/tools/emboss_5/emboss_fuzztran.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 101 lines · 93 code · 8 blank · 0 comment · 0 complexity · 7ddd4269ac0177d4ca83453a506f6a91 MD5 · raw file
- <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" size="5" type="text" value="">
- <label>Search pattern</label>
- </param>
- <param name="mismatch" size="5" 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**
-
- 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>