Mercurial > repos > xuebing > sharplabtool
comparison tools/emboss_5/emboss_epestfind.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: epestfind29" name="epestfind" version="5.0.0"> | |
| 2 <description>Finds PEST motifs as potential proteolytic cleavage sites</description> | |
| 3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
| 4 <command interpreter="perl">emboss_single_outputfile_wrapper.pl epestfind -sequence $input1 -goutfile $ofile2 -outfile $ofile1 -window $window -order $order -potential $potential -poor $poor | |
| 5 -invalid $invalid -map $map -graph png -auto</command> | |
| 6 <inputs> | |
| 7 <param format="data" name="input1" type="data"> | |
| 8 <label>Sequence</label> | |
| 9 </param> | |
| 10 <param name="window" size="4" type="text" value="10"> | |
| 11 <label>Minimal distance between positively charged amino acids</label> | |
| 12 </param> | |
| 13 <param name="order" type="select"> | |
| 14 <label>Sort by</label> | |
| 15 <option value="3">Score</option> | |
| 16 <option value="1">Length</option> | |
| 17 <option value="2">Position</option> | |
| 18 </param> | |
| 19 <param name="threshold" size="4" type="text" value="5.0"> | |
| 20 <label>Threshold value to discriminate weak from potential PEST motifs.</label> | |
| 21 </param> | |
| 22 <param name="potential" type="select"> | |
| 23 <label>Decide whether potential PEST motifs should be printed</label> | |
| 24 <option value="yes">Yes</option> | |
| 25 <option value="no">No</option> | |
| 26 </param> | |
| 27 <param name="poor" type="select"> | |
| 28 <label>Decide whether poor PEST motifs should be printed</label> | |
| 29 <option value="yes">Yes</option> | |
| 30 <option value="no">No</option> | |
| 31 </param> | |
| 32 <param name="invalid" type="select"> | |
| 33 <label>Decide whether invalid PEST motifs should be printed</label> | |
| 34 <option value="no">No</option> | |
| 35 <option value="yes">Yes</option> | |
| 36 </param> | |
| 37 <param name="map" type="select"> | |
| 38 <label>Decide whether PEST motifs should be mapped to sequence</label> | |
| 39 <option value="yes">Yes</option> | |
| 40 <option value="no">No</option> | |
| 41 </param> | |
| 42 </inputs> | |
| 43 <outputs> | |
| 44 <data format="png" name="ofile2" /> | |
| 45 <data format="epestfind" name="ofile1" /> | |
| 46 </outputs> | |
| 47 <!-- <tests> | |
| 48 <test> | |
| 49 <param name="input1" value="2.fasta"/> | |
| 50 <param name="window" value="10"/> | |
| 51 <param name="order" value="3"/> | |
| 52 <param name="threshold" value="5.0"/> | |
| 53 <param name="potential" value="yes"/> | |
| 54 <param name="poor" value="yes"/> | |
| 55 <param name="invalid" value="no"/> | |
| 56 <param name="map" value="yes"/> | |
| 57 <output name="ofile1" file="emboss_epestfind_out.epestfind"/> | |
| 58 </test> | |
| 59 </tests> output file contains file location info --> | |
| 60 <help> | |
| 61 You can view the original documentation here_. | |
| 62 | |
| 63 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/epestfind.html | |
| 64 </help> | |
| 65 </tool> |