/tools/emboss_5/emboss_tranalign.xml

 1<tool id="EMBOSS: tranalign100" name="tranalign" version="5.0.0">
 2  <description>Align nucleic coding regions given the aligned proteins</description>
 3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 4  <command>tranalign -asequence $input1 -bsequence $input2 -outseq $out_file1 -table $table -osformat3 $out_format1 -auto</command>
 5  <inputs>
 6    <param format="fasta" name="input1" type="data">
 7      <label>Nucleic Sequences</label>
 8    </param>
 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>
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="out_format1" type="select">
34      <label>Output Sequence File Format</label>
35      <option value="fasta">FASTA (m)</option>
36      <option value="acedb">ACeDB (m)</option>
37      <option value="asn1">ASN.1 (m)</option>
38      <option value="clustal">Clustal (m)</option>
39      <option value="codata">CODATA (m)</option>
40      <option value="embl">EMBL (m)</option>
41      <option value="fitch">Fitch (m)</option>
42      <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
43      <option value="genbank">GENBANK (m)</option>
44      <option value="gff">GFF (m)</option>
45      <option value="hennig86">Hennig86 (m)</option>
46      <option value="ig">Intelligenetics (m)</option>
47      <option value="jackknifer">Jackknifer (m)</option>
48      <option value="jackknifernon">Jackknifernon (m)</option>
49      <option value="mega">Mega (m)</option>
50      <option value="meganon">Meganon (m)</option>
51      <option value="msf">Wisconsin Package GCG's MSF (m)</option>
52      <option value="pir">NBRF (PIR) (m)</option>
53      <option value="ncbi">NCBI style FASTA (m)</option>
54      <option value="nexus">Nexus/PAUP (m)</option>
55      <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
56      <option value="phylip">PHYLIP interleaved (m)</option>
57      <option value="phylipnon">PHYLIP non-interleaved (m)</option>
58      <option value="selex">SELEX (m)</option>
59      <option value="staden">Staden (s)</option>
60      <option value="strider">DNA strider (m)</option>
61      <option value="swiss">SwisProt entry (m)</option>
62      <option value="text">Plain sequence (s)</option>
63      <option value="treecon">Treecon (m)</option>
64    </param>
65  </inputs>
66  <outputs>
67    <data format="fasta" name="out_file1" />
68  </outputs>
69  <tests>
70    <test>
71      <param name="input1" value="3.fasta"/>
72      <param name="input2" value="2.pep"/>
73      <param name="table" value="0"/>
74      <param name="out_format1" value="fasta"/>
75      <output name="out_file1" file="emboss_tranalign_out.fasta"/>
76    </test>
77  </tests>
78  <code file="emboss_format_corrector.py" />
79  <help>
80    You can view the original documentation here_.
81    
82    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/tranalign.html
83
84------
85
86**Citation**
87
88If 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;`_
89  </help>
90</tool>