Mercurial > repos > xuebing > sharplabtool
comparison tools/emboss_5/emboss_sigcleave.xml @ 0:9071e359b9a3
Uploaded
| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:9071e359b9a3 |
|---|---|
| 1 <tool id="EMBOSS: sigcleave88" name="sigcleave" version="5.0.0"> | |
| 2 <description>Reports protein signal cleavage sites</description> | |
| 3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
| 4 <command>sigcleave -sequence $input1 -outfile $out_file1 -minweight "$minweight" -prokaryote $prokaryote -rformat2 $out_format1 -auto</command> | |
| 5 <inputs> | |
| 6 <param format="data" name="input1" type="data"> | |
| 7 <label>Sequences</label> | |
| 8 </param> | |
| 9 <param name="minweight" size="4" type="text" value="3.5"> | |
| 10 <label>Minimum scoring weight value for the predicted cleavage site</label> | |
| 11 </param> | |
| 12 <param name="prokaryote" type="select"> | |
| 13 <label>Specifies the sequence is prokaryotic and changes the default scoring data file</label> | |
| 14 <option value="no">No</option> | |
| 15 <option value="yes">Yes</option> | |
| 16 </param> | |
| 17 <param name="out_format1" type="select"> | |
| 18 <label>Output Report File Format</label> | |
| 19 <option value="motif">Motif</option> | |
| 20 <option value="embl">EMBL</option> | |
| 21 <option value="genbank">GENBANK</option> | |
| 22 <option value="gff">GFF</option> | |
| 23 <option value="pir">PIR</option> | |
| 24 <option value="swiss">SwissProt</option> | |
| 25 <option value="dbmotif">DbMotif</option> | |
| 26 <option value="diffseq">Diffseq</option> | |
| 27 <option value="excel">Excel (tab delimited)</option> | |
| 28 <option value="feattable">FeatTable</option> | |
| 29 <option value="regions">Regions</option> | |
| 30 <option value="seqtable">SeqTable</option> | |
| 31 <option value="simple">SRS Simple</option> | |
| 32 <option value="srs">SRS</option> | |
| 33 <option value="table">Table</option> | |
| 34 <option value="tagseq">TagSeq</option> | |
| 35 </param> | |
| 36 </inputs> | |
| 37 <outputs> | |
| 38 <data format="motif" name="out_file1" /> | |
| 39 </outputs> | |
| 40 <tests> | |
| 41 <test> | |
| 42 <param name="input1" value="2.fasta"/> | |
| 43 <param name="minweight" value="3.5"/> | |
| 44 <param name="prokaryote" value="no"/> | |
| 45 <param name="out_format1" value="excel"/> | |
| 46 <output name="out_file1" file="emboss_sigcleave_out.tabular"/> | |
| 47 </test> | |
| 48 </tests> | |
| 49 <code file="emboss_format_corrector.py" /> | |
| 50 <help> | |
| 51 You can view the original documentation here_. | |
| 52 | |
| 53 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/sigcleave.html | |
| 54 </help> | |
| 55 </tool> |