Mercurial > repos > xuebing > sharplabtool
comparison tools/emboss_5/emboss_fuzztran.xml @ 0:9071e359b9a3
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 <tool id="EMBOSS: fuzztran39" name="fuzztran" version="5.0.0"> | |
| 2 <description>Protein pattern search after translation</description> | |
| 3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
| 4 <command>fuzztran -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -frame $frame -table $table -rformat2 $out_format1 -auto</command> | |
| 5 <inputs> | |
| 6 <param format="fasta" name="input1" type="data"> | |
| 7 <label>Sequences</label> | |
| 8 </param> | |
| 9 <param name="pattern" size="5" type="text" value=""> | |
| 10 <label>Search pattern</label> | |
| 11 </param> | |
| 12 <param name="mismatch" size="5" type="text" value="0"> | |
| 13 <label>Number of mismatches</label> | |
| 14 </param> | |
| 15 <param name="frame" type="select"> | |
| 16 <label>Frame(s) to translate</label> | |
| 17 <option value="1">Frame 1</option> | |
| 18 <option value="2">Frame 2</option> | |
| 19 <option value="3">Frame 3</option> | |
| 20 <option value="F">Forward three frames</option> | |
| 21 <option value="-1">Frame -1</option> | |
| 22 <option value="-2">Frame -2</option> | |
| 23 <option value="-3">Frame -3</option> | |
| 24 <option value="R">Reverse three frames</option> | |
| 25 <option value="6">All six frames</option> | |
| 26 </param> | |
| 27 <param name="table" type="select"> | |
| 28 <label>Code to use</label> | |
| 29 <option value="0">Standard</option> | |
| 30 <option value="1">Standard (with alternative initiation codons)</option> | |
| 31 <option value="2">Vertebrate Mitochondrial</option> | |
| 32 <option value="3">Yeast Mitochondrial</option> | |
| 33 <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option> | |
| 34 <option value="5">Invertebrate Mitochondrial</option> | |
| 35 <option value="6">Ciliate Macronuclear and Dasycladacean</option> | |
| 36 <option value="9">Echinoderm Mitochondrial</option> | |
| 37 <option value="10">Euplotid Nuclear</option> | |
| 38 <option value="11">Bacterial</option> | |
| 39 <option value="12">Alternative Yeast Nuclear</option> | |
| 40 <option value="13">Ascidian Mitochondrial</option> | |
| 41 <option value="14">Flatworm Mitochondrial</option> | |
| 42 <option value="15">Blepharisma Macronuclear</option> | |
| 43 <option value="16">Chlorophycean Mitochondrial</option> | |
| 44 <option value="21">Trematode Mitochondrial</option> | |
| 45 <option value="22">Scenedesmus obliquus</option> | |
| 46 <option value="23">Thraustochytrium Mitochondrial</option> | |
| 47 </param> | |
| 48 <param name="out_format1" type="select"> | |
| 49 <label>Output Report File Format</label> | |
| 50 <option value="table">Table</option> | |
| 51 <option value="embl">EMBL</option> | |
| 52 <option value="genbank">GENBANK</option> | |
| 53 <option value="gff">GFF</option> | |
| 54 <option value="pir">PIR</option> | |
| 55 <option value="swiss">SwissProt</option> | |
| 56 <option value="dbmotif">DbMotif</option> | |
| 57 <option value="diffseq">Diffseq</option> | |
| 58 <option value="excel">Excel (tab delimited)</option> | |
| 59 <option value="feattable">FeatTable</option> | |
| 60 <option value="motif">Motif</option> | |
| 61 <option value="regions">Regions</option> | |
| 62 <option value="seqtable">SeqTable</option> | |
| 63 <option value="simple">SRS Simple</option> | |
| 64 <option value="srs">SRS</option> | |
| 65 <option value="tagseq">TagSeq</option> | |
| 66 </param> | |
| 67 </inputs> | |
| 68 <outputs> | |
| 69 <data format="fuzztran" name="out_file1" /> | |
| 70 </outputs> | |
| 71 <tests> | |
| 72 <test> | |
| 73 <param name="input1" value="1.fasta"/> | |
| 74 <param name="pattern" value="AA"/> | |
| 75 <param name="mismatch" value="0"/> | |
| 76 <param name="frame" value="6"/> | |
| 77 <param name="table" value="0"/> | |
| 78 <param name="out_format1" value="excel"/> | |
| 79 <output name="out_file1" file="emboss_fuzztran_out.tabular"/> | |
| 80 </test> | |
| 81 </tests> | |
| 82 <code file="emboss_format_corrector.py" /> | |
| 83 <help> | |
| 84 | |
| 85 .. class:: warningmark | |
| 86 | |
| 87 The input dataset needs to be sequences. | |
| 88 | |
| 89 ----- | |
| 90 | |
| 91 You can view the original documentation here_. | |
| 92 | |
| 93 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzztran.html | |
| 94 </help> | |
| 95 </tool> |