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