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annotate simtext_app.xml @ 1:429b1df6b7a9 draft

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"planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
author dlalgroup
date Thu, 24 Sep 2020 04:32:14 +0000
parents 34ed44f3f85c
children d7b190591e63
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34ed44f3f85c "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
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1 <tool id="simtext_app" name="simtext_app" tool_type="interactive" version="@VERSION@">
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2 <description>Interactive shiny app to explore SimText output data</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 <entry_points>
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8 <entry_point name="SimText App" requires_domain="true">
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9 <port>8888</port>
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10 </entry_point>
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11 </entry_points>
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12 <expand macro="stdio"/>
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13 <command><![CDATA[Rscript
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14 '${__tool_directory__}/simtext_app.R'
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15 --input '$input'
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16 --matrix '$matrix'
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17 --host '0.0.0.0'
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18 --port '8888'
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19 ]]>
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20 </command>
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21 <inputs>
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22 <param argument="--input" label="Input file" name="input" optional="false" type="data" format="tabular" help="input"/>
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23 <param argument="--matrix" label="matrix file" name="matrix" optional="false" type="data" format="tabular" help="matrix"/>
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24 </inputs>
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25 <outputs>
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26 <data format="tabular" name="output" />
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27 </outputs>
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28 <tests><!-- cannot test interactive tools yet
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29 <test>
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30 <param name="input" value="test_data" ftype="tabular"/>
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31 <param name="matrix" value="text_to_wordmatrix_output"/>
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32 </test>-->
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33 </tests>
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34 <help><![CDATA[
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35
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36 The tool enables the exploration of data generated by ‘text_to_wordmatrix’ or ‘pmids_to_pubtator_matrix’ tools in a Shiny local instance. The following features can be generated: 1) word clouds for each initial search query, 2) dimension reduction and hierarchical clustering of binary matrices, and 3) tables with words and their frequency in the search queries.
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37
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38 Input 1, a table with:
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39 - A column with initial search queries starting with "ID\_" (e.g., "ID_gene" if initial search queries were genes).
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40 - Column(s) with grouping factor(s) to compare pre-existing categories of the initial search queries with the grouping based on text. The column names should start with "GROUPING\_". If the column name is "GROUPING_disorder", "disorder" will be shown as a grouping variable in the app.
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41 Input 2:
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42 The output of 'text_to_wordmatrix' or 'pmids_to_pubtator_matrix' tools, or a binary matrix.
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43
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44
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45 ]]></help>
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46 <expand macro="citations"/>
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47 </tool>