<tool id="deseq" name="DE Seq">
	<description>Run Differential Expression analysis from SAM To Count data</description>

	<command interpreter="python">
		 stderr_wrapper.py Rscript ${GALAXY_DATA_INDEX_DIR}/deseq.R $counts $column_types $comparison $top_table $diagnostic_html "$diagnostic_html.files_path" "$counts.name"
	</command>

	<inputs>
		<param format="tabular" name="counts" type="data" optional="false" label="Counts file (from sam2counts)" help="Must have same number of samples as the column types field. E.g. if the column types field is 'kidney,kidney,liver,liver', then there must be 4 sample columns in the counts file."/>

		<param name="column_types" type="text" size="40" optional="false" label="Column Types in counts file" help="A comma separated list (no spaces) of the types of the data columns using the same name for replicates.  E.g. kidney,kidney,kidney,liver,liver,liver">
			<validator type="empty_field"/>
			<validator type="regex" message="Must be a comma-separated list with no spaces">^(\w+,)+\w+$</validator>
		</param>

		<param name="comparison" type="text" size="30" optional="false" label="Comparison type" help="A comma separated tuple (no spaces) of the comparison you want to do.  Must use the names from the Column Types list.  E.g. comparing kidney to liver: kidney,liver.  Comparing liver to kidney: liver,kidney">
			<validator type="empty_field"/>
			<validator type="regex" message="Must be a comma-separated tuple with no spaces">^\w+,\w+$</validator>
		</param>
	</inputs>

	<outputs>
		<data format="tabular" name="top_table" label="Top Table from ${tool.name} on ${on_string}"/>
		<data format="html" name="diagnostic_html" label="Diagnostic Plots for ${tool.name} on ${on_string}"/>
	</outputs>

	<help>
		NOTE: This DEseq Galaxy tool can only be run on counts files that are created from SAM files that have been aligned to a transcriptome.
	</help>

</tool>