[2] | 1 | <tool id="EMBOSS: fuzznuc37" name="fuzznuc" version="5.0.1">
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| 2 | <description>Nucleic acid pattern search</description>
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| 3 | <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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| 4 | <command>fuzznuc -sequence $input1 -outfile $out_file1 -pattern '$pattern' -pmismatch $mismatch -complement $complement -rformat2 $out_format1 -auto</command>
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| 5 | <inputs>
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| 6 | <param format="fasta" name="input1" type="data">
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| 7 | <label>Sequences</label>
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| 8 | </param>
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| 9 | <param name="pattern" size="5" type="text" value="">
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| 10 | <label>Search pattern</label>
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| 11 | <sanitizer>
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| 12 | <valid initial="string.printable">
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| 13 | <remove value="'"/>
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| 14 | </valid>
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| 15 | <mapping initial="none">
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| 16 | <add source="'" target=""/>
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| 17 | </mapping>
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| 18 | </sanitizer>
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| 19 | </param>
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| 20 | <param name="mismatch" size="5" type="text" value="0">
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| 21 | <label>Number of mismatches</label>
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| 22 | </param>
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| 23 | <param name="complement" type="select">
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| 24 | <label>Search complementary strand</label>
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| 25 | <option value="no">No</option>
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| 26 | <option value="yes">Yes</option>
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| 27 | </param>
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| 28 | <param name="out_format1" type="select">
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| 29 | <label>Output Report File Format</label>
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| 30 | <option value="seqtable">SeqTable</option>
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| 31 | <option value="embl">EMBL</option>
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| 32 | <option value="genbank">GENBANK</option>
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| 33 | <option value="gff">GFF</option>
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| 34 | <option value="pir">PIR</option>
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| 35 | <option value="swiss">SwissProt</option>
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| 36 | <option value="dbmotif">DbMotif</option>
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| 37 | <option value="diffseq">Diffseq</option>
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| 38 | <option value="excel">Excel (tab delimited)</option>
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| 39 | <option value="feattable">FeatTable</option>
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| 40 | <option value="motif">Motif</option>
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| 41 | <option value="regions">Regions</option>
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| 42 | <option value="simple">SRS Simple</option> |
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| 43 | <option value="fuzznuc">Fuzznuc Output File</option>
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| 44 | <option value="srs">SRS</option>
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| 45 | <option value="table">Table</option>
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| 46 | <option value="tagseq">TagSeq</option>
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| 47 | </param>
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| 48 | </inputs>
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| 49 | <outputs>
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| 50 | <data format="fuzznuc" name="out_file1" />
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| 51 | </outputs> |
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| 52 | <tests> |
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| 53 | <test> |
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| 54 | <param name="input1" value="2.fasta"/> |
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| 55 | <param name="pattern" value="AA"/> |
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| 56 | <param name="mismatch" value="0"/> |
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| 57 | <param name="complement" value="no"/> |
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| 58 | <param name="out_format1" value="excel"/> |
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| 59 | <output name="out_file1" file="emboss_fuzznuc_out.tabular"/> |
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| 60 | </test> |
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| 61 | </tests>
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| 62 | <code file="emboss_format_corrector.py" />
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| 63 | <help> |
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| 64 | |
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| 65 | .. class:: warningmark |
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| 66 | |
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| 67 | The input dataset needs to be sequences. |
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| 68 | |
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| 69 | ----- |
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| 70 | |
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| 71 | You can view the original documentation here_. |
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| 72 | |
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| 73 | .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzznuc.html |
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| 74 | </help> |
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| 75 | </tool> |
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