<tool id="importMatrixData" name="Import custom data" version="1.0.0">

    <description>Quality control and normalization of a custom matrix expression data</description>

    <requirements>
        <requirement type="package">bioconductor-biobase</requirement>
        <requirement type="package">bioconductor-limma</requirement>
        <requirement type="package">bioconductor-affy</requirement>
        <requirement type="package">bioconductor-affyplm</requirement>
        <requirement type="package">r-jsonlite</requirement>
        <requirement type="package">r-dplyr</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__}/ImportDataFromMatrix.R
            --input $input
            --normalization $normalization
            --annotations $annotations
            --rdataoutput $result_export_eset
            --htmloutput $result_html
            --htmloutputpath $result_html.files_path
            --htmltemplate ${__tool_directory__}/ImportDataFromMatrix_tpl.html
        ]]>
        </command>

    <inputs>
        <param name="input" type="data" format="tabular" label="Input data" help="Input data"/>
        <param name="normalization" type="select" label="Preprocessing/normalization">
            <option value="quantile">quantile normalization + log2</option>
            <option value="log2">log2 only</option>
            <option value="none">none</option>
        </param>
        <param name="annotations" type="text" label="Annotation GPL code" help="GPL code for annotations"/>		
    </inputs>

    <outputs>
        <data format="rdata" name="result_export_eset" label="export normalized expressionSet"/>		
        <data format="html" name="result_html" label="QC result"/>
    </outputs>

    <help>
<![CDATA[ 
**What it does**
		     	
This tool imports data stored in a tabular text file. 
Column titles (chip IDs) must match the IDs of the .cond file.
GPL annotation code is also required to fetch annotations from GEO.

**Exemple**

Header of input tabular text file
::


""	"GSM80460"	"GSM80461"	"GSM80462"	"GSM80463"	"GSM80464"
"1007_s_at"	-0.0513991525066443	0.306845500314283	0.0854246562526777	-0.142417044615852	0.0854246562526777
"1053_at"	-0.187707155126729	-0.488026018218199	-0.282789700980404	0.160920188181103	0.989865622866287
"117_at"	0.814755482809874	-2.15842936260448	-0.125006361067033	-0.256700472111743	0.0114956388378294
"121_at"	-0.0558912008920451	-0.0649174766813385	0.49467161164755	-0.0892673380970874	0.113700499164728
"1294_at"	0.961993677420255	-0.0320936297098533	-0.169744675832317	-0.0969617298870879	-0.181149439104566
"1316_at"	0.0454429707611671	0.43616183931445	-0.766111939825723	-0.182786075741673	0.599317793698226
"1405_i_at"	2.23450132056221	0.369606070031838	-1.06190243892591	-0.190997225060914	0.595503660502742


The .cond file should look like this 
::

 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**
	- Boxplots and MA plots 
	- Rdata object containing the data for further analysis.
]]>
    </help>

</tool>