Mercurial > repos > iuc > syndiva
annotate syndiva.xml @ 0:0254731f047b draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
| author | iuc |
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| date | Thu, 23 Jun 2022 22:32:13 +0000 |
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| rev | line source |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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changeset
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1 <tool id="syndiva" name="syndiva" version="1.0" profile="21.05"> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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2 <description> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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3 diversity analysis of synthetic libraries of a Fibronectin domain |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
parents:
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4 </description> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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5 <macros> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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6 <import>macros.xml</import> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
parents:
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7 </macros> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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8 <expand macro="requirements"> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
parents:
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9 <expand macro="matplotlib_requirement" /> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
parents:
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10 <expand macro="biopython_requirement"/> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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11 </expand> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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12 <command detect_errors="exit_code"> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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13 <![CDATA[ |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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14 mkdir -p '$report.extra_files_path' && |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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15 python '$__tool_directory__/syndiva.py' |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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16 -i '$fasta_file' |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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17 -p '$pattern' |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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18 -5 '$restriction_site_5' |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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19 -3 '$restriction_site_3' |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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20 -o '$report.extra_files_path' |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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21 && cp '${report.extra_files_path}'/*\.html output.html |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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22 ]]> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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23 </command> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
parents:
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24 <inputs> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
parents:
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25 <param name="fasta_file" type="data" format="fasta" label="DNA FASTA file"/> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
parents:
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26 <param name="pattern" type="text" area="true" label="Sequence pattern" > |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
parents:
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27 <validator type="empty_field" /> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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28 <validator type="regex" message="An expression is required and is allowed to contain only protein alphabet letters (ACDEFGHIKLMNPQRSTVWY), numbers and the characters -:* ">^[ACDEFGHIKLMNPQRSTVWY\d\-:*]+$</validator> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
parents:
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29 </param> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
parents:
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30 <param name="restriction_site_5" type="text" label="5' Restriction sites" help="Sequence of the restrict" > |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
parents:
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31 <validator type="empty_field" /> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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32 <validator type="regex" message="An expression is required and is allowed to contain only DNA alphabet letters (ATGC)">^[ATGC]{4,10}$</validator> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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33 </param> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
parents:
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34 <param name="restriction_site_3" type="text" label="3' Restriction sites" help="Sequence of the restrict" > |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
parents:
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35 <validator type="empty_field" /> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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36 <validator type="regex" message="An expression is required and is allowed to contain only DNA alphabet letters (ATGC)">^[ATGC]{4,10}$</validator> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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37 </param> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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38 </inputs> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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39 <outputs> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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40 <data format="html" name="report" from_work_dir="output.html" /> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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41 </outputs> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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42 <tests> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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43 <test> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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44 <param name="fasta_file" value="syndiva_datatest.fasta"/> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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45 <param name="pattern" value="AAAGSSVSSVPTKLEVVAATPTSLLISWDA:4-6:V:1:YYRITYGETGGNSPVQEFTVPG:3:TATISGLSPGVDYTITVYA:11-12:PISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIRAETVESCLAKSHTENSFTNVWKDDKTLDRYANYE"/> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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46 <param name="restriction_site_5" value="GCGGCCGC"/> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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47 <param name="restriction_site_3" value="GGTACC"/> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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48 <output name="report" file="syndiva_report.html" ftype="html" lines_diff="2"/> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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49 </test> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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50 </tests> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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51 <help> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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52 <![CDATA[ |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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53 - **Scientific context** |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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54 |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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55 - *SynDivA* was developed to analyze the diversity of synthetic libraries of a Fibronectin domain. |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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56 - This diversity is generated in the context of a project of directed evolution using a phage display approach, to obtain ligands with high affinity and specificity for biological targets. It was introduced in three loops of the domain. It is both a variation of amino acids and a variation of the lengths of loops. |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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57 - *SynDivA* is used before the step of selecting banks of interest, by ensuring quality - and therefore of diversity - of the bank by determining, by projection, the number of unique and functional sequences. |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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58 |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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59 - **Description** |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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60 |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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61 - *SynDivA* is implemented in Python. |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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62 |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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63 - The computations are divided into three steps: |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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64 |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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65 1. Pre-processing of the input data (determination of the orientation of the sequences, determination of the reading frame, translation of nucleotide sequences in protein sequences, elimination of the sequences "wastes" containing stop codons in variable regions) |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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66 2. Alignment of sequences 2-2 |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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67 3. Statistics calculations on the alignments (distances) |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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68 |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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69 - The results are presented as an HTML report. |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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70 |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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71 - **Example** |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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72 |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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73 - Pattern : AAAGSSVSSVPTKLEVVAATPTSLLISWDA:4-6:V:1:YYRITYGETGGNSPVQEFTVPG:3:TATISGLSPGVDYTITVYA:11-12:PISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIRAETVESCLAKSHTENSFTNVWKDDKTLDRYANYE |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
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74 - 5' restriction site : GCGGCCGC |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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changeset
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75 - 3' restriction site : GGTACC |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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76 |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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77 ]]></help> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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78 <expand macro="citations" /> |
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0254731f047b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA commit 90c5ec603e2c6b8c49d2dc7ec1b1e97f9d8fb92c
iuc
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79 </tool> |