/tools/emboss_5/emboss_matcher.xml
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1<tool id="EMBOSS: matcher52" name="matcher" version="5.0.0"> 2 <description>Finds the best local alignments between two sequences</description> 3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 4 <command>matcher -asequence $input1 -bsequence $input2 -outfile $out_file1 -alternatives $alternatives -gapopen $gapopen -gapextend $gapextend -aformat3 $out_format1 -auto</command> 5 <inputs> 6 <param format="data" name="input1" type="data"> 7 <label>Sequence 1</label> 8 </param> 9 <param format="data" name="input2" type="data"> 10 <label>Sequence 2</label> 11 </param> 12 <param name="alternatives" size="4" type="text" value="1"> 13 <label>Number of alternative matches</label> 14 </param> 15 <param name="gapopen" size="4" type="text" value="16"> 16 <label>Gap penalty</label> 17 </param> 18 <param name="gapextend" size="4" type="text" value="4"> 19 <label>Gap length (extension) penalty</label> 20 </param> 21 <param name="out_format1" type="select"> 22 <label>Output Alignment File Format</label> 23 <option value="markx0">Markx0 (p)</option> 24 <option value="simple">Simple (m)</option> 25 <option value="fasta">FASTA (m)</option> 26 <option value="msf">MSF (m)</option> 27 <option value="srs">SRS (m)</option> 28 <option value="pair">Pair (p)</option> 29 <option value="markx1">Markx1 (p)</option> 30 <option value="markx2">Markx2 (p)</option> 31 <option value="markx3">Markx3 (p)</option> 32 <option value="markx10">Markx10 (p)</option> 33 <option value="srspair">SRS pair (p)</option> 34 <option value="score">Score (p)</option> 35 </param> 36 </inputs> 37 <outputs> 38 <data format="markx0" name="out_file1" /> 39 </outputs> 40 <tests> 41 <test> 42 <param name="input1" value="2.fasta"/> 43 <param name="input2" value="1.fasta"/> 44 <param name="alternatives" value="1"/> 45 <param name="gapopen" value="16"/> 46 <param name="gapextend" value="4"/> 47 <param name="out_format1" value="fasta"/> 48 <output name="out_file1" file="emboss_matcher_out.fasta"/> 49 </test> 50 </tests> 51 <code file="emboss_format_corrector.py" /> 52 <help> 53 You can view the original documentation here_. 54 55 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/matcher.html 56 57------ 58 59**Citation** 60 61If 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>`_ 62 </help> 63</tool>