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Björn Grüning
68 lines
2.6 KiB
XML
68 lines
2.6 KiB
XML
<tool id="interactive_tool_simtext_app" name="SimText" tool_type="interactive" version="0.0.2" license="MIT">
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<description>Interactive shiny app to explore SimText output data</description>
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<requirements>
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<container type="docker">dlalgroup/simtext:2.0</container>
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</requirements>
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<entry_points>
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<entry_point name="SimText App" requires_domain="true">
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<port>8888</port>
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</entry_point>
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</entry_points>
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<command><![CDATA[
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Rscript
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'${__tool_directory__}/simtext_app.R'
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--input '$input'
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--matrix '$matrix'
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--host '0.0.0.0'
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--port '8888'
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]]>
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</command>
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<inputs>
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<param argument="--input" label="Input file" name="input" type="data" format="tabular"/>
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<param argument="--matrix" label="Matrix file" name="matrix" type="data" format="tabular"/>
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</inputs>
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<outputs>
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<data format="tabular" name="output" />
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</outputs>
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<tests><!-- cannot test interactive tools yet
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<test>
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<param name="input" value="test_data" ftype="tabular"/>
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<param name="matrix" value="text_to_wordmatrix_output"/>
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</test>-->
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</tests>
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<help><![CDATA[
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**What it does**
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The tool enables the exploration of data generated by ‘text_to_wordmatrix’ or ‘pmids_to_pubtator_matrix’ tools in a Shiny local instance.
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The following features can be generated: 1) word clouds for each initial search query, 2) dimension reduction and hierarchical clustering of
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binary matrices, and 3) tables with words and their frequency in the search queries.
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-----
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**How it works**
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- Input 1, a table with:
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- A column with initial search queries starting with "ID\_" (e.g., "ID_gene" if initial search queries were genes).
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- 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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| ID_gene | GROUPING_disorder
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| SCN1A | epilepsy
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| ANKRD11 | autism
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- Input 2:
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- The output of 'text_to_wordmatrix' or 'pmids_to_pubtator_matrix' tools, or a binary matrix.
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| scn8a | neuro | patient | spectrum | brain | grin2a
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| 1 | 1 | 1 | 0 | 1 | 1
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| 0 | 1 | 0 | 1 | 1 | 0
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]]></help>
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<citations>
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<citation type="doi">10.1101/2020.07.06.190629</citation>
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</citations>
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</tool>
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