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