<tool id="sam2counts_edger" name="SAM/BAM To Counts">
  <requirements>
      <requirement version="2.7">python</requirement>
  </requirements>
  <description> - Create a digital expression matrix by counting reads aligned to transcripts</description>
  <command interpreter="python">
	sam2counts_galaxy_edger.py 
	## Inputs.
	#set $gnum=1
        #for $group in $group_analysis
 		--group G$gnum --treatment '${group.group}' --sample-name '${group.sample_init}' 
		--bam-file ${group.file_init} --file-type ${group.file_init.ext}
      		#for $input_files in $group.input_files:
       			--group G$gnum --treatment '${group.group}' --sample-name '${input_files.sample}' 
			    --bam-file ${input_files.file} --file-type ${group.file_init.ext}
        	#end for
		#set $gnum = $gnum + 1
        #end for

	$use_ref

	-o $output
  </command>

  <inputs>
	<param name="use_ref" type="boolean" label="Files have headers?" checked="true" truevalue="" falsevalue="-r" />

        <repeat name="group_analysis" title="Group" min="1" default="1">
		<param name="group" title="Group name" type="text" optional="false" label="Group name (no spaces, commas, or quotes)">
			<validator type="empty_field" />
			<validator type="regex" message="No spaces, commas, or quotes allowed">^[^\s,\'\"]+$</validator>
		</param>
		<param name="sample_init" title="Sample name" type="text" optional="false" label="Sample name (no spaces, commas, or quotes)">
			<validator type="empty_field" />
			<validator type="regex" message="No spaces, commas, or quotes allowed">^[^\s,\'\"]+$</validator>
		</param>
		<param format="sam,bam" name="file_init" type="data" label="SAM/BAM File" optional="false" help="">
			<validator type="empty_field" />
		</param>
		<repeat name="input_files" title="Replicate" min="1" default="1">
		    <param name="sample" title="Sample name" type="text" optional="false" label="Sample name (no spaces, commas, or quotes)">
			<validator type="empty_field" />
			<validator type="regex" message="No spaces, commas, or quotes allowed">^[^\s,\'\"]+$</validator>
		    </param>
		    <param format="sam,bam" name="file" type="data" label="Add file" help=""/>
		</repeat>
	</repeat>
  </inputs>
  
  <outputs>
    	<data format="tabular" name="output" label="Read Counts for ${tool.name} on ${on_string}"/>
  </outputs>
  	
  <help>
Sample names must be unique.
  </help>  
  
</tool>