Mercurial > repos > xuebing > sharplabtool
comparison tools/emboss_5/emboss_seqmatchall.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: seqmatchall83" name="seqmatchall" version="5.0.0"> | |
| 2 <description>All-against-all comparison of a set of sequences</description> | |
| 3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
| 4 <command>seqmatchall -sequence $input1 -outfile $out_file1 -wordsize $wordsize -aformat2 $out_format1 -auto</command> | |
| 5 <inputs> | |
| 6 <param format="fasta" name="input1" type="data"> | |
| 7 <label>Sequences</label> | |
| 8 </param> | |
| 9 <param name="wordsize" size="4" type="text" value="4"> | |
| 10 <label>Word size</label> | |
| 11 </param> | |
| 12 <param name="out_format1" type="select"> | |
| 13 <label>Output Alignment File Format</label> | |
| 14 <option value="match">Match (m)</option> | |
| 15 <option value="simple">Simple (m)</option> | |
| 16 <option value="fasta">FASTA (m)</option> | |
| 17 <option value="msf">MSF (m)</option> | |
| 18 <option value="srs">SRS (m)</option> | |
| 19 <option value="pair">Pair (p)</option> | |
| 20 <option value="markx0">Markx0 (p)</option> | |
| 21 <option value="markx1">Markx1 (p)</option> | |
| 22 <option value="markx2">Markx2 (p)</option> | |
| 23 <option value="markx3">Markx3 (p)</option> | |
| 24 <option value="markx10">Markx10 (p)</option> | |
| 25 <option value="srspair">SRS pair (p)</option> | |
| 26 <option value="score">Score (p)</option> | |
| 27 <option value="seqmatchall">Seqmatchall Output File</option> | |
| 28 </param> | |
| 29 </inputs> | |
| 30 <outputs> | |
| 31 <data format="seqmatchall" name="out_file1" />. | |
| 32 </outputs> | |
| 33 <tests> | |
| 34 <test> | |
| 35 <param name="input1" value="2.fasta"/> | |
| 36 <param name="wordsize" value="2"/> | |
| 37 <param name="out_format1" value="fasta"/> | |
| 38 <output name="out_file1" file="emboss_seqmatchall_out.fasta"/> | |
| 39 </test> | |
| 40 </tests> | |
| 41 <code file="emboss_format_corrector.py" /> | |
| 42 <help> | |
| 43 | |
| 44 .. class:: warningmark | |
| 45 | |
| 46 The input dataset needs to be sequences. | |
| 47 | |
| 48 ----- | |
| 49 | |
| 50 You can view the original documentation here_. | |
| 51 | |
| 52 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/seqmatchall.html | |
| 53 </help> | |
| 54 </tool> |