/tools/emboss_5/emboss_wordmatch.xml
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1<tool id="EMBOSS: wordmatch110" name="wordmatch" version="5.0.0"> 2 <description>Finds all exact matches of a given size between 2 sequences</description> 3 <command>wordmatch -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize "$wordsize" -aformat3 $out_format1 -offormat4 $out_format2 4 -offormat5 $out_format3 -auto</command> 5 <inputs> 6 <param format="fasta" name="input1" type="data"> 7 <label>Sequence 1</label> 8 </param> 9 <param format="fasta" name="input2" type="data"> 10 <label>Sequence 2</label> 11 </param> 12 <param name="wordsize" size="5" type="text" value="4"> 13 <label>Word size</label> 14 </param> 15 <param name="out_format1" type="select"> 16 <label>Output Alignment File Format</label> 17 <option value="match">Match (m)</option> 18 <option value="simple">Simple (m)</option> 19 <option value="fasta">FASTA (m)</option> 20 <option value="msf">MSF (m)</option> 21 <option value="srs">SRS (m)</option> 22 <option value="pair">Pair (p)</option> 23 <option value="markx0">Markx0 (p)</option> 24 <option value="markx1">Markx1 (p)</option> 25 <option value="markx2">Markx2 (p)</option> 26 <option value="markx3">Markx3 (p)</option> 27 <option value="markx10">Markx10 (p)</option> 28 <option value="srspair">SRS pair (p)</option> 29 <option value="score">Score (p)</option> 30 </param> 31 <param name="out_format2" type="select"> 32 <label>Output Feature 1 File Format</label> 33 <option value="gff">GFF</option> 34 <option value="embl">EMBL</option> 35 <option value="swiss">SwissProt</option> 36 </param> 37 <param name="out_format3" type="select"> 38 <label>Output Feature 2 File Format</label> 39 <option value="gff">GFF</option> 40 <option value="embl">EMBL</option> 41 <option value="swiss">SwissProt</option> 42 </param> 43 </inputs> 44 <outputs> 45 <data format="match" name="out_file1" /> 46 <data format="gff" name="out_file2" /> 47 <data format="gff" name="out_file3" /> 48 </outputs> 49 <!-- <tests> 50 <test> 51 <param name="input1" value="2.fasta"/> 52 <param name="input2" value="1.fasta"/> 53 <param name="wordsize" value="4"/> 54 <param name="out_format1" value="fasta"/> 55 <param name="out_format2" value="gff"/> 56 <param name="out_format3" value="gff"/> 57 <output name="ofile2" file="emboss_wordmatch_out.embl"/> 58 </test> 59 </tests> test takes a long time to run--> 60 <code file="emboss_format_corrector.py" /> 61 <help> 62 63.. class:: warningmark 64 65The input datasets need to be sequences. 66 67----- 68 69 You can view the original documentation here_. 70 71 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/wordmatch.html 72 </help> 73</tool>