Mercurial > repos > iuc > lcrgenie
annotate lcrgenie.xml @ 0:a2eb8a8af800 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
author | iuc |
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date | Fri, 02 Dec 2022 13:56:16 +0000 |
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a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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1 <tool id="lcrgenie" name="Ligase Chain Reaction Genie" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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2 <description>Web-based tool for supporting the design of bridging oligos</description> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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3 <macros> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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4 <token name="@TOOL_VERSION@">1.0.2</token> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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5 <token name="@VERSION_SUFFIX@">0</token> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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6 </macros> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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7 <requirements> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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8 <requirement type="package" version="@TOOL_VERSION@">lcr_genie</requirement> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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9 </requirements> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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10 <stdio> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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11 <regex match="WARNING:" level="warning" /> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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12 <regex match="ERROR:" level="fatal" /> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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13 </stdio> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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14 <command detect_errors="exit_code"><![CDATA[ |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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15 python -m lcr_genie |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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16 '$LCR_input' |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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17 'out.xlsx' |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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18 --melting_temp '$adv.melting_temp' |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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19 && mv 'out.xlsx' '$LCR_output' |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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20 ]]></command> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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21 <inputs> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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22 <param name="LCR_input" type="data" format="xml" label="Constructs" help="SBOL file containing constructs designs and sequences" /> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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23 <section name="adv" title="Advanced Options" expanded="false"> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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24 <param name="melting_temp" value="60.0" type="float" label="Melting temperature" help="Target melting temperature for the bridging oligos"/> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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25 </section> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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26 </inputs> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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27 <outputs> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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28 <data name="LCR_output" format="xlsx" label="LCR Genie: Assembly Plan" /> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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29 </outputs> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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30 <tests> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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31 <test> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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32 <!-- test 1: check if identical outputs are produced with default parameters --> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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33 <param name="LCR_input" value="LCR_input_lycopene.xml" /> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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34 <output name="LCR_output" > |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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35 <assert_contents> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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36 <has_size value="58196" delta="100" /> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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37 </assert_contents> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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38 </output> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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39 </test> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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40 </tests> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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41 <help><![CDATA[ |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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42 LCRGenie |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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43 ======== |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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44 |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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45 LCR Genie is a web-based tool for supporting the design of bridging oligos, which are required for annealing together individual synthetic DNA parts (designed by PartsGenie) into multi-gene plasmid assemblies, designed by OptDoE. |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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46 |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
iuc
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47 Enzyme identifiers are randomly chosen and combined with the aforementioned parts to explore the combinatorics of possible constructs. |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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48 |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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49 LCR Genie takes as input an SBOL (Synthetic Biology Open Language) document containing numerous combinatorial plasmid assemblies, and designing bridging oligos necessary for assembly via the ligase cycling reaction method. The LCR Genie node performs analogous functionality to the `DNA weaver <https://github.com/Edinburgh-Genome-Foundry/DnaWeaver>`_ node (supporting multi-part assembly but by a different experimental method) and as such, its output format matches that of DNA Weaver. |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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50 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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51 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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52 Input |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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53 ----- |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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54 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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55 * **Constructs**\ : SBOL (Synthetic Biology Open Language) file containing constructs designs and sequences |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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56 * **Melting temperature**\ : (float) is the target melting temperature for the bridging oligos (default=60.0) |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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57 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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58 Output |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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59 ------ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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60 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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61 * **Assembly Plan**\ : Output spreadsheet |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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62 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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63 Project Links |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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64 --------------------- |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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65 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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66 * `GitHub <https://github.com/neilswainston/LCRGenie/>`_ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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67 |
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68 License |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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69 ------- |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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70 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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71 `MIT <https://github.com/neilswainston/LCRGenie/blob/master/LICENSE>`_ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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72 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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73 ]]></help> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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74 <creator> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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75 <person givenName="Neil" familyName="Swainston" identifier="https://orcid.org/0000-0001-7020-1236" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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76 <person givenName="Joan" familyName="Hérisson" email="joan.herisson@univ-evry.fr" identifier="https://orcid.org/0000-0001-9741-0847" /> |
a2eb8a8af800
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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77 </creator> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie commit dbe26a79ce78bd8e4eb44df0b533364127c2015b
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78 </tool> |