Mercurial > repos > xuebing > sharplabtool
comparison tools/emboss_5/emboss_palindrome.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: palindrome65" name="palindrome" version="5.0.0"> | |
| 2 <description>Looks for inverted repeats in a nucleotide sequence</description> | |
| 3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
| 4 <command>palindrome -sequence $input1 -outfile $out_file1 -minpallen $minpallen -maxpallen $maxpallen -gaplimit $gaplimit -nummismatches $nummismatches -overlap $overlap -auto</command> | |
| 5 <inputs> | |
| 6 <param format="fasta" name="input1" type="data"> | |
| 7 <label>Sequences</label> | |
| 8 </param> | |
| 9 <param name="minpallen" size="4" type="text" value="10"> | |
| 10 <label>Minimum length of palindrome</label> | |
| 11 </param> | |
| 12 <param name="maxpallen" size="4" type="text" value="100"> | |
| 13 <label>Maximum length of palindrome</label> | |
| 14 </param> | |
| 15 <param name="gaplimit" size="4" type="text" value="100"> | |
| 16 <label>Maximum gap between repeated regions</label> | |
| 17 </param> | |
| 18 <param name="nummismatches" size="4" type="text" value="0"> | |
| 19 <label>Number of mismatches allowed</label> | |
| 20 </param> | |
| 21 <param name="overlap" type="select"> | |
| 22 <label>Report overlapping matches</label> | |
| 23 <option value="yes">Yes</option> | |
| 24 <option value="no">No</option> | |
| 25 </param> | |
| 26 </inputs> | |
| 27 <outputs> | |
| 28 <data format="palindrome" name="out_file1" /> | |
| 29 </outputs> | |
| 30 <tests> | |
| 31 <test> | |
| 32 <param name="input1" value="2.fasta"/> | |
| 33 <param name="minpallen" value="10"/> | |
| 34 <param name="maxpallen" value="100"/> | |
| 35 <param name="gaplimit" value="100"/> | |
| 36 <param name="nummismatches" value="0"/> | |
| 37 <param name="overlap" value="yes"/> | |
| 38 <output name="out_file1" file="emboss_palindrome_out.palindrome"/> | |
| 39 </test> | |
| 40 </tests> | |
| 41 <help> | |
| 42 | |
| 43 .. class:: warningmark | |
| 44 | |
| 45 The input dataset needs to be sequences. | |
| 46 | |
| 47 ----- | |
| 48 | |
| 49 You can view the original documentation here_. | |
| 50 | |
| 51 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/palindrome.html | |
| 52 </help> | |
| 53 </tool> |