Mercurial > repos > devteam > emboss_5
view emboss_5/emboss_equicktandem.xml @ 5:2cf967772a40
Fix for emboss_format_corrector.py. Datatypes should be changed before the job is run.
author | Daniel Blankenberg <dan@bx.psu.edu> |
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date | Fri, 11 Oct 2013 14:10:00 -0400 |
parents | b94ca591877b |
children | b810c96613ee |
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<tool id="EMBOSS: equicktandem31" name="equicktandem" version="5.0.0"> <description>Finds tandem repeats</description> <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> <command>equicktandem -sequence $input1 -outfile $out_file1 -origfile $ofile2 -maxrepeat $maxrepeat -threshold $threshold -rformat2 $out_format1 -auto</command> <inputs> <param format="fasta" name="input1" type="data"> <label>Sequence</label> </param> <param name="maxrepeat" size="4" type="text" value="600"> <label>Maximum repeat size</label> </param> <param name="threshold" size="4" type="text" value="20"> <label>Threshold score</label> </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> </inputs> <outputs> <data format="table" name="out_file1" /> <data format="equicktandem" name="ofile2" /> </outputs> <tests> <test> <param name="input1" value="1.fasta"/> <param name="maxrepeat" value="600"/> <param name="threshold" value="20"/> <param name="out_format1" value="table"/> <output name="ofile2" file="emboss_equicktandem_out.equicktandem"/> </test> </tests> <code file="emboss_format_corrector.py" /> <help> .. class:: warningmark The input dataset needs to be sequences. ----- You can view the original documentation here_. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/equicktandem.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>`_ </help> </tool>