<tool id="sam2counts" name="SAM To Counts">
	<description>Produce count data from SAM files</description>

	<requirements>
		<requirement type="python-module">sam2counts_galaxy.py</requirement>
	</requirements>

	<command interpreter="python">
		sam2counts_galaxy.py 

		${first_input}
		#for $input_file in $input_files:
		  ${input_file.additional_input}
		#end for

		-o $counts
		-l $colnames
	</command>

	<inputs>
                <param name="colnames" type="text" size="30" label="Short names for samples" help="A comma-separated list of short names for the samples in order">
                        <validator type="empty_field"/>
                        <validator type="regex" message="Must be a comma-separated tuple with no spaces">^(\w+,)+\w+$</validator>
                </param>

        	<param format="sam" name="first_input" type="data" label="SAM file" help=""/>
        	<repeat name="input_files" title="Additional SAM Files">
            		<param format="sam" name="additional_input" type="data" label="SAM file" help=""/>
        	</repeat>
	</inputs>

	<outputs>
		<data format="tabular" name="counts"/>
	</outputs>

	<help>
	</help>

</tool>