Mercurial > repos > devteam > emboss_5
diff emboss_sirna.xml @ 11:0e2484b6829b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
| author | iuc |
|---|---|
| date | Mon, 30 Jan 2017 13:27:40 -0500 |
| parents | 9b98d3d903c6 |
| children | 27c43fb015f0 |
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--- a/emboss_sirna.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_sirna.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,92 +1,87 @@ -<tool id="EMBOSS: sirna89" name="sirna" version="5.0.0"> - <description>Finds siRNA duplexes in mRNA</description> - <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> - <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 format="fasta" name="input1" type="data"> - <label>Sequences</label> - </param> - <param name="poliii" type="select"> - <label>Select only the 21 base probes that start with a purine (Pol III expression vectors)</label> - <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</label> - <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</label> - <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</label> - <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</label> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <param name="out_format1" type="select"> - <label>Output Report File Format</label> - <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</label> - <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 format="table" name="ofile1" /> - <data format="fasta" name="ofile2" /> +<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> @@ -101,10 +96,8 @@ <param name="out_format2" value="fasta"/> <output name="ofile2" file="emboss_sirna_out.fasta"/> </test> - </tests> - <code file="emboss_format_corrector.py" /> + </tests> <help> - .. class:: warningmark The input dataset needs to be sequences. @@ -112,15 +105,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/sirna.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/sirna.html </help> + <expand macro="citations" /> </tool>