/tools/emboss_5/emboss_transeq.xml
XML | 128 lines | 120 code | 8 blank | 0 comment | 0 complexity | 5750776352de454da1c2151e69f010b3 MD5 | raw file
1<tool id="EMBOSS: transeq101" name="transeq" version="5.0.0"> 2 <description>Translate nucleic acid sequences</description> 3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 4 <command>transeq -sequence $input1 -outseq $out_file1 -frame $frame -table $table -regions "$regions" -trim $trim -clean $clean -alternative $alternative -osformat2 $out_format1 -auto</command> 5 <inputs> 6 <param format="fasta" name="input1" type="data"> 7 <label>Sequences</label> 8 </param> 9 <param name="frame" type="select"> 10 <label>Frame(s) to translate</label> 11 <option value="1">Frame 1</option> 12 <option value="2">Frame 2</option> 13 <option value="3">Frame 3</option> 14 <option value="F">Forward three frames</option> 15 <option value="-1">Frame -1</option> 16 <option value="-2">Frame -2</option> 17 <option value="-3">Frame -3</option> 18 <option value="R">Reverse three frames</option> 19 <option value="6">All six frames</option> 20 </param> 21 <param name="table" type="select"> 22 <label>Code to use</label> 23 <option value="0">Standard</option> 24 <option value="1">Standard (with alternative initiation codons)</option> 25 <option value="2">Vertebrate Mitochondrial</option> 26 <option value="3">Yeast Mitochondrial</option> 27 <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option> 28 <option value="5">Invertebrate Mitochondrial</option> 29 <option value="6">Ciliate Macronuclear and Dasycladacean</option> 30 <option value="9">Echinoderm Mitochondrial</option> 31 <option value="10">Euplotid Nuclear</option> 32 <option value="11">Bacterial</option> 33 <option value="12">Alternative Yeast Nuclear</option> 34 <option value="13">Ascidian Mitochondrial</option> 35 <option value="14">Flatworm Mitochondrial</option> 36 <option value="15">Blepharisma Macronuclear</option> 37 <option value="16">Chlorophycean Mitochondrial</option> 38 <option value="21">Trematode Mitochondrial</option> 39 <option value="22">Scenedesmus obliquus</option> 40 <option value="23">Thraustochytrium Mitochondrial</option> 41 </param> 42 <param name="regions" size="10" type="text" value=""> 43 <label>Regions to translate</label> 44 </param> 45 <param name="trim" type="select"> 46 <label>Remove all 'X' and '*' characters from the right end of the translation</label> 47 <option value="no">No</option> 48 <option value="yes">Yes</option> 49 </param> 50 <param name="clean" type="select"> 51 <label>Change all STOP codon positions from the '*' character to 'X'</label> 52 <option value="no">No</option> 53 <option value="yes">Yes</option> 54 </param> 55 <param name="alternative" type="select"> 56 <label>Define frame '-1' as using the set of codons starting with the last codon of the sequence</label> 57 <option value="no">No</option> 58 <option value="yes">Yes</option> 59 </param> 60 <param name="out_format1" type="select"> 61 <label>Output Sequence File Format</label> 62 <option value="fasta">FASTA (m)</option> 63 <option value="acedb">ACeDB (m)</option> 64 <option value="asn1">ASN.1 (m)</option> 65 <option value="clustal">Clustal (m)</option> 66 <option value="codata">CODATA (m)</option> 67 <option value="embl">EMBL (m)</option> 68 <option value="fitch">Fitch (m)</option> 69 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option> 70 <option value="genbank">GENBANK (m)</option> 71 <option value="gff">GFF (m)</option> 72 <option value="hennig86">Hennig86 (m)</option> 73 <option value="ig">Intelligenetics (m)</option> 74 <option value="jackknifer">Jackknifer (m)</option> 75 <option value="jackknifernon">Jackknifernon (m)</option> 76 <option value="mega">Mega (m)</option> 77 <option value="meganon">Meganon (m)</option> 78 <option value="msf">Wisconsin Package GCG's MSF (m)</option> 79 <option value="pir">NBRF (PIR) (m)</option> 80 <option value="ncbi">NCBI style FASTA (m)</option> 81 <option value="nexus">Nexus/PAUP (m)</option> 82 <option value="nexusnon">Nexusnon/PAUPnon (m)</option> 83 <option value="phylip">PHYLIP interleaved (m)</option> 84 <option value="phylipnon">PHYLIP non-interleaved (m)</option> 85 <option value="selex">SELEX (m)</option> 86 <option value="staden">Staden (s)</option> 87 <option value="strider">DNA strider (m)</option> 88 <option value="swiss">SwisProt entry (m)</option> 89 <option value="text">Plain sequence (s)</option> 90 <option value="treecon">Treecon (m)</option> 91 </param> 92 </inputs> 93 <outputs> 94 <data format="fasta" name="out_file1" /> 95 </outputs> 96 <tests> 97 <test> 98 <param name="input1" value="2.fasta"/> 99 <param name="frame" value="1"/> 100 <param name="table" value="0"/> 101 <param name="regions" value=""/> 102 <param name="trim" value="no"/> 103 <param name="clean" value="no"/> 104 <param name="alternative" value="no"/> 105 <param name="out_format1" value="fasta"/> 106 <output name="out_file1" file="emboss_transeq_out.fasta"/> 107 </test> 108 </tests> 109 <code file="emboss_format_corrector.py" /> 110 <help> 111 112.. class:: warningmark 113 114The input dataset needs to be sequences. 115 116----- 117 118 You can view the original documentation here_. 119 120 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/transeq.html 121 122------ 123 124**Citation** 125 126If 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>`_ 127 </help> 128</tool>