
|
55 <param name="uppercase" size="50" type="text" value="">
|
|
|
56 <label>Regions to put in uppercase</label>
|
|
|
57 </param>
|
|
|
58 <param name="number" type="select">
|
|
|
59 <label>Number the sequence at the beginning and the end of each line</label>
|
|
|
60 <option value="yes">Yes</option>
|
|
|
61 <option value="no">No</option>
|
|
|
62 </param>
|
|
|
63 <param name="width" size="4" type="text" value="60">
|
|
|
64 <label>Number of nucleotides displayed on each line</label>
|
|
|
65 </param>
|
|
|
66 <param name="length" size="4" type="text" value="0">
|
|
|
67 <label>Line length of page</label>
|
|
|
68 </param>
|
|
|
69 <param name="margin" size="4" type="text" value="10">
|
|
|
70 <label>Margin around sequence for numbering</label>
|
|
|
71 </param>
|
|
|
72 <param name="disp_name" type="select">
|
|
|
73 <label>Display the ID name of the sequence</label>
|
|
|
74 <option value="yes">Yes</option>
|
|
|
75 <option value="no">No</option>
|
|
|
76 </param>
|
|
|
77 <param name="description" type="select">
|
|
|
78 <label>Display the description of the sequence</label>
|
|
|
79 <option value="yes">Yes</option>
|
|
|
80 <option value="no">No</option>
|
|
|
81 </param>
|
|
|
82 <param name="offset" size="4" type="text" value="1">
|
|
|
83 <label>Number from which you want the DNA sequence to be numbered</label>
|
|
|
84 </param>
|
|
|
85 <param name="html_out1" type="select">
|
|
|
86 <label>Format output as an HTML table</label>
|
|
|
87 <option value="no">No</option>
|
|
|
88 <option value="yes">Yes</option>
|
|
|
89 </param>
|
|
|
90 <param name="out_format2" type="select">
|
|
|
91 <label>Output Sequence File Format</label>
|
|
|
92 <option value="fasta">FASTA (m)</option>
|
|
|
93 <option value="acedb">ACeDB (m)</option>
|
|
|
94 <option value="asn1">ASN.1 (m)</option>
|
|
|
95 <option value="clustal">Clustal (m)</option>
|
|
|
96 <option value="codata">CODATA (m)</option>
|
|
|
97 <option value="embl">EMBL (m)</option>
|
|
|
98 <option value="fitch">Fitch (m)</option>
|
|
|
99 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
|
|
|
100 <option value="genbank">GENBANK (m)</option>
|
|
|
101 <option value="gff">GFF (m)</option>
|
|
|
102 <option value="hennig86">Hennig86 (m)</option>
|
|
|
103 <option value="ig">Intelligenetics (m)</option>
|
|
|
104 <option value="jackknifer">Jackknifer (m)</option>
|
|
|
105 <option value="jackknifernon">Jackknifernon (m)</option>
|
|
|
106 <option value="mega">Mega (m)</option>
|
|
|
107 <option value="meganon">Meganon (m)</option>
|
|
|
108 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
|
|
|
109 <option value="pir">NBRF (PIR) (m)</option>
|
|
|
110 <option value="ncbi">NCBI style FASTA (m)</option>
|
|
|
111 <option value="nexus">Nexus/PAUP (m)</option>
|
|
|
112 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
|
|
|
113 <option value="phylip">PHYLIP interleaved (m)</option>
|
|
|
114 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
|
|
|
115 <option value="selex">SELEX (m)</option>
|
|
|
116 <option value="staden">Staden (s)</option>
|
|
|
117 <option value="strider">DNA strider (m)</option>
|
|
|
118 <option value="swiss">SwisProt entry (m)</option>
|
|
|
119 <option value="text">Plain sequence (s)</option>
|
|
|
120 <option value="treecon">Treecon (m)</option>
|
|
|
121 </param>
|
|
|
122 </inputs>
|
|
|
123 <outputs>
|
|
|
124 <data format="sixpack" name="ofile1" />
|
|
|
125 <data format="fasta" name="ofile2" />
|
|
|
126 </outputs>
|
|
|
127 <!-- <tests>
|
|
|
128 <test>
|
|
|
129 <param name="input1" value="2.fasta"/>
|
|
|
130 <param name="table" value="0"/>
|
|
|
131 <param name="firstorf" value="no"/>
|
|
|
132 <param name="lastorf" value="no"/>
|
|
|
133 <param name="mstart" value="no"/>
|
|
|
134 <param name="reverse" value="no"/>
|
|
|
135 <param name="orfminsize" value="1"/>
|
|
|
136 <param name="uppercase" value=""/>
|
|
|
137 <param name="number" value="no"/>
|
|
|
138 <param name="width" value="60"/>
|
|
|
139 <param name="length" value="0"/>
|
|
|
140 <param name="margin" value="10"/>
|
|
|
141 <param name="disp_name" value="no"/>
|
|
|
142 <param name="description" value="no"/>
|
|
|
143 <param name="offset" value="1"/>
|
|
|
144 <param name="html_out1" value="no"/>
|
|
|
145 <param name="out_format2" value="fasta"/>
|
|
|
146 <output name="ofile2" file="emboss_sixpack_out.fasta"/>
|
|
|
147 </test>
|
|
|
148 </tests> -->
|
|
|
149 <code file="emboss_format_corrector.py" />
|
|
|
150 <help>
|
|
|
151
|
|
|
152 .. class:: warningmark
|
|
|
153
|
|
|
154 The input dataset needs to be sequences.
|
|
|
155
|
|
|
156 -----
|
|
|
157
|
|
|
158 You can view the original documentation here_.
|
|
|
159
|
|
|
160 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/sixpack.html
|
|
|
161 </help>
|
|
|
162 </tool>
|
