Mercurial > repos > xuebing > sharplabtool
comparison tools/emboss_5/emboss_wordmatch.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: wordmatch110" name="wordmatch" version="5.0.0"> | |
| 2 <description>Finds all exact matches of a given size between 2 sequences</description> | |
| 3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
| 4 <command>wordmatch -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize "$wordsize" -aformat3 $out_format1 -offormat4 $out_format2 | |
| 5 -offormat5 $out_format3 -auto</command> | |
| 6 <inputs> | |
| 7 <param format="fasta" name="input1" type="data"> | |
| 8 <label>Sequence 1</label> | |
| 9 </param> | |
| 10 <param format="fasta" name="input2" type="data"> | |
| 11 <label>Sequence 2</label> | |
| 12 </param> | |
| 13 <param name="wordsize" size="5" type="text" value="4"> | |
| 14 <label>Word size</label> | |
| 15 </param> | |
| 16 <param name="out_format1" type="select"> | |
| 17 <label>Output Alignment File Format</label> | |
| 18 <option value="match">Match (m)</option> | |
| 19 <option value="simple">Simple (m)</option> | |
| 20 <option value="fasta">FASTA (m)</option> | |
| 21 <option value="msf">MSF (m)</option> | |
| 22 <option value="srs">SRS (m)</option> | |
| 23 <option value="pair">Pair (p)</option> | |
| 24 <option value="markx0">Markx0 (p)</option> | |
| 25 <option value="markx1">Markx1 (p)</option> | |
| 26 <option value="markx2">Markx2 (p)</option> | |
| 27 <option value="markx3">Markx3 (p)</option> | |
| 28 <option value="markx10">Markx10 (p)</option> | |
| 29 <option value="srspair">SRS pair (p)</option> | |
| 30 <option value="score">Score (p)</option> | |
| 31 </param> | |
| 32 <param name="out_format2" type="select"> | |
| 33 <label>Output Feature 1 File Format</label> | |
| 34 <option value="gff">GFF</option> | |
| 35 <option value="embl">EMBL</option> | |
| 36 <option value="swiss">SwissProt</option> | |
| 37 </param> | |
| 38 <param name="out_format3" type="select"> | |
| 39 <label>Output Feature 2 File Format</label> | |
| 40 <option value="gff">GFF</option> | |
| 41 <option value="embl">EMBL</option> | |
| 42 <option value="swiss">SwissProt</option> | |
| 43 </param> | |
| 44 </inputs> | |
| 45 <outputs> | |
| 46 <data format="match" name="out_file1" /> | |
| 47 <data format="gff" name="out_file2" /> | |
| 48 <data format="gff" name="out_file3" /> | |
| 49 </outputs> | |
| 50 <!-- <tests> | |
| 51 <test> | |
| 52 <param name="input1" value="2.fasta"/> | |
| 53 <param name="input2" value="1.fasta"/> | |
| 54 <param name="wordsize" value="4"/> | |
| 55 <param name="out_format1" value="fasta"/> | |
| 56 <param name="out_format2" value="gff"/> | |
| 57 <param name="out_format3" value="gff"/> | |
| 58 <output name="ofile2" file="emboss_wordmatch_out.embl"/> | |
| 59 </test> | |
| 60 </tests> test takes a long time to run--> | |
| 61 <code file="emboss_format_corrector.py" /> | |
| 62 <help> | |
| 63 | |
| 64 .. class:: warningmark | |
| 65 | |
| 66 The input datasets need to be sequences. | |
| 67 | |
| 68 ----- | |
| 69 | |
| 70 You can view the original documentation here_. | |
| 71 | |
| 72 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/wordmatch.html | |
| 73 </help> | |
| 74 </tool> |