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comparison emboss_transeq.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 d5c3794bd246
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10:9b98d3d903c6 11:0e2484b6829b
1 <tool id="EMBOSS: transeq101" name="transeq" version="5.0.0"> 1 <tool id="EMBOSS: transeq101" name="transeq" version="5.0.0">
2 <description>Translate nucleic acid sequences</description> 2 <description>Translate nucleic acid sequences</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
4 <command><![CDATA[ 8 <command><![CDATA[
5 transeq 9 transeq
6 -sequence '$input1' 10 -sequence '$input1'
7 -outseq '$out_file1' 11 -outseq '$out_file1'
8 -frame $frame 12 -frame $frame
9 -table $table 13 -table $table
10 #if str($regions).strip(): 14 #if str($regions).strip():
11 -regions "$regions" 15 -regions '$regions'
12 #end if 16 #end if
13 -trim $trim 17 -trim $trim
14 -clean $clean 18 -clean $clean
15 -alternative $alternative 19 -alternative $alternative
16 -osformat2 '$out_format1' 20 -osformat2 '$out_format1'
17 -auto 21 -auto
18 ]]> 22 ]]>
19 </command> 23 </command>
20 <inputs> 24 <inputs>
21 <param format="fasta" name="input1" type="data"> 25 <param name="input1" type="data" format="fasta" label="Sequences" />
22 <label>Sequences</label> 26 <param name="frame" type="select" label="Frame(s) to translate">
23 </param>
24 <param name="frame" type="select">
25 <label>Frame(s) to translate</label>
26 <option value="1">Frame 1</option> 27 <option value="1">Frame 1</option>
27 <option value="2">Frame 2</option> 28 <option value="2">Frame 2</option>
28 <option value="3">Frame 3</option> 29 <option value="3">Frame 3</option>
29 <option value="F">Forward three frames</option> 30 <option value="F">Forward three frames</option>
30 <option value="-1">Frame -1</option> 31 <option value="-1">Frame -1</option>
31 <option value="-2">Frame -2</option> 32 <option value="-2">Frame -2</option>
32 <option value="-3">Frame -3</option> 33 <option value="-3">Frame -3</option>
33 <option value="R">Reverse three frames</option> 34 <option value="R">Reverse three frames</option>
34 <option value="6">All six frames</option> 35 <option value="6">All six frames</option>
35 </param> 36 </param>
36 <param name="table" type="select"> 37 <param name="table" type="select" label="Code to use">
37 <label>Code to use</label>
38 <option value="0">Standard</option> 38 <option value="0">Standard</option>
39 <option value="1">Standard (with alternative initiation codons)</option> 39 <option value="1">Standard (with alternative initiation codons)</option>
40 <option value="2">Vertebrate Mitochondrial</option> 40 <option value="2">Vertebrate Mitochondrial</option>
41 <option value="3">Yeast Mitochondrial</option> 41 <option value="3">Yeast Mitochondrial</option>
42 <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option> 42 <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
52 <option value="16">Chlorophycean Mitochondrial</option> 52 <option value="16">Chlorophycean Mitochondrial</option>
53 <option value="21">Trematode Mitochondrial</option> 53 <option value="21">Trematode Mitochondrial</option>
54 <option value="22">Scenedesmus obliquus</option> 54 <option value="22">Scenedesmus obliquus</option>
55 <option value="23">Thraustochytrium Mitochondrial</option> 55 <option value="23">Thraustochytrium Mitochondrial</option>
56 </param> 56 </param>
57 <param name="regions" type="text" value=""> 57 <param name="regions" type="text" value="" label="Regions to translate" />
58 <label>Regions to translate</label> 58 <param name="trim" type="select" label="Remove all 'X' and '*' characters from the right end of the translation">
59 </param>
60 <param name="trim" type="select">
61 <label>Remove all 'X' and '*' characters from the right end of the translation</label>
62 <option value="no">No</option> 59 <option value="no">No</option>
63 <option value="yes">Yes</option> 60 <option value="yes">Yes</option>
64 </param> 61 </param>
65 <param name="clean" type="select"> 62 <param name="clean" type="select" label="Change all STOP codon positions from the '*' character to 'X'">
66 <label>Change all STOP codon positions from the '*' character to 'X'</label>
67 <option value="no">No</option> 63 <option value="no">No</option>
68 <option value="yes">Yes</option> 64 <option value="yes">Yes</option>
69 </param> 65 </param>
70 <param name="alternative" type="select"> 66 <param name="alternative" type="select" label="Define frame '-1' as using the set of codons starting with the last codon of the sequence">
71 <label>Define frame '-1' as using the set of codons starting with the last codon of the sequence</label>
72 <option value="no">No</option> 67 <option value="no">No</option>
73 <option value="yes">Yes</option> 68 <option value="yes">Yes</option>
74 </param> 69 </param>
75 <param name="out_format1" type="select"> 70 <param name="out_format1" type="select" label="Output sequence file format">
76 <label>Output Sequence File Format</label>
77 <option value="fasta">FASTA (m)</option> 71 <option value="fasta">FASTA (m)</option>
78 <option value="acedb">ACeDB (m)</option> 72 <option value="acedb">ACeDB (m)</option>
79 <option value="asn1">ASN.1 (m)</option> 73 <option value="asn1">ASN.1 (m)</option>
80 <option value="clustal">Clustal (m)</option> 74 <option value="clustal">Clustal (m)</option>
81 <option value="codata">CODATA (m)</option> 75 <option value="codata">CODATA (m)</option>
104 <option value="text">Plain sequence (s)</option> 98 <option value="text">Plain sequence (s)</option>
105 <option value="treecon">Treecon (m)</option> 99 <option value="treecon">Treecon (m)</option>
106 </param> 100 </param>
107 </inputs> 101 </inputs>
108 <outputs> 102 <outputs>
109 <data format="fasta" name="out_file1" /> 103 <data name="out_file1" format="fasta" />
110 </outputs> 104 </outputs>
111 <tests> 105 <tests>
112 <test> 106 <test>
113 <param name="input1" value="2.fasta"/> 107 <param name="input1" value="2.fasta"/>
114 <param name="frame" value="1"/> 108 <param name="frame" value="1"/>
119 <param name="alternative" value="no"/> 113 <param name="alternative" value="no"/>
120 <param name="out_format1" value="fasta"/> 114 <param name="out_format1" value="fasta"/>
121 <output name="out_file1" file="emboss_transeq_out.fasta"/> 115 <output name="out_file1" file="emboss_transeq_out.fasta"/>
122 </test> 116 </test>
123 </tests> 117 </tests>
124 <code file="emboss_format_corrector.py" />
125 <help> 118 <help>
126
127 .. class:: warningmark 119 .. class:: warningmark
128 120
129 The input dataset needs to be sequences. 121 The input dataset needs to be sequences.
130 122
131 ----- 123 -----
132 124
133 You can view the original documentation here_. 125 You can view the original documentation here_.
134
135 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/transeq.html
136 126
137 ------ 127 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/transeq.html
138
139 **Citation**
140
141 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;`_
142
143 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;`_
144 </help> 128 </help>
129 <expand macro="citations" />
145 </tool> 130 </tool>