view edgeR_Design_Matrix.xml @ 2:521bfa975110 draft

Uploaded

<?xml version="1.0" encoding="UTF-8"?>
<tool id="edger_design_matrix" name="edgeR Design Creator">
	<description>Create the experimental design for edgeR by a few clicks in Galaxy</description>
	
	<command interpreter="python">
		edgeR_Design_Matrix.py
			-o $contrast_matrix
			-u
				#for $unpaired_sample in $unpaired_samples
					${unpaired_sample}
				#end for
			-p
				#for $paired_sample in $paired_samples
					#for $sample in $paired_sample.samples
						${sample.sample}
					#end for
					:
				#end for
			-t
				#for $treatment in $check.treatments
					#for $factor in $treatment.factors
						"$factor.name"
						$factor.samples
					#end for
					:
				#end for
			-n
				#for $unpaired_sample in $unpaired_samples
					"${unpaired_sample}:${unpaired_sample.name}"
				#end for
				#for $paired_sample in $paired_samples
					#for $sample in $paired_sample.samples
						"${sample.sample}:${sample.sample.name}"
					#end for
				#end for
	</command>
	
	<code file="edgeR_Design_Matrix.listing.py" />
	
	<inputs>
		<param name="unpaired_samples" type="data" format="tabular" label="Unpaired read-count dataset" help="from featureCounts/DEXSeq-count/HTSeq-count, etc.  Press [ctrl] and click the sample to unselect it." multiple="true" />
		
		<repeat name="paired_samples" title="Add paired samples; per patient">
			<repeat name="samples" title="Add sample for patient" min="2">
				<param name="sample" type="data" format="tabular" label="Read-count dataset that belongs to a pair" help="from featureCounts/DEXSeq-count/HTSeq-count, etc." />
			</repeat>
		</repeat>
		
		<conditional name="check">
			<param name="continue" help="When clicking this variable, the treatment menu will appear" type="boolean" truevalue="yes" />
			
			<when value="yes">	
				<repeat name="treatments" title="Treatments" min="1">
					<repeat name="factors" title="Factor" min="2" help="e.g. 'normal' or 'tumor', 'untreated', 'recurrent', 'metastatic', or 'group_1',...,'group_n' etc.">
						<param name="name" type="text" />
						<param name="samples" type="select" label="Corresponding samples" multiple="true" dynamic_options="listfiles(unpaired_samples,paired_samples)"  />
					</repeat>
				</repeat>
			</when>
		</conditional>
		
	</inputs>
	
	<outputs>
		<data format="tabular" name="contrast_matrix" label="Contrast matrix" />
	</outputs>
	
	<help>
Examples::
	 2 group, unpaired::
		Group name 1 = Healthy
		Group name 2 = Tumor
	
	</help>
</tool>