--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/simtext_app.xml	Thu Sep 24 02:17:05 2020 +0000
@@ -0,0 +1,47 @@
+<tool id="simtext_app" name="simtext_app" tool_type="interactive" version="@VERSION@">
+    <description>Interactive shiny app to explore SimText output data</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <entry_points>
+        <entry_point name="SimText App" requires_domain="true">
+            <port>8888</port>
+        </entry_point>
+    </entry_points>
+    <expand macro="stdio"/>
+    <command><![CDATA[Rscript 
+      '${__tool_directory__}/simtext_app.R'
+      --input '$input'
+      --matrix '$matrix'
+      --host '0.0.0.0'
+      --port '8888'
+      ]]>
+    </command>
+    <inputs>
+      <param argument="--input" label="Input file" name="input" optional="false" type="data" format="tabular" help="input"/>
+      <param argument="--matrix" label="matrix file" name="matrix" optional="false" type="data" format="tabular" help="matrix"/>
+    </inputs>
+    <outputs>
+      <data format="tabular" name="output" />
+    </outputs>
+    <tests><!-- cannot test interactive tools yet
+        <test>
+          <param name="input" value="test_data" ftype="tabular"/>
+          <param name="matrix" value="text_to_wordmatrix_output"/>
+        </test>-->
+    </tests>
+    <help><![CDATA[
+
+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.
+
+Input 1, a table with:
+    - A column with initial search queries starting with "ID\_" (e.g., "ID_gene" if initial search queries were genes).
+    - 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.
+Input 2:
+  The output of 'text_to_wordmatrix' or 'pmids_to_pubtator_matrix' tools, or a binary matrix.
+
+
+        ]]></help>
+    <expand macro="citations"/>
+</tool>
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