diff vst_transformation.xml @ 0:a48dde9abecf draft

Uploaded initial version

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vst_transformation.xml	Wed Jul 17 04:06:12 2013 -0400
@@ -0,0 +1,73 @@
+<tool id="vsttransform" name="Variance stabilizing transformation" version="1.0.0">
+    <description>
+		using DESeq
+    </description>
+    
+    <requirements>
+		<requirement type="package" version="3.0.1">package_r3</requirement>
+		<requirement type="package" version="1.0.0">r_additions</requirement>
+		<requirement type="package" version="2.12">biocbasics</requirement>
+	</requirements>
+    
+    <command interpreter="perl">
+		vst_transformation.pl ${parameters}
+    </command> 
+   
+    <inputs>
+	<param format="tabular" name="counttable" type="data" label="Count table" help="Count table generated by HTSeq-count on mapped RNA-seq data" /> 
+	<param name="header_row" type="boolean" checked="TRUE" truevalue="TRUE" falsevalue="FALSE" label="Does the table has a header row" /> 
+	<param name="header_columns" type="boolean" checked="TRUE" truevalue="TRUE" falsevalue="FALSE"  label="Does the first column contains identifiers" /> 
+	
+	<repeat name="replicates" title="Replicate group">
+		<param name="repl_group_name" type="text" value="" size="50" label="Replicate group name">
+			<sanitizer invalid_char="">
+				<valid initial="string.letters,string.digits"><add value="_" /> </valid>
+			</sanitizer>
+		</param>
+		<param name="rep_columns" label="Select replicates" type="data_column" data_ref="counttable" numerical="True" 
+	         		multiple="true" use_header_names="true" size="120" display="checkboxes">
+        		<validator type="no_options" message="Please select at least one column."/>
+		</param>  <!-- $replicates contains a comma-separated list of number -->
+	</repeat>
+    </inputs>
+
+    <outputs>
+		<data format="tabular" name="outtab" label="${tool.name} of ${on_string}"/>
+		<data format="html" name="html_file" label="Histogram of ${tool.name} of ${on_string}"/>		
+    </outputs>
+
+	<configfiles>
+		<configfile name="parameters">
+			## first we pass some galaxy environment variables
+			counttable==$counttable
+			header_row==$header_row
+			header_columns==$header_columns
+			outtab==$outtab
+			html_file==$html_file
+			
+			##REPEAT BLOCK
+			#for $i, $s in enumerate( $replicates )
+			replicates_$s.repl_group_name==$s.rep_columns
+			#end for
+		</configfile>
+
+	</configfiles> 
+
+	<tests>
+		<test>
+			<param name="counttable" value="counttable1.tsv" ftype="tabular" />
+			<param name="header_row" value="TRUE" />
+			<param name="header_columns" value="TRUE" />
+			<param name="repl_group_name" value="can" />
+			<param name="rep_columns" value="2,3" />
+			<output name="outtab" file="vst_transf_tabout.txt" ftype="tabular" />
+			<output name="html_file" file="vst_transf_htmlout.html" ftype="html" lines_diff="6"/>
+		</test>
+	</tests>
+
+    <help>
+**Variance stabilizing transformation**
+
+This tool takes in raw count data per feature and applies a variance stabilizing transformation using DESeq.
+    </help>
+</tool>