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comparison emboss_sixpack.xml @ 10:9b98d3d903c6 draft

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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
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9:18a63c800a4d 10:9b98d3d903c6
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" 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" 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" type="text" value="60">
64 <label>Number of nucleotides displayed on each line</label>
65 </param>
66 <param name="length" type="text" value="0">
67 <label>Line length of page</label>
68 </param>
69 <param name="margin" 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" 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
162 ------
163
164 **Citation**
165
166 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;`_
167
168 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;`_
169 </help>
170 </tool>