view rdata_extractor.xml @ 0:10212598b005 draft

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<tool id="Rdata_exctract" name="Rdata parser" version="0.1">
    <requirements>
        <requirement type="package" version="1.20.0">r-getopt</requirement>
        <requirement type="package" version="7.0">readline</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        mkdir outputs &&
	Rscript '$__tool_directory__/rdata_extractor.R' '$rdata' $selectedattributes '$summary' '$other' '$bind_dataframe'
]]>
    </command>
    <inputs>
        <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"/>
            </options>
        </param>
        <param name="bind_dataframe" label="Bind variables in a single tabular when its possible" type="boolean" truevalue="bind" falsevalue="nobind" checked="true"/>
    </inputs>
    <outputs>
        <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"/>
        </data>
    </outputs>
    <help><![CDATA[

.. 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:  http://www.sthda.com/english/wiki/saving-data-into-r-data-format-rds-and-rdata&gt.

More informations concerning R Data format and save / load functions can be found here:  http://www.sthda.com/english/wiki/saving-data-into-r-data-format-rds-and-rdata&gt.


|

**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.

    ]]></help>
</tool>