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1 <tool id="plant_tribes_gene_family_scaffold_loader" name="Load PlantTribes scaffold" version="@WRAPPER_VERSION@.0.0">
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2 <description>into Galaxy PlantTribes database</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 <command detect_errors="exit_code"><![CDATA[
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7 python '$__tool_directory__/gene_family_scaffold_loader.py'
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8 --database_connection_string '$__app__.config.plant_tribes_database_connection'
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9 --output '$output'
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10 --scaffold_path '$GALAXY_DATA_INDEX_DIR/plant_tribes/scaffolds/$scaffold']]></command>
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11 <inputs>
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12 <expand macro="param_scaffold" />
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13 </inputs>
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14 <outputs>
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15 <data name="output" format="txt"/>
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16 </outputs>
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17 <tests>
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18 <test>
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19 <!--Testing this tool is a bit difficult at the current time.-->
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20 </test>
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21 </tests>
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22 <help>
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23 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary
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24 analyses of genome-scale gene families and transcriptomes. This tool analyzes scaffolds installed into Galaxy by the
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25 PlantTribes Scaffolds Downloader data manager tool and inserts information about them into the Galaxy PlantTribes database
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26 for querying and additional analysis.
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27
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28 -----
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29
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30 **Required options**
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31
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32 * **Gene family scaffold** - one of the PlantTribes gene family scaffolds, installed into Galaxy by the PlantTribes Scaffold Data Manager tool, that has not yet been analyzed and loaded into the Galaxy PlantTribes database.
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33 </help>
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34 <citations>
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35 <citation type="bibtex">
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36 @unpublished{None,
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37 author = {Greg Von Kuster,Eric Wafula},
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38 title = {None},
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39 year = {None},
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40 eprint = {None},
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41 url = {https://github.com/dePamphilis/PlantTribes}}
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42 </citation>
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43 </citations>
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44 </tool>
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