Mercurial > repos > xuebing > sharplabtool
comparison tools/emboss_5/emboss_patmatdb.xml @ 0:9071e359b9a3
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 <tool id="EMBOSS: patmatdb67" name="patmatdb" version="5.0.0"> | |
| 2 <description>Search a protein sequence with a motif</description> | |
| 3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
| 4 <command>patmatdb -sequence $input1 -outfile $out_file1 -motif "$motif" -rformat3 $out_format1 -auto</command> | |
| 5 <inputs> | |
| 6 <param format="data" name="input1" type="data"> | |
| 7 <label>Main sequence</label> | |
| 8 </param> | |
| 9 <param name="motif" size="4" type="text" value=""> | |
| 10 <label>Motif to search for</label> | |
| 11 </param> | |
| 12 <param name="out_format1" type="select"> | |
| 13 <label>Output Report File Format</label> | |
| 14 <option value="dbmotif">DbMotif</option> | |
| 15 <option value="embl">EMBL</option> | |
| 16 <option value="genbank">GENBANK</option> | |
| 17 <option value="gff">GFF</option> | |
| 18 <option value="pir">PIR</option> | |
| 19 <option value="swiss">SwissProt</option> | |
| 20 <option value="diffseq">Diffseq</option> | |
| 21 <option value="excel">Excel (tab delimited)</option> | |
| 22 <option value="feattable">FeatTable</option> | |
| 23 <option value="motif">Motif</option> | |
| 24 <option value="regions">Regions</option> | |
| 25 <option value="seqtable">SeqTable</option> | |
| 26 <option value="simple">SRS Simple</option> | |
| 27 <option value="srs">SRS</option> | |
| 28 <option value="table">Table</option> | |
| 29 <option value="tagseq">TagSeq</option> | |
| 30 </param> | |
| 31 </inputs> | |
| 32 <outputs> | |
| 33 <data format="dbmotif" name="out_file1" /> | |
| 34 </outputs> | |
| 35 <tests> | |
| 36 <test> | |
| 37 <param name="input1" value="2.fasta"/> | |
| 38 <param name="motif" value="aa"/> | |
| 39 <param name="out_format1" value="excel"/> | |
| 40 <output name="out_file1" file="emboss_patmatdb_out.tabular"/> | |
| 41 </test> | |
| 42 </tests> | |
| 43 <code file="emboss_format_corrector.py" /> | |
| 44 <help> | |
| 45 You can view the original documentation here_. | |
| 46 | |
| 47 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/patmatdb.html | |
| 48 </help> | |
| 49 </tool> |