Mercurial > repos > devteam > emboss_5
diff emboss_fuzztran.xml @ 10:9b98d3d903c6 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
author | devteam |
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date | Fri, 12 Aug 2016 19:17:10 -0400 |
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children | 0e2484b6829b |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/emboss_fuzztran.xml Fri Aug 12 19:17:10 2016 -0400 @@ -0,0 +1,103 @@ +<tool id="EMBOSS: fuzztran39" name="fuzztran" version="5.0.0"> + <description>Protein pattern search after translation</description> + <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> + <command>fuzztran -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -frame $frame -table $table -rformat2 $out_format1 -auto</command> + <inputs> + <param format="fasta" name="input1" type="data"> + <label>Sequences</label> + </param> + <param name="pattern" type="text" value=""> + <label>Search pattern</label> + </param> + <param name="mismatch" type="text" value="0"> + <label>Number of mismatches</label> + </param> + <param name="frame" type="select"> + <label>Frame(s) to translate</label> + <option value="1">Frame 1</option> + <option value="2">Frame 2</option> + <option value="3">Frame 3</option> + <option value="F">Forward three frames</option> + <option value="-1">Frame -1</option> + <option value="-2">Frame -2</option> + <option value="-3">Frame -3</option> + <option value="R">Reverse three frames</option> + <option value="6">All six frames</option> + </param> + <param name="table" type="select"> + <label>Code to use</label> + <option value="0">Standard</option> + <option value="1">Standard (with alternative initiation codons)</option> + <option value="2">Vertebrate Mitochondrial</option> + <option value="3">Yeast Mitochondrial</option> + <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option> + <option value="5">Invertebrate Mitochondrial</option> + <option value="6">Ciliate Macronuclear and Dasycladacean</option> + <option value="9">Echinoderm Mitochondrial</option> + <option value="10">Euplotid Nuclear</option> + <option value="11">Bacterial</option> + <option value="12">Alternative Yeast Nuclear</option> + <option value="13">Ascidian Mitochondrial</option> + <option value="14">Flatworm Mitochondrial</option> + <option value="15">Blepharisma Macronuclear</option> + <option value="16">Chlorophycean Mitochondrial</option> + <option value="21">Trematode Mitochondrial</option> + <option value="22">Scenedesmus obliquus</option> + <option value="23">Thraustochytrium Mitochondrial</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> + </inputs> + <outputs> + <data format="fuzztran" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="input1" value="1.fasta"/> + <param name="pattern" value="AA"/> + <param name="mismatch" value="0"/> + <param name="frame" value="6"/> + <param name="table" value="0"/> + <param name="out_format1" value="excel"/> + <output name="out_file1" file="emboss_fuzztran_out.tabular"/> + </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/fuzztran.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>