deep_process_template.xml

<?xml version="1.0"?>
<?xml-stylesheet type="text/css" href="http://deep.mpi-inf.mpg.de/DAC/files/style/deep_process_style.css"?>
<!-- Header above: leave that unchanged -->

<!-- Process documentation: change as necessary -->
<process>
	<!-- Process name: by convention, should be 3 capital letters -->
    <name>PROC</name>
	<!-- Process version: by convention, (single-digit) number, increment by one after update -->
	<version>0</version>
	<!-- Process author: state full name and valid institutional e-mail address -->
	<author>
		<name>Author_Name</name>
		<email>Author_Email</email>
	</author>
	<!-- Process description: free-text field, describe what, how and why this analysis does.
	 If you have to use special characters like ">" or "&", remember to escape them properly. -->
    <description>
        Description
	</description>

	<!-- Process input files: you can copy the "filetype" block as often as necessary -->
	<inputs>
		<filetype>
			<identifier>Input_ID1</identifier>
			<format>format</format>
			<quantity>single</quantity>
			<comment>Comment_1</comment>
		</filetype>
	</inputs>

	<!-- Process reference files: you can copy the "filetype" block as often as necessary -->
	<references>
		<filetype>
			<identifier>Reference_ID1</identifier>
			<format>format</format>
			<quantity>single</quantity>
			<comment>Comment_2</comment>
		</filetype>
	</references>

	<!-- Process output files: you can copy the "filetype" block as often as necessary; you only need to document
	 output files that are stored, i.e., that are available in downstream analysis. Do not list intermediate or
	 temporary files that are anyway discarded after a successful pipeline run -->
	<outputs>
		<filetype>
			<identifier>Output_ID1</identifier>
			<format>format</format>
			<quantity>collection</quantity>
			<comment>Comment_3</comment>
		</filetype>
	</outputs>

	<!-- Process step-by-step instructions: you can copy the "tool" block as often as necessary.
	 Note that special characters as part of the command line must not be escaped. Enclosing the
	 command line in a <![CDATA[  ]]> block avoids interpretation of its content as XML stream. -->
	<software>
		<tool>
			<name>Tool_Name</name>
			<version>Tool_Version</version>
			<command_line>
				<![CDATA[
					CMDLINE
				]]>
			</command_line>
			<!-- looping: can the above command line be executed in parallel, e.g., for each
			 chromosome separately? If so, please specify the corresponding identifier
			 from the command line here -->
            <loop>no_looping</loop>
			<comment>Comment_4</comment>
		</tool>
	</software>

</process>