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view emboss_sirna.xml @ 12:832c20329690 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
author | iuc |
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date | Mon, 23 Apr 2018 13:05:09 -0400 |
parents | d49956b87f7e |
children | 8992d258e42f |
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<tool id="EMBOSS: sirna89" name="sirna" version="5.0.0"> <description>Finds siRNA duplexes in mRNA</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <code file="emboss_format_corrector.py" /> <command>sirna -sequence '$input1' -outfile '$ofile1' -outseq '$ofile2' -poliii $poliii -aa $aa -tt $tt -polybase $polybase -context $context -rformat2 $out_format1 -osformat3 $out_format2 -auto</command> <inputs> <param name="input1" type="data" format="fasta" label="Sequences" /> <param name="poliii" type="select" label="Select only the 21 base probes that start with a purine (Pol III expression vectors)"> <option value="no">No</option> <option value="yes">Yes</option> </param> <param name="aa" type="select" label="Select only those 23 base regions that start with AA"> <option value="no">No</option> <option value="yes">Yes</option> </param> <param name="tt" type="select" label="Select only those 23 base regions that end with TT"> <option value="no">No</option> <option value="yes">Yes</option> </param> <param name="polybase" type="select" label="Report more than those 23 base regions that have no repeat of 4 or more of any bases in a row"> <option value="yes">Yes</option> <option value="no">No</option> </param> <param name="context" type="select" label="Displays the whole 23 bases of the region with the first two bases in brackets"> <option value="no">No</option> <option value="yes">Yes</option> </param> <param name="out_format1" type="select" label="Output report file format"> <option value="table">Table</option> <option value="embl">EMBL</option> <option value="genbank">GENBANK</option> <option value="gff">GFF</option> <option value="pir">PIR</option> <option value="swiss">SwissProt</option> <option value="dbmotif">DbMotif</option> <option value="diffseq">Diffseq</option> <option value="excel">Excel (tab delimited)</option> <option value="feattable">FeatTable</option> <option value="motif">Motif</option> <option value="regions">Regions</option> <option value="seqtable">SeqTable</option> <option value="simple">SRS Simple</option> <option value="srs">SRS</option> <option value="tagseq">TagSeq</option> </param> <param name="out_format2" type="select" label="Output sequence file format"> <option value="fasta">FASTA (m)</option> <option value="acedb">ACeDB (m)</option> <option value="asn1">ASN.1 (m)</option> <option value="clustal">Clustal (m)</option> <option value="codata">CODATA (m)</option> <option value="embl">EMBL (m)</option> <option value="fitch">Fitch (m)</option> <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option> <option value="genbank">GENBANK (m)</option> <option value="gff">GFF (m)</option> <option value="hennig86">Hennig86 (m)</option> <option value="ig">Intelligenetics (m)</option> <option value="jackknifer">Jackknifer (m)</option> <option value="jackknifernon">Jackknifernon (m)</option> <option value="mega">Mega (m)</option> <option value="meganon">Meganon (m)</option> <option value="msf">Wisconsin Package GCG's MSF (m)</option> <option value="pir">NBRF (PIR) (m)</option> <option value="ncbi">NCBI style FASTA (m)</option> <option value="nexus">Nexus/PAUP (m)</option> <option value="nexusnon">Nexusnon/PAUPnon (m)</option> <option value="phylip">PHYLIP interleaved (m)</option> <option value="phylipnon">PHYLIP non-interleaved (m)</option> <option value="selex">SELEX (m)</option> <option value="staden">Staden (s)</option> <option value="strider">DNA strider (m)</option> <option value="swiss">SwisProt entry (m)</option> <option value="text">Plain sequence (s)</option> <option value="treecon">Treecon (m)</option> </param> </inputs> <outputs> <data name="ofile1" format="table" /> <data name="ofile2" format="fasta" /> </outputs> <tests> <test> <param name="input1" value="2.fasta"/> <param name="poliii" value="no"/> <param name="aa" value="no"/> <param name="tt" value="no"/> <param name="polybase" value="yes"/> <param name="context" value="no"/> <param name="mismatchpercent" value="0"/> <param name="out_format1" value="gff"/> <param name="out_format2" value="fasta"/> <output name="ofile2" file="emboss_sirna_out.fasta"/> </test> </tests> <help> .. class:: warningmark The input dataset needs to be sequences. ----- You can view the original documentation here_. .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/sirna.html </help> <expand macro="citations" /> </tool>