view rdata_extractor.xml @ 1:5184899fd06e draft default tip

author mnhn65mo
date Tue, 07 Aug 2018 08:23:15 -0400
parents 10212598b005
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<tool id="Rdata_exctract" name="Rdata parser" version="0.1">
        <requirement type="package" version="1.20.0">r-getopt</requirement>
        <requirement type="package" version="7.0">readline</requirement>
    <command detect_errors="exit_code"><![CDATA[
        mkdir outputs &&
	Rscript '$__tool_directory__/rdata_extractor.R' '$rdata' $selectedattributes '$summary' '$other' '$bind_dataframe'
        <param name="rdata" type="data" label="Rdata file to explore" format="rdata"/>
        <param name="rdata_attributes" type="data" label="File with .Rdata content details" format="tabular"/>

        <param name="selectedattributes" label="Select which attribute(s) you want to extract" type="select" display="checkboxes" multiple="true">
            <options from_dataset="rdata_attributes">
                <column name="value" index="0"/>
        <param name="bind_dataframe" label="Bind variables in a single tabular when its possible" type="boolean" truevalue="bind" falsevalue="nobind" checked="true"/>
        <data name="summary" from_work_dir="summary.tabular" format="tabular" label="Summary"/>
        <data name="other">
            <discover_datasets pattern="__designation_and_ext__" visible="true" directory="outputs"/>

.. class:: infomark 

Rdata parser
**What it does**        

The Rdata parser tool allows to extract informations from a binary R file in .RData format. 

It produces a summary file and extract the selected dimensions. 
More informations concerning R Data format and save / load functions can be found here:

More informations concerning R Data format and save / load functions can be found here:


**How to use it**

First use the Rdata reader tool to get the list of dimensions available in the binary file.

Use the reader tool output to select the dimension(s) you want to extract.

If the selected variables can be displayed alongside in a tabular files the option \"Bind\" will try to do so.