<tool id="GEOQuery" name="GEOQuery" version="1.0.0">

    <description>GEOQuery wrapper</description>

    <requirements>
        <requirement type="package" version="2.46.0">bioconductor-geoquery</requirement>
        <requirement type="package">r-optparse</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
        <regex match="Warning" source="both" level="warning"/>
    </stdio>

    <command>
        <![CDATA[ 
        Rscript --vanilla
        ${__tool_directory__}/GEOQuery.R 
            --id ${GEOQueryID} 
            --transformation ${transformation}
            --data ${GEOQueryData} 
            --rdata ${GEOQueryRData} 
            --conditions ${conditions}
        ]]>
    </command>

    <inputs>
        <param name="GEOQueryID" type="text" size="12" optional="false" label="GEOQuery ID" help="">
            <validator type="empty_field"/>
        </param>
        <param name="transformation" type="select" label="log2 transformation">
            <option value="auto">auto</option>
            <option value="yes">yes</option>
            <option value="no">no</option>
        </param>
    </inputs>

    <outputs>
        <data format="tabular" name="GEOQueryData" label="GEOQuery Data of ${GEOQueryID}"/>
        <data format="cond" name="conditions" label="conditions of ${GEOQueryID}"/>
        <data format="rdata" name="GEOQueryRData" label="GEOQuery RData of ${GEOQueryID}"/>
    </outputs>

    <tests>
        <test>
            <param name="GEOQueryID" value="GSE3524"/>
            <param name="transformation" value="auto"/>
            <output name="conditions" file="conditions.cond" ftype="cond"/>
        </test>
    </tests>

    <help>
<![CDATA[ 
**What it does**     	

This tool fetches microarray data directly from GEO database, based on the GEOQuery R package. Given a GSE accession ID, it returns an Rdata object containing the data and a text file (.cond file) summarizing the conditions of the experiment. 
The .cond file is a text file containing one line per sample in the experiment. Each line is made of 3 columns:

	- Sample ID 
	- Condition of the biological sample
	- Description of the biological sample

**Example** of .cond file      	
::

 GSM80460	series of 16 tumors	GSM80460 OSCE-2T SERIES OF 16 TUMORS
 GSM80461	series of 16 tumors	GSM80461 OSCE-4T Series of 16 Tumors
 GSM80462	series of 16 tumors	GSM80462 OSCE-6T Series of 16 Tumors
 GSM80476	series of 4 normals	GSM80476 OSCE-2N Series of 4 Normals
 GSM80477	series of 4 normals	GSM80477 OSCE-9N Series of 4 Normals
    
**Results**
	
- Rdata object containing data for further analysis
- Condition (.cond) file summarizing conditions of the experiment
- Tabular (.txt) file containing expression data for each sample
]]> 		
    </help>

</tool>