[2] | 1 | <tool id="EMBOSS: wordmatch110" name="wordmatch" version="5.0.0">
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| 2 | <description>Finds all exact matches of a given size between 2 sequences</description>
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| 3 | <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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| 4 | <command>wordmatch -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize "$wordsize" -aformat3 $out_format1 -offormat4 $out_format2
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| 5 | -offormat5 $out_format3 -auto</command>
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| 6 | <inputs>
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| 7 | <param format="fasta" name="input1" type="data">
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| 8 | <label>Sequence 1</label>
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| 9 | </param>
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| 10 | <param format="fasta" name="input2" type="data"> |
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| 11 | <label>Sequence 2</label>
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| 12 | </param>
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| 13 | <param name="wordsize" size="5" type="text" value="4">
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| 14 | <label>Word size</label>
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| 15 | </param>
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| 16 | <param name="out_format1" type="select">
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| 17 | <label>Output Alignment File Format</label>
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| 18 | <option value="match">Match (m)</option>
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| 19 | <option value="simple">Simple (m)</option>
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| 20 | <option value="fasta">FASTA (m)</option>
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| 21 | <option value="msf">MSF (m)</option>
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| 22 | <option value="srs">SRS (m)</option>
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| 23 | <option value="pair">Pair (p)</option>
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| 24 | <option value="markx0">Markx0 (p)</option>
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| 25 | <option value="markx1">Markx1 (p)</option>
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| 26 | <option value="markx2">Markx2 (p)</option>
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| 27 | <option value="markx3">Markx3 (p)</option>
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| 28 | <option value="markx10">Markx10 (p)</option>
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| 29 | <option value="srspair">SRS pair (p)</option>
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| 30 | <option value="score">Score (p)</option>
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| 31 | </param>
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| 32 | <param name="out_format2" type="select">
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| 33 | <label>Output Feature 1 File Format</label>
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| 34 | <option value="gff">GFF</option>
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| 35 | <option value="embl">EMBL</option>
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| 36 | <option value="swiss">SwissProt</option>
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| 37 | </param>
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| 38 | <param name="out_format3" type="select">
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| 39 | <label>Output Feature 2 File Format</label>
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| 40 | <option value="gff">GFF</option>
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| 41 | <option value="embl">EMBL</option>
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| 42 | <option value="swiss">SwissProt</option>
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| 43 | </param>
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| 44 | </inputs>
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| 45 | <outputs>
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| 46 | <data format="match" name="out_file1" />
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| 47 | <data format="gff" name="out_file2" />
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| 48 | <data format="gff" name="out_file3" />
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| 49 | </outputs> |
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| 50 | <!-- <tests> |
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| 51 | <test> |
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| 52 | <param name="input1" value="2.fasta"/> |
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| 53 | <param name="input2" value="1.fasta"/> |
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| 54 | <param name="wordsize" value="4"/> |
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| 55 | <param name="out_format1" value="fasta"/> |
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| 56 | <param name="out_format2" value="gff"/> |
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| 57 | <param name="out_format3" value="gff"/> |
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| 58 | <output name="ofile2" file="emboss_wordmatch_out.embl"/> |
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| 59 | </test> |
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| 60 | </tests> test takes a long time to run-->
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| 61 | <code file="emboss_format_corrector.py" />
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| 62 | <help> |
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| 63 | |
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| 64 | .. class:: warningmark |
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| 65 | |
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| 66 | The input datasets need to be sequences. |
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| 67 | |
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| 68 | ----- |
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| 69 | |
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| 70 | You can view the original documentation here_. |
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| 71 | |
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| 72 | .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/wordmatch.html |
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| 73 | </help> |
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| 74 | </tool>
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