changeset 0:d468482eb206 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/edgeR_Design_Matrix.xml	Thu Jan 09 02:43:41 2014 -0500
@@ -0,0 +1,75 @@
+<?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>