Mercurial > repos > xuebing > sharplabtool
comparison tools/emboss_5/emboss_diffseq.xml @ 0:9071e359b9a3
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| author | xuebing |
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| 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: diffseq22" name="diffseq" version="5.0.0"> | |
| 2 <description>Find differences between nearly identical sequences</description> | |
| 3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
| 4 <command>diffseq -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize $wordsize -globaldifferences $globaldifferences -rformat3 | |
| 5 $out_format1 -offormat4 $out_format2 -offormat5 $out_format3 -auto</command> | |
| 6 <inputs> | |
| 7 <param format="data" name="input1" type="data"> | |
| 8 <label>Sequence 1</label> | |
| 9 </param> | |
| 10 <param format="data" name="input2" type="data"> | |
| 11 <label>Sequence 2</label> | |
| 12 </param> | |
| 13 <param name="wordsize" size="4" type="text" value="20"> | |
| 14 <label>Wordsize</label> | |
| 15 </param> | |
| 16 <param name="globaldifferences" type="select"> | |
| 17 <label>Report differences at the ends</label> | |
| 18 <option value="no">No</option> | |
| 19 <option value="yes">Yes</option> | |
| 20 </param> | |
| 21 <param name="out_format1" type="select"> | |
| 22 <label>Output Report File Format</label> | |
| 23 <option value="diffseq">Diffseq</option> | |
| 24 <option value="embl">EMBL</option> | |
| 25 <option value="genbank">GENBANK</option> | |
| 26 <option value="gff">GFF</option> | |
| 27 <option value="pir">PIR</option> | |
| 28 <option value="swiss">SwissProt</option> | |
| 29 <option value="dbmotif">DbMotif</option> | |
| 30 <option value="excel">Excel (tab delimited)</option> | |
| 31 <option value="feattable">FeatTable</option> | |
| 32 <option value="motif">Motif</option> | |
| 33 <option value="regions">Regions</option> | |
| 34 <option value="seqtable">SeqTable</option> | |
| 35 <option value="simple">SRS Simple</option> | |
| 36 <option value="srs">SRS</option> | |
| 37 <option value="table">Table</option> | |
| 38 <option value="tagseq">TagSeq</option> | |
| 39 </param> | |
| 40 <param name="out_format2" type="select"> | |
| 41 <label>Sequence 1 Output Feature File Format</label> | |
| 42 <option value="gff">GFF</option> | |
| 43 <option value="embl">EMBL</option> | |
| 44 <option value="swiss">SwissProt</option> | |
| 45 </param> | |
| 46 <param name="out_format3" type="select"> | |
| 47 <label>Sequence 2 Output Feature File Format</label> | |
| 48 <option value="gff">GFF</option> | |
| 49 <option value="embl">EMBL</option> | |
| 50 <option value="swiss">SwissProt</option> | |
| 51 </param> | |
| 52 </inputs> | |
| 53 <outputs> | |
| 54 <data format="diffseq" name="out_file1" /> | |
| 55 <data format="gff" name="out_file2" /> | |
| 56 <data format="gff" name="out_file3" /> | |
| 57 </outputs> | |
| 58 <code file="emboss_format_corrector.py" /> | |
| 59 <help> | |
| 60 You can view the original documentation here_. | |
| 61 | |
| 62 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/diffseq.html | |
| 63 </help> | |
| 64 </tool> |