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1 <tool id="GSEA" name="Gene Set Enrichment Analysis" version="0.1.0">
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1
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2
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3 <requirements>
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4 <requirement type="package" version="1.4.0">bioconductor-fgsea</requirement>
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5 <requirement type="package" version="1.20.0">r-getopt</requirement>
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6 <!-- required for alpha function used with plotMD -->
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7 <requirement type="package" version="0.12.13">r-rcpp</requirement>
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8 </requirements>
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9
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10 <command detect_errors="exit_code"><![CDATA[
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11 Rscript '$__tool_directory__/GSEA.R' --input1 '$Ranked_list' --input2 '$Pathway_database' --output '$output'
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12 ]]></command>
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13 <inputs>
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14 <param type="data" name="Ranked_list" format="txt" />
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15 <param type="data" name="Pathway_database" format="txt" />
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16 </inputs>
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17 <outputs>
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18 <data name="output" format="txt" />
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="Ranked_list" value="ranked_genes_list.rnk"/>
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23 <param name="Pathway_database" value="ouse.gmt"/>
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24 <output name="output" file="GSEA_results.txt"/>
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25 </test>
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26 </tests>
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27 <help><![CDATA[
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28 Write the tool help section here.
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29 ]]></help>
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30 <citations>
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31 <citation type="bibtex">
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32 @misc{github01_mismatch_removal,
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33 author = {LastTODO, FirstTODO},
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34 year = {TODO},
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35 title = {01_mismatch_removal},
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36 publisher = {GitHub},
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37 journal = {GitHub repository},
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38 url = {https://github.com/dktanwar/Galaxy_Tools/tree/master/01_mismatch_removal},
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39 }</citation>
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40 </citations>
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41 </tool>
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