[2] | 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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