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1 <tool id="EMBOSS: patmatdb67" name="patmatdb" version="5.0.0">
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2 <description>Search a protein sequence with a motif</description>
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3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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4 <command>patmatdb -sequence $input1 -outfile $out_file1 -motif "$motif" -rformat3 $out_format1 -auto</command>
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5 <inputs>
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6 <param format="data" name="input1" type="data">
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7 <label>Main sequence</label>
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8 </param>
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9 <param name="motif" size="4" type="text" value="">
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10 <label>Motif to search for</label>
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11 </param>
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12 <param name="out_format1" type="select">
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13 <label>Output Report File Format</label>
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14 <option value="dbmotif">DbMotif</option>
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15 <option value="embl">EMBL</option>
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16 <option value="genbank">GENBANK</option>
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17 <option value="gff">GFF</option>
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18 <option value="pir">PIR</option>
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19 <option value="swiss">SwissProt</option>
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20 <option value="diffseq">Diffseq</option>
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21 <option value="excel">Excel (tab delimited)</option>
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22 <option value="feattable">FeatTable</option>
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23 <option value="motif">Motif</option>
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24 <option value="regions">Regions</option>
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25 <option value="seqtable">SeqTable</option>
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26 <option value="simple">SRS Simple</option>
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27 <option value="srs">SRS</option>
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28 <option value="table">Table</option>
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29 <option value="tagseq">TagSeq</option>
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30 </param>
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31 </inputs>
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32 <outputs>
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33 <data format="dbmotif" name="out_file1" />
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="input1" value="2.fasta"/>
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38 <param name="motif" value="aa"/>
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39 <param name="out_format1" value="excel"/>
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40 <output name="out_file1" file="emboss_patmatdb_out.tabular"/>
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41 </test>
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42 </tests>
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43 <code file="emboss_format_corrector.py" />
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44 <help>
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45 You can view the original documentation here_.
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46
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47 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/patmatdb.html
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48 </help>
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49 </tool> |
