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comparison emboss_sixpack.xml @ 11:0e2484b6829b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
author iuc
date Mon, 30 Jan 2017 13:27:40 -0500
parents 9b98d3d903c6
children 27c43fb015f0
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10:9b98d3d903c6 11:0e2484b6829b
1 <tool id="EMBOSS: sixpack90" name="sixpack" version="5.0.0"> 1 <tool id="EMBOSS: sixpack90" name="sixpack" version="5.0.0.1">
2 <!-- tool adds file description and timestamp to output data --> 2 <!-- tool adds file description and timestamp to output data -->
3 <description>Display a DNA sequence with 6-frame translation and ORFs</description> 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> 4 <macros>
5 <command>sixpack -sequence $input1 -outfile $ofile1 -outseq $ofile2 -table $table -firstorf $firstorf -lastorf $lastorf -mstart $mstart -reverse $reverse -orfminsize $orfminsize -uppercase 5 <import>macros.xml</import>
6 "$uppercase" -number $number -width "$width" -length "$length" -margin "$margin" -name $disp_name -description $description -offset "$offset" -html $html_out1 -osformat $out_format2 -auto</command> 6 </macros>
7 <expand macro="requirements" />
8 <code file="emboss_format_corrector.py" />
9 <command>sixpack -sequence '$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>
7 <inputs> 11 <inputs>
8 <param format="fasta" name="input1" type="data"> 12 <param name="input1" type="data" format="fasta" label="Sequences" />
9 <label>Sequences</label> 13 <param name="table" type="select" label="Code to use">
10 </param>
11 <param name="table" type="select">
12 <label>Code to use</label>
13 <option value="0">Standard</option> 14 <option value="0">Standard</option>
14 <option value="1">Standard (with alternative initiation codons)</option> 15 <option value="1">Standard (with alternative initiation codons)</option>
15 <option value="2">Vertebrate Mitochondrial</option> 16 <option value="2">Vertebrate Mitochondrial</option>
16 <option value="3">Yeast Mitochondrial</option> 17 <option value="3">Yeast Mitochondrial</option>
17 <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option> 18 <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
27 <option value="16">Chlorophycean Mitochondrial</option> 28 <option value="16">Chlorophycean Mitochondrial</option>
28 <option value="21">Trematode Mitochondrial</option> 29 <option value="21">Trematode Mitochondrial</option>
29 <option value="22">Scenedesmus obliquus</option> 30 <option value="22">Scenedesmus obliquus</option>
30 <option value="23">Thraustochytrium Mitochondrial</option> 31 <option value="23">Thraustochytrium Mitochondrial</option>
31 </param> 32 </param>
32 <param name="firstorf" type="select"> 33 <param name="firstorf" type="select" label="Count the beginning of a sequence as a possible ORF">
33 <label>Count the beginning of a sequence as a possible ORF</label>
34 <option value="yes">Yes</option> 34 <option value="yes">Yes</option>
35 <option value="no">No</option> 35 <option value="no">No</option>
36 </param> 36 </param>
37 <param name="lastorf" type="select"> 37 <param name="lastorf" type="select" label="Count the end of a sequence as a possible ORF">
38 <label>Count the end of a sequence as a possible ORF</label>
39 <option value="yes">Yes</option> 38 <option value="yes">Yes</option>
40 <option value="no">No</option> 39 <option value="no">No</option>
41 </param> 40 </param>
42 <param name="mstart" type="select"> 41 <param name="mstart" type="select" label="Displays only ORFs starting with an M">
43 <label>Displays only ORFs starting with an M</label>
44 <option value="no">No</option> 42 <option value="no">No</option>
45 <option value="yes">Yes</option> 43 <option value="yes">Yes</option>
46 </param> 44 </param>
47 <param name="reverse" type="select"> 45 <param name="reverse" type="select" label="Display the translation of the DNA sequence in the 3 reverse frames">
48 <label>Display the translation of the DNA sequence in the 3 reverse frames</label>
49 <option value="yes">Yes</option> 46 <option value="yes">Yes</option>
50 <option value="no">No</option> 47 <option value="no">No</option>
51 </param> 48 </param>
52 <param name="orfminsize" type="text" value="1"> 49 <param name="orfminsize" type="integer" value="1" label="Minimum size of Open Reading Frames (ORFs) to display in the translations" />
53 <label>Minimum size of Open Reading Frames (ORFs) to display in the translations</label> 50 <param name="uppercase" type="text" value="" label="Regions to put in uppercase" />
54 </param> 51 <param name="number" type="select" label="Number the sequence at the beginning and the end of each line">
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> 52 <option value="yes">Yes</option>
61 <option value="no">No</option> 53 <option value="no">No</option>
62 </param> 54 </param>
63 <param name="width" type="text" value="60"> 55 <param name="width" type="integer" value="60" label="Number of nucleotides displayed on each line" />
64 <label>Number of nucleotides displayed on each line</label> 56 <param name="length" type="integer" value="0" label="Line length of page" />
65 </param> 57 <param name="margin" type="integer" value="10" label="Margin around sequence for numbering" />
66 <param name="length" type="text" value="0"> 58 <param name="disp_name" type="select" label="Display the ID name of the sequence">
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> 59 <option value="yes">Yes</option>
75 <option value="no">No</option> 60 <option value="no">No</option>
76 </param> 61 </param>
77 <param name="description" type="select"> 62 <param name="description" type="select" label="Display the description of the sequence">
78 <label>Display the description of the sequence</label>
79 <option value="yes">Yes</option> 63 <option value="yes">Yes</option>
80 <option value="no">No</option> 64 <option value="no">No</option>
81 </param> 65 </param>
82 <param name="offset" type="text" value="1"> 66 <param name="offset" type="integer" value="1" label="Number from which you want the DNA sequence to be numbered" />
83 <label>Number from which you want the DNA sequence to be numbered</label> 67 <param name="html_out1" type="select" label="Format output as an HTML table">
84 </param>
85 <param name="html_out1" type="select">
86 <label>Format output as an HTML table</label>
87 <option value="no">No</option> 68 <option value="no">No</option>
88 <option value="yes">Yes</option> 69 <option value="yes">Yes</option>
89 </param> 70 </param>
90 <param name="out_format2" type="select"> 71 <param name="out_format2" type="select" label="Output sequence file format">
91 <label>Output Sequence File Format</label>
92 <option value="fasta">FASTA (m)</option> 72 <option value="fasta">FASTA (m)</option>
93 <option value="acedb">ACeDB (m)</option> 73 <option value="acedb">ACeDB (m)</option>
94 <option value="asn1">ASN.1 (m)</option> 74 <option value="asn1">ASN.1 (m)</option>
95 <option value="clustal">Clustal (m)</option> 75 <option value="clustal">Clustal (m)</option>
96 <option value="codata">CODATA (m)</option> 76 <option value="codata">CODATA (m)</option>
119 <option value="text">Plain sequence (s)</option> 99 <option value="text">Plain sequence (s)</option>
120 <option value="treecon">Treecon (m)</option> 100 <option value="treecon">Treecon (m)</option>
121 </param> 101 </param>
122 </inputs> 102 </inputs>
123 <outputs> 103 <outputs>
124 <data format="sixpack" name="ofile1" /> 104 <data name="ofile1" format="sixpack" />
125 <data format="fasta" name="ofile2" /> 105 <data name="ofile2" format="fasta" />
126 </outputs> 106 </outputs>
127 <!-- <tests> 107 <!-- <tests>
128 <test> 108 <test>
129 <param name="input1" value="2.fasta"/> 109 <param name="input1" value="2.fasta"/>
130 <param name="table" value="0"/> 110 <param name="table" value="0"/>
144 <param name="html_out1" value="no"/> 124 <param name="html_out1" value="no"/>
145 <param name="out_format2" value="fasta"/> 125 <param name="out_format2" value="fasta"/>
146 <output name="ofile2" file="emboss_sixpack_out.fasta"/> 126 <output name="ofile2" file="emboss_sixpack_out.fasta"/>
147 </test> 127 </test>
148 </tests> --> 128 </tests> -->
149 <code file="emboss_format_corrector.py" />
150 <help> 129 <help>
151
152 .. class:: warningmark 130 .. class:: warningmark
153 131
154 The input dataset needs to be sequences. 132 The input dataset needs to be sequences.
155 133
156 ----- 134 -----
157 135
158 You can view the original documentation here_. 136 You can view the original documentation here_.
159
160 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/sixpack.html
161 137
162 ------ 138 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/sixpack.html
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> 139 </help>
140 <expand macro="citations" />
170 </tool> 141 </tool>