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comparison simtext_app.xml @ 0:34ed44f3f85c 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 02:17:05 +0000
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-1:000000000000 0:34ed44f3f85c
1 <tool id="simtext_app" name="simtext_app" tool_type="interactive" version="@VERSION@">
2 <description>Interactive shiny app to explore SimText output data</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <entry_points>
8 <entry_point name="SimText App" requires_domain="true">
9 <port>8888</port>
10 </entry_point>
11 </entry_points>
12 <expand macro="stdio"/>
13 <command><![CDATA[Rscript
14 '${__tool_directory__}/simtext_app.R'
15 --input '$input'
16 --matrix '$matrix'
17 --host '0.0.0.0'
18 --port '8888'
19 ]]>
20 </command>
21 <inputs>
22 <param argument="--input" label="Input file" name="input" optional="false" type="data" format="tabular" help="input"/>
23 <param argument="--matrix" label="matrix file" name="matrix" optional="false" type="data" format="tabular" help="matrix"/>
24 </inputs>
25 <outputs>
26 <data format="tabular" name="output" />
27 </outputs>
28 <tests><!-- cannot test interactive tools yet
29 <test>
30 <param name="input" value="test_data" ftype="tabular"/>
31 <param name="matrix" value="text_to_wordmatrix_output"/>
32 </test>-->
33 </tests>
34 <help><![CDATA[
35
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.
37
38 Input 1, a table with:
39 - A column with initial search queries starting with "ID\_" (e.g., "ID_gene" if initial search queries were genes).
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.
41 Input 2:
42 The output of 'text_to_wordmatrix' or 'pmids_to_pubtator_matrix' tools, or a binary matrix.
43
44
45 ]]></help>
46 <expand macro="citations"/>
47 </tool>