Mercurial > repos > devteam > emboss_5
comparison emboss_tranalign.xml @ 11:0e2484b6829b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
author | iuc |
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date | Mon, 30 Jan 2017 13:27:40 -0500 |
parents | 9b98d3d903c6 |
children | d5c3794bd246 |
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10:9b98d3d903c6 | 11:0e2484b6829b |
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1 <tool id="EMBOSS: tranalign100" name="tranalign" version="5.0.0"> | 1 <tool id="EMBOSS: tranalign100" name="tranalign" version="5.0.0"> |
2 <description>Align nucleic coding regions given the aligned proteins</description> | 2 <description>Align nucleic coding regions given the aligned proteins</description> |
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | 3 <macros> |
4 <command>tranalign -asequence $input1 -bsequence $input2 -outseq $out_file1 -table $table -osformat3 $out_format1 -auto</command> | 4 <import>macros.xml</import> |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <code file="emboss_format_corrector.py" /> | |
8 <command>tranalign -asequence '$input1' -bsequence '$input2' -outseq '$out_file1' -table $table -osformat3 $out_format1 -auto</command> | |
5 <inputs> | 9 <inputs> |
6 <param format="fasta" name="input1" type="data"> | 10 <param name="input1" type="data" format="fasta" label="Nucleic sequences" /> |
7 <label>Nucleic Sequences</label> | 11 <param name="input2" type="data" format="data" label="Protein sequences" /> |
8 </param> | 12 <param name="table" type="select" label="Code to use"> |
9 <param format="data" name="input2" type="data"> | |
10 <label>Protein Sequences</label> | |
11 </param> | |
12 <param name="table" type="select"> | |
13 <label>Code to use</label> | |
14 <option value="0">Standard</option> | 13 <option value="0">Standard</option> |
15 <option value="1">Standard (with alternative initiation codons)</option> | 14 <option value="1">Standard (with alternative initiation codons)</option> |
16 <option value="2">Vertebrate Mitochondrial</option> | 15 <option value="2">Vertebrate Mitochondrial</option> |
17 <option value="3">Yeast Mitochondrial</option> | 16 <option value="3">Yeast Mitochondrial</option> |
18 <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option> | 17 <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option> |
28 <option value="16">Chlorophycean Mitochondrial</option> | 27 <option value="16">Chlorophycean Mitochondrial</option> |
29 <option value="21">Trematode Mitochondrial</option> | 28 <option value="21">Trematode Mitochondrial</option> |
30 <option value="22">Scenedesmus obliquus</option> | 29 <option value="22">Scenedesmus obliquus</option> |
31 <option value="23">Thraustochytrium Mitochondrial</option> | 30 <option value="23">Thraustochytrium Mitochondrial</option> |
32 </param> | 31 </param> |
33 <param name="out_format1" type="select"> | 32 <param name="out_format1" type="select" label="Output sequence file format"> |
34 <label>Output Sequence File Format</label> | |
35 <option value="fasta">FASTA (m)</option> | 33 <option value="fasta">FASTA (m)</option> |
36 <option value="acedb">ACeDB (m)</option> | 34 <option value="acedb">ACeDB (m)</option> |
37 <option value="asn1">ASN.1 (m)</option> | 35 <option value="asn1">ASN.1 (m)</option> |
38 <option value="clustal">Clustal (m)</option> | 36 <option value="clustal">Clustal (m)</option> |
39 <option value="codata">CODATA (m)</option> | 37 <option value="codata">CODATA (m)</option> |
62 <option value="text">Plain sequence (s)</option> | 60 <option value="text">Plain sequence (s)</option> |
63 <option value="treecon">Treecon (m)</option> | 61 <option value="treecon">Treecon (m)</option> |
64 </param> | 62 </param> |
65 </inputs> | 63 </inputs> |
66 <outputs> | 64 <outputs> |
67 <data format="fasta" name="out_file1" /> | 65 <data name="out_file1" format="fasta" /> |
68 </outputs> | 66 </outputs> |
69 <tests> | 67 <tests> |
70 <test> | 68 <test> |
71 <param name="input1" value="3.fasta"/> | 69 <param name="input1" value="3.fasta"/> |
72 <param name="input2" value="2.pep"/> | 70 <param name="input2" value="2.pep"/> |
73 <param name="table" value="0"/> | 71 <param name="table" value="0"/> |
74 <param name="out_format1" value="fasta"/> | 72 <param name="out_format1" value="fasta"/> |
75 <output name="out_file1" file="emboss_tranalign_out.fasta"/> | 73 <output name="out_file1" file="emboss_tranalign_out.fasta"/> |
76 </test> | 74 </test> |
77 </tests> | 75 </tests> |
78 <code file="emboss_format_corrector.py" /> | |
79 <help> | 76 <help> |
80 You can view the original documentation here_. | 77 You can view the original documentation here_. |
81 | |
82 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/tranalign.html | |
83 | 78 |
84 ------ | 79 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/tranalign.html |
85 | |
86 **Citation** | |
87 | |
88 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. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ | |
89 | |
90 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. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ | |
91 </help> | 80 </help> |
81 <expand macro="citations" /> | |
92 </tool> | 82 </tool> |