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comparison emboss_sixpack.xml @ 10:d49956b87f7e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author iuc
date Wed, 08 Feb 2017 12:42:22 -0500
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children 8992d258e42f
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9:511429456d3c 10:d49956b87f7e
1 <tool id="EMBOSS: sixpack90" name="sixpack" version="5.0.0.1">
2 <!-- tool adds file description and timestamp to output data -->
3 <description>Display a DNA sequence with 6-frame translation and ORFs</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <code file="emboss_format_corrector.py" />
9 <command>sixpack -sequence '$input1' -outfile '$ofile1' -outseq '$ofile2' -table $table -firstorf $firstorf -lastorf $lastorf -mstart $mstart -reverse $reverse -orfminsize $orfminsize -uppercase
10 '$uppercase' -number $number -width $width -length $length -margin $margin -name $disp_name -description $description -offset $offset -html $html_out1 -osformat $out_format2 -auto</command>
11 <inputs>
12 <param name="input1" type="data" format="fasta" label="Sequences" />
13 <param name="table" type="select" label="Code to use">
14 <option value="0">Standard</option>
15 <option value="1">Standard (with alternative initiation codons)</option>
16 <option value="2">Vertebrate Mitochondrial</option>
17 <option value="3">Yeast Mitochondrial</option>
18 <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
19 <option value="5">Invertebrate Mitochondrial</option>
20 <option value="6">Ciliate Macronuclear and Dasycladacean</option>
21 <option value="9">Echinoderm Mitochondrial</option>
22 <option value="10">Euplotid Nuclear</option>
23 <option value="11">Bacterial</option>
24 <option value="12">Alternative Yeast Nuclear</option>
25 <option value="13">Ascidian Mitochondrial</option>
26 <option value="14">Flatworm Mitochondrial</option>
27 <option value="15">Blepharisma Macronuclear</option>
28 <option value="16">Chlorophycean Mitochondrial</option>
29 <option value="21">Trematode Mitochondrial</option>
30 <option value="22">Scenedesmus obliquus</option>
31 <option value="23">Thraustochytrium Mitochondrial</option>
32 </param>
33 <param name="firstorf" type="select" label="Count the beginning of a sequence as a possible ORF">
34 <option value="yes">Yes</option>
35 <option value="no">No</option>
36 </param>
37 <param name="lastorf" type="select" label="Count the end of a sequence as a possible ORF">
38 <option value="yes">Yes</option>
39 <option value="no">No</option>
40 </param>
41 <param name="mstart" type="select" label="Displays only ORFs starting with an M">
42 <option value="no">No</option>
43 <option value="yes">Yes</option>
44 </param>
45 <param name="reverse" type="select" label="Display the translation of the DNA sequence in the 3 reverse frames">
46 <option value="yes">Yes</option>
47 <option value="no">No</option>
48 </param>
49 <param name="orfminsize" type="integer" value="1" label="Minimum size of Open Reading Frames (ORFs) to display in the translations" />
50 <param name="uppercase" type="text" value="" label="Regions to put in uppercase" />
51 <param name="number" type="select" label="Number the sequence at the beginning and the end of each line">
52 <option value="yes">Yes</option>
53 <option value="no">No</option>
54 </param>
55 <param name="width" type="integer" value="60" label="Number of nucleotides displayed on each line" />
56 <param name="length" type="integer" value="0" label="Line length of page" />
57 <param name="margin" type="integer" value="10" label="Margin around sequence for numbering" />
58 <param name="disp_name" type="select" label="Display the ID name of the sequence">
59 <option value="yes">Yes</option>
60 <option value="no">No</option>
61 </param>
62 <param name="description" type="select" label="Display the description of the sequence">
63 <option value="yes">Yes</option>
64 <option value="no">No</option>
65 </param>
66 <param name="offset" type="integer" value="1" label="Number from which you want the DNA sequence to be numbered" />
67 <param name="html_out1" type="select" label="Format output as an HTML table">
68 <option value="no">No</option>
69 <option value="yes">Yes</option>
70 </param>
71 <param name="out_format2" type="select" label="Output sequence file format">
72 <option value="fasta">FASTA (m)</option>
73 <option value="acedb">ACeDB (m)</option>
74 <option value="asn1">ASN.1 (m)</option>
75 <option value="clustal">Clustal (m)</option>
76 <option value="codata">CODATA (m)</option>
77 <option value="embl">EMBL (m)</option>
78 <option value="fitch">Fitch (m)</option>
79 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
80 <option value="genbank">GENBANK (m)</option>
81 <option value="gff">GFF (m)</option>
82 <option value="hennig86">Hennig86 (m)</option>
83 <option value="ig">Intelligenetics (m)</option>
84 <option value="jackknifer">Jackknifer (m)</option>
85 <option value="jackknifernon">Jackknifernon (m)</option>
86 <option value="mega">Mega (m)</option>
87 <option value="meganon">Meganon (m)</option>
88 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
89 <option value="pir">NBRF (PIR) (m)</option>
90 <option value="ncbi">NCBI style FASTA (m)</option>
91 <option value="nexus">Nexus/PAUP (m)</option>
92 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
93 <option value="phylip">PHYLIP interleaved (m)</option>
94 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
95 <option value="selex">SELEX (m)</option>
96 <option value="staden">Staden (s)</option>
97 <option value="strider">DNA strider (m)</option>
98 <option value="swiss">SwisProt entry (m)</option>
99 <option value="text">Plain sequence (s)</option>
100 <option value="treecon">Treecon (m)</option>
101 </param>
102 </inputs>
103 <outputs>
104 <data name="ofile1" format="sixpack" />
105 <data name="ofile2" format="fasta" />
106 </outputs>
107 <!-- <tests>
108 <test>
109 <param name="input1" value="2.fasta"/>
110 <param name="table" value="0"/>
111 <param name="firstorf" value="no"/>
112 <param name="lastorf" value="no"/>
113 <param name="mstart" value="no"/>
114 <param name="reverse" value="no"/>
115 <param name="orfminsize" value="1"/>
116 <param name="uppercase" value=""/>
117 <param name="number" value="no"/>
118 <param name="width" value="60"/>
119 <param name="length" value="0"/>
120 <param name="margin" value="10"/>
121 <param name="disp_name" value="no"/>
122 <param name="description" value="no"/>
123 <param name="offset" value="1"/>
124 <param name="html_out1" value="no"/>
125 <param name="out_format2" value="fasta"/>
126 <output name="ofile2" file="emboss_sixpack_out.fasta"/>
127 </test>
128 </tests> -->
129 <help>
130 .. class:: warningmark
131
132 The input dataset needs to be sequences.
133
134 -----
135
136 You can view the original documentation here_.
137
138 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/sixpack.html
139 </help>
140 <expand macro="citations" />
141 </tool>