/tools/emboss_5/emboss_tranalign.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 90 lines · 86 code · 4 blank · 0 comment · 0 complexity · ee7b17910fc23c7ab23d397b4071e098 MD5 · raw file
- <tool id="EMBOSS: tranalign100" name="tranalign" version="5.0.0">
- <description>Align nucleic coding regions given the aligned proteins</description>
- <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
- <command>tranalign -asequence $input1 -bsequence $input2 -outseq $out_file1 -table $table -osformat3 $out_format1 -auto</command>
- <inputs>
- <param format="fasta" name="input1" type="data">
- <label>Nucleic Sequences</label>
- </param>
- <param format="data" name="input2" type="data">
- <label>Protein Sequences</label>
- </param>
- <param name="table" type="select">
- <label>Code to use</label>
- <option value="0">Standard</option>
- <option value="1">Standard (with alternative initiation codons)</option>
- <option value="2">Vertebrate Mitochondrial</option>
- <option value="3">Yeast Mitochondrial</option>
- <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
- <option value="5">Invertebrate Mitochondrial</option>
- <option value="6">Ciliate Macronuclear and Dasycladacean</option>
- <option value="9">Echinoderm Mitochondrial</option>
- <option value="10">Euplotid Nuclear</option>
- <option value="11">Bacterial</option>
- <option value="12">Alternative Yeast Nuclear</option>
- <option value="13">Ascidian Mitochondrial</option>
- <option value="14">Flatworm Mitochondrial</option>
- <option value="15">Blepharisma Macronuclear</option>
- <option value="16">Chlorophycean Mitochondrial</option>
- <option value="21">Trematode Mitochondrial</option>
- <option value="22">Scenedesmus obliquus</option>
- <option value="23">Thraustochytrium Mitochondrial</option>
- </param>
- <param name="out_format1" type="select">
- <label>Output Sequence File Format</label>
- <option value="fasta">FASTA (m)</option>
- <option value="acedb">ACeDB (m)</option>
- <option value="asn1">ASN.1 (m)</option>
- <option value="clustal">Clustal (m)</option>
- <option value="codata">CODATA (m)</option>
- <option value="embl">EMBL (m)</option>
- <option value="fitch">Fitch (m)</option>
- <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
- <option value="genbank">GENBANK (m)</option>
- <option value="gff">GFF (m)</option>
- <option value="hennig86">Hennig86 (m)</option>
- <option value="ig">Intelligenetics (m)</option>
- <option value="jackknifer">Jackknifer (m)</option>
- <option value="jackknifernon">Jackknifernon (m)</option>
- <option value="mega">Mega (m)</option>
- <option value="meganon">Meganon (m)</option>
- <option value="msf">Wisconsin Package GCG's MSF (m)</option>
- <option value="pir">NBRF (PIR) (m)</option>
- <option value="ncbi">NCBI style FASTA (m)</option>
- <option value="nexus">Nexus/PAUP (m)</option>
- <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
- <option value="phylip">PHYLIP interleaved (m)</option>
- <option value="phylipnon">PHYLIP non-interleaved (m)</option>
- <option value="selex">SELEX (m)</option>
- <option value="staden">Staden (s)</option>
- <option value="strider">DNA strider (m)</option>
- <option value="swiss">SwisProt entry (m)</option>
- <option value="text">Plain sequence (s)</option>
- <option value="treecon">Treecon (m)</option>
- </param>
- </inputs>
- <outputs>
- <data format="fasta" name="out_file1" />
- </outputs>
- <tests>
- <test>
- <param name="input1" value="3.fasta"/>
- <param name="input2" value="2.pep"/>
- <param name="table" value="0"/>
- <param name="out_format1" value="fasta"/>
- <output name="out_file1" file="emboss_tranalign_out.fasta"/>
- </test>
- </tests>
- <code file="emboss_format_corrector.py" />
- <help>
- You can view the original documentation here_.
-
- .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/tranalign.html
-
- ------
-
- **Citation**
-
- 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>`_
- </help>
- </tool>