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

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

	<command interpreter="python">
		sam2counts_galaxy.py 

		#if str($filetype.ftype_select) == "sam":
		${first_input_sam}
		#for $input_file_sam in $filetype.input_files_sam:
		  ${input_file_sam.additional_input_sam}
		#end for
		#end if

		#if str($filetype.ftype_select) == "bam":
		-b

		${first_input_bam}
		#for $input_file_bam in $filetype.input_files_bam:
		  ${input_file_bam.additional_input_bam}
		#end for
		#end if

		-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>

		<conditional name="filetype">

		<param name="ftype_select" type="select" label="Are the input files SAM or BAM format?">
			<option value="sam">SAM</option>
			<option value="bam">BAM</option>
		</param>

		<when value="sam">
        		<param format="sam" name="first_input_sam" type="data" label="SAM file" help=""/>
        		<repeat name="input_files_sam" title="Additional SAM Files">
            			<param format="sam" name="additional_input_sam" type="data" label="SAM file" help=""/>
        		</repeat>
		</when>

		<when value="bam">
                        <param format="bam" name="first_input_bam" type="data" label="BAM file" help=""/>
                        <repeat name="input_files_bam" title="Additional BAM Files">
                                <param format="bam" name="additional_input_bam" type="data" label="BAM file" help=""/>
                        </repeat>
                </when>

		</conditional>
	</inputs>

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

	<help>
	</help>

</tool>