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1 <tool id="EMBOSS: sirna89" name="sirna" version="5.0.0">
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2 <description>Finds siRNA duplexes in mRNA</description>
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3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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4 <command>sirna -sequence $input1 -outfile $ofile1 -outseq $ofile2 -poliii $poliii -aa $aa -tt $tt -polybase $polybase -context $context -rformat2 $out_format1 -osformat3 $out_format2
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5 -auto</command>
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6 <inputs>
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7 <param format="fasta" name="input1" type="data">
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8 <label>Sequences</label>
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9 </param>
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10 <param name="poliii" type="select">
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11 <label>Select only the 21 base probes that start with a purine (Pol III expression vectors)</label>
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12 <option value="no">No</option>
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13 <option value="yes">Yes</option>
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14 </param>
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15 <param name="aa" type="select">
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16 <label>Select only those 23 base regions that start with AA</label>
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17 <option value="no">No</option>
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18 <option value="yes">Yes</option>
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19 </param>
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20 <param name="tt" type="select">
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21 <label>Select only those 23 base regions that end with TT</label>
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22 <option value="no">No</option>
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23 <option value="yes">Yes</option>
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24 </param>
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25 <param name="polybase" type="select">
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26 <label>Report more than those 23 base regions that have no repeat of 4 or more of any bases in a row</label>
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27 <option value="yes">Yes</option>
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28 <option value="no">No</option>
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29 </param>
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30 <param name="context" type="select">
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31 <label>Displays the whole 23 bases of the region with the first two bases in brackets</label>
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32 <option value="no">No</option>
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33 <option value="yes">Yes</option>
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34 </param>
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35 <param name="out_format1" type="select">
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36 <label>Output Report File Format</label>
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37 <option value="table">Table</option>
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38 <option value="embl">EMBL</option>
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39 <option value="genbank">GENBANK</option>
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40 <option value="gff">GFF</option>
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41 <option value="pir">PIR</option>
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42 <option value="swiss">SwissProt</option>
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43 <option value="dbmotif">DbMotif</option>
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44 <option value="diffseq">Diffseq</option>
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45 <option value="excel">Excel (tab delimited)</option>
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46 <option value="feattable">FeatTable</option>
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47 <option value="motif">Motif</option>
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48 <option value="regions">Regions</option>
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49 <option value="seqtable">SeqTable</option>
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50 <option value="simple">SRS Simple</option>
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51 <option value="srs">SRS</option>
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52 <option value="tagseq">TagSeq</option>
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53 </param>
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54 <param name="out_format2" type="select">
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55 <label>Output Sequence File Format</label>
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56 <option value="fasta">FASTA (m)</option>
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57 <option value="acedb">ACeDB (m)</option>
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58 <option value="asn1">ASN.1 (m)</option>
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59 <option value="clustal">Clustal (m)</option>
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60 <option value="codata">CODATA (m)</option>
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61 <option value="embl">EMBL (m)</option>
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62 <option value="fitch">Fitch (m)</option>
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63 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
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64 <option value="genbank">GENBANK (m)</option>
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65 <option value="gff">GFF (m)</option>
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66 <option value="hennig86">Hennig86 (m)</option>
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67 <option value="ig">Intelligenetics (m)</option>
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68 <option value="jackknifer">Jackknifer (m)</option>
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69 <option value="jackknifernon">Jackknifernon (m)</option>
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70 <option value="mega">Mega (m)</option>
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71 <option value="meganon">Meganon (m)</option>
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72 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
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73 <option value="pir">NBRF (PIR) (m)</option>
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74 <option value="ncbi">NCBI style FASTA (m)</option>
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75 <option value="nexus">Nexus/PAUP (m)</option>
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76 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
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77 <option value="phylip">PHYLIP interleaved (m)</option>
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78 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
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79 <option value="selex">SELEX (m)</option>
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80 <option value="staden">Staden (s)</option>
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81 <option value="strider">DNA strider (m)</option>
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82 <option value="swiss">SwisProt entry (m)</option>
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83 <option value="text">Plain sequence (s)</option>
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84 <option value="treecon">Treecon (m)</option>
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85 </param>
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86 </inputs>
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87 <outputs>
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88 <data format="table" name="ofile1" />
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89 <data format="fasta" name="ofile2" />
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90 </outputs>
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91 <tests>
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92 <test>
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93 <param name="input1" value="2.fasta"/>
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94 <param name="poliii" value="no"/>
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95 <param name="aa" value="no"/>
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96 <param name="tt" value="no"/>
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97 <param name="polybase" value="yes"/>
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98 <param name="context" value="no"/>
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99 <param name="mismatchpercent" value="0"/>
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100 <param name="out_format1" value="gff"/>
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101 <param name="out_format2" value="fasta"/>
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102 <output name="ofile2" file="emboss_sirna_out.fasta"/>
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103 </test>
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104 </tests>
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105 <code file="emboss_format_corrector.py" />
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106 <help>
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107
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108 .. class:: warningmark
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109
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110 The input dataset needs to be sequences.
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111
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112 -----
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113
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114 You can view the original documentation here_.
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115
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116 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/sirna.html
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117 </help>
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118 </tool>
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