<tool id="sartools_edger" name="SARTools edgeR" version="1.0.0">
    
    <!-- [REQUIRED] Tool description displayed after the tool name -->
    <description>Compare two or more biological conditions in a RNA-Seq framework with edgeR</description>
    
    <macros>
    	<import>macros.xml</import>
    </macros>
    
    <expand macro="requirements"/>
    <expand macro="stdio"/>

    
    <!-- [REQUIRED] The command to execute -->
    <command interpreter="python"><![CDATA[
	
	abims_sartools_edger_wrapper.py
	## parameters
	@COMMAND_BASIC_PARAMETERS@
    	#if str( $advanced_parameters.adv_param ) == "show":
            @COMMAND_BATCH_PARAM@
	    --alpha $advanced_parameters.alpha
	    --pAdjustMethod $advanced_parameters.pAdjustMethod
	    --cpmCutoff $advanced_parameters.cpmCutoff
	    --geneSelection $advanced_parameters.geneSelection
	    --normalizationMethod $advanced_parameters.normalizationMethod
	    --colors $advanced_parameters.colors
    	#end if
	## ouputs
	@COMMAND_OUTPUTS@
        
    ]]></command>
    
    <!-- [REQUIRED] Input files and tool parameters -->
    <inputs>
        
        <expand macro="basic_parameters" />
 
        <conditional name="advanced_parameters" >
            <param name="adv_param" type="select" label="Advanced Parameters" help="" >
                <option value="hide" selected="true">Hide</option>
                <option value="show">Show</option>
            </param>
            <when value="hide" />
            <when value="show">
		<expand macro="batch_param" />
		<expand macro="alpha_param" />
		<expand macro="padjustmethod_param" />
		<param name="cpmCutoff" type="integer" value="1" min="0" label="Counts-per-million cut-off to filter low counts" help="(-m, --cpmCutoff) Set to 0 to disable filtering. Default is 1." />
		<param name="geneSelection" type="select" label="Selection of the features in MDSPlot" help="(-g, --gene.selection) Default is 'pairwise'." >
                	<option value="pairwise" selected="true">pairwise</option>
                	<option value="common">common</option>
		</param>
		<param name="normalizationMethod" type="select" label="Normalization method in calcNormFactors" help="(-n, --normalizationMethod) 'TMM' (default), 'RLE' (DESeq method) or 'upperquartile'." >
                	<option value="TMM" selected="true">TMM</option>
                	<option value="RLE">RLE</option>
                	<option value="upperquartile">upperquartile</option>
		</param>
		<expand macro="colors_param" />
            </when>
        </conditional>

    </inputs>
    
    <!-- [REQUIRED] Output files -->
    <outputs>
        
        <expand macro="outputs" /> 
              
    </outputs>
    
    <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
    <tests>
        <!-- [HELP] Test files have to be in the ~/test-data directory -->
        <test>
	    <!-- Test with 2 conditions, 2 replicates, 10 features -->
            <param name="targetFile" dbkey="?" value="target_small.txt" />
            <param name="rawDir" value="raw_small.zip" dbkey="?" ftype="zip"/>
	        <param name="adv_param" value="show"/>
            <output name="log">
                <assert_contents>
                    <has_text text="KO vs WT    5      4    9" />
                    <has_text text="HTML report created" />
                </assert_contents>
            </output>
        </test>
<!--        <test>
-->        <!-- NOT WORKING YET: Test with 3 conditions, 3 replicates, 10 features, with batch effect -->
<!--            <param name="targetFile" dbkey="?" value="targetT048_small.txt" />
            <param name="rawDir"   value="rawT048_small.zip" dbkey="?" ftype="no_unzip.zip"/>
	    <param name="condRef" value="T0"/>
	    <param name="adv_param" value="show"/>
	    <param name="condition" value="true"/>
            <output name="tables_html" file="SARTools_edgeR_targetT048_small_tables.html" lines_diff="12">
            	<extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_edgeR_T4vsT0_small.complete.txt"/>
            	<extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_edgeR_T8vsT0_small.complete.txt"/>
            	<extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_edgeR_T8vsT4_small.complete.txt"/>
	    </output>
        </test>
-->        <test>
        <!-- Test with 2 conditions, 2 replicates, 8217 features -->
            <param name="targetFile" dbkey="?" value="target.txt" />
            <param name="rawDir"   value="raw.zip" dbkey="?" ftype="zip"/>
	        <param name="adv_param" value="show"/>
            <output name="log">
                <assert_contents>
                    <has_text text="KO vs WT    2691   2713 5404" />
                    <has_text text="HTML report created" />
                </assert_contents>
            </output>
        </test>
<!--        <test>
-->        <!-- NOT WORKING YET: Test with 3 conditions, 3 replicates, 10160 features, with batch effect -->
<!--            <param name="targetFile" dbkey="?" value="targetT048.txt" />
            <param name="rawDir"   value="rawT048.zip" dbkey="?" ftype="no_unzip.zip"/>
	    <param name="condRef" value="T0"/>
	    <param name="adv_param" value="show"/>
	    <param name="condition" value="true"/>
            <output name="tables_html" file="SARTools_edgeR_targetT048_tables.html" lines_diff="14">
            	<extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_edgeR_T4vsT0.complete.txt"/>
            	<extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_edgeR_T8vsT0.complete.txt"/>
            	<extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_edgeR_T8vsT4.complete.txt"/>
	    </output>
        </test>
-->    </tests>
    
    <!-- [OPTIONAL] Help displayed in Galaxy -->
    <help><![CDATA[

@HELP_AUTHORS@

==============
SARTools edgeR
==============

-----------
Description
-----------

@HELP_DESCRIPTION@


-----------
Input files
-----------

@HELP_INPUT_FILES@


----------
Parameters
----------

	@HELP_BASIC_PARAMETERS@
	* **batch:** adjustment variable to use as a batch effect, must be a column of the target file (NULL if no batch effect needs to be taken into account);
	* **alpha:** significance threshold applied to the adjusted p-values to select the differentially expressed features (default is 0.05);
	* **pAdjustMethod:** p-value adjustment method for multiple testing [4, 5] ("BH" by default, "BY" or any value of p.adjust.methods);
	* **cpmCutoff:** counts-per-million cut-off to filter low counts (default is 1, set to 0 to disable filtering);
	* **gene.selection:** method of selection of the features for the MultiDimensional Scaling plot ("pairwise" by default or common);
	* **normalizationMethod:** normalization method in calcNormFactors(): "TMM" (default), "RLE" (DESeq method) or "upperquartile";
	* **colors:** colors used for the figures (one per biological condition), 8 are given by default.


------------
Output files
------------

@HELP_OUTPUT_FILES@

		
---------------------------------------------------

[1] G.-K. Smyth. Limma: linear models for microarray data. In R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, and W. Huber, editors, Bioinformatics and Computational Biology Solutions Using R and Bioconductor, pages 397–420. Springer, New York, 2005.

[2] S. Anders. HTSeq: Analysing high-throughput sequencing data with Python. http://www-huber.embl.de/users/anders/HTSeq/, 2011.

[3] S. Anders, P.-T. Pyl, and W. Huber. HTSeq - A Python framework to work with high-throughput sequencing data. bioRxiv preprint, 2014. URL: http://dx.doi.org/10.1101/002824.

[4] Y. Benjamini and Y. Hochberg. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society B, 57:289–300, 1995.

[5] Y. Benjamini and D. Yekutieli. The control of the false discovery rate in multiple testing under dependency. Ann. Statist., 29(4):1165–1188, 2001.


   ]]></help>

   <citations>
        <expand macro="common_citations" /> 
   </citations>
    
</tool>