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104 lines
4.4 KiB
XML
104 lines
4.4 KiB
XML
<tool id="EMBOSS: sirna89" name="sirna">
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<description>Finds siRNA duplexes in mRNA</description>
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<command>sirna -sequence $input1 -outfile $out_file1 -outseq $out_file2 -poliii $poliii -aa $aa -tt $tt -polybase $polybase -context $context -rformat2 $out_format1 -osformat3 $out_format2
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-auto</command>
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<inputs>
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<param format="fasta" name="input1" type="data">
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<label>Sequences</label>
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</param>
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<param name="poliii" type="select">
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<label>Select only the 21 base probes that start with a purine (Pol III expression vectors)</label>
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<option value="no">No</option>
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<option value="yes">Yes</option>
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</param>
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<param name="aa" type="select">
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<label>Select only those 23 base regions that start with AA</label>
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<option value="no">No</option>
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<option value="yes">Yes</option>
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</param>
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<param name="tt" type="select">
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<label>Select only those 23 base regions that end with TT</label>
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<option value="no">No</option>
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<option value="yes">Yes</option>
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</param>
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<param name="polybase" type="select">
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<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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<option value="yes ">Yes</option>
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<option value="no">No</option>
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</param>
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<param name="context" type="select">
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<label>Displays the whole 23 bases of the region with the first two bases in brackets</label>
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<option value="no">No</option>
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<option value="yes">Yes</option>
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</param>
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<param name="out_format1" type="select">
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<label>Output Report File Format</label>
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<option value="table">Table</option>
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<option value="embl">EMBL</option>
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<option value="genbank">GENBANK</option>
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<option value="gff">GFF</option>
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<option value="pir">PIR</option>
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<option value="swiss">SwissProt</option>
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<option value="dbmotif">DbMotif</option>
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<option value="diffseq">Diffseq</option>
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<option value="excel">Excel (tab delimited)</option>
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<option value="feattable">FeatTable</option>
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<option value="motif">Motif</option>
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<option value="regions">Regions</option>
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<option value="seqtable">SeqTable</option>
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<option value="simple">SRS Simple</option>
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<option value="srs">SRS</option>
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<option value="tagseq">TagSeq</option>
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</param>
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<param name="out_format2" type="select">
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<label>Output Sequence File Format</label>
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<option value="fasta">FASTA (m)</option>
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<option value="acedb">ACeDB (m)</option>
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<option value="asn1">ASN.1 (m)</option>
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<option value="clustal">Clustal (m)</option>
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<option value="codata">CODATA (m)</option>
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<option value="embl">EMBL (m)</option>
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<option value="fitch">Fitch (m)</option>
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<option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
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<option value="genbank">GENBANK (m)</option>
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<option value="gff">GFF (m)</option>
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<option value="hennig86">Hennig86 (m)</option>
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<option value="ig">Intelligenetics (m)</option>
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<option value="jackknifer">Jackknifer (m)</option>
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<option value="jackknifernon">Jackknifernon (m)</option>
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<option value="mega">Mega (m)</option>
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<option value="meganon">Meganon (m)</option>
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<option value="msf">Wisconsin Package GCG's MSF (m)</option>
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<option value="pir">NBRF (PIR) (m)</option>
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<option value="ncbi">NCBI style FASTA (m)</option>
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<option value="nexus">Nexus/PAUP (m)</option>
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<option value="nexusnon">Nexusnon/PAUPnon (m)</option>
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<option value="phylip">PHYLIP interleaved (m)</option>
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<option value="phylipnon">PHYLIP non-interleaved (m)</option>
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<option value="selex">SELEX (m)</option>
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<option value="staden">Staden (s)</option>
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<option value="strider">DNA strider (m)</option>
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<option value="swiss">SwisProt entry (m)</option>
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<option value="text">Plain sequence (s)</option>
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<option value="treecon">Treecon (m)</option>
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</param>
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</inputs>
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<outputs>
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<data format="table" name="out_file1" />
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<data format="fasta" name="out_file2" />
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</outputs>
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<code file="emboss_format_corrector.py" />
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<help>
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.. class:: warningmark
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The input dataset needs to be sequences.
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-----
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You can view the original documentation here_.
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.. _here: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/sirna.html
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</help>
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</tool>
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