annotate emboss_epestfind.xml @ 18:63dd26468588 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 18de4aa9ba00124b1b3e3afe14219e46931e58a9"
author iuc
date Fri, 09 Jul 2021 18:36:34 +0000
parents 8992d258e42f
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8992d258e42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753
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1 <tool id="EMBOSS: epestfind29" name="epestfind" version="@VERSION@.1">
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2 <description>Finds PEST motifs as potential proteolytic cleavage sites</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' epestfind -sequence '$input1' -goutfile '$ofile2' -outfile '$ofile1' -window $window -order $order -potential $potential -poor $poor
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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8 -invalid $invalid -map $map -graph png -auto</command>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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9 <inputs>
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10 <param name="input1" type="data" format="data" label="Sequence" />
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11 <param name="window" type="integer" value="10" label="Minimal distance between positively charged amino acids" />
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12 <param name="order" type="select" label="Sort by">
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13 <option value="3">Score</option>
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14 <option value="1">Length</option>
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15 <option value="2">Position</option>
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16 </param>
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17 <param name="threshold" type="float" value="5.0" label="Threshold value to discriminate weak from potential PEST motifs" />
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18 <param name="potential" type="select" label="Decide whether potential PEST motifs should be printed">
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19 <option value="yes">Yes</option>
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20 <option value="no">No</option>
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21 </param>
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22 <param name="poor" type="select" label="Decide whether poor PEST motifs should be printed">
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23 <option value="yes">Yes</option>
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24 <option value="no">No</option>
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25 </param>
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26 <param name="invalid" type="select" label="Decide whether invalid PEST motifs should be printed">
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27 <option value="no">No</option>
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28 <option value="yes">Yes</option>
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29 </param>
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30 <param name="map" type="select" label="Decide whether PEST motifs should be mapped to sequence">
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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31 <option value="yes">Yes</option>
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32 <option value="no">No</option>
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33 </param>
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34 </inputs>
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35 <outputs>
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36 <data name="ofile2" format="png" />
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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37 <data name="ofile1" format="epestfind" />
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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38 </outputs>
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39 <!-- <tests>
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40 <test>
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41 <param name="input1" value="2.fasta"/>
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42 <param name="window" value="10"/>
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43 <param name="order" value="3"/>
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44 <param name="threshold" value="5.0"/>
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45 <param name="potential" value="yes"/>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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46 <param name="poor" value="yes"/>
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47 <param name="invalid" value="no"/>
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48 <param name="map" value="yes"/>
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49 <output name="ofile1" file="emboss_epestfind_out.epestfind"/>
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50 </test>
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51 </tests> output file contains file location info -->
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52 <help>
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53 You can view the original documentation here_.
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54
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55 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/epestfind.html
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56 </help>
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57 <expand macro="citations" />
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58 </tool>