supp_file_2_process_css.xml

<?xml version="1.0"?>
<?xml-stylesheet type="text/css" href="supp_file_3_style.css"?>
<process>
    <name>EXAMPLE</name>
	<version>1</version>
	<author>
		<name>John Doe</name>
		<email>john@doe.org</email>
	</author>
    <description>
        This file illustrates the basic specification of a process. The example analysis in this process counts - in a rather complicated way - the number
        of lines in an input file that contain two specified words and checks if this number is equal to the number of lines in a reference file. The output file generated by an analysis run of this process contains a yes/no answer.
        This process describes an analysis that can be executed on most computers running a common Linux installation such as Debian. All command lines listed below can be tested in a shell.
	</description>
	<inputs>
		<filetype>
			<identifier>input_file</identifier>
			<format>txt</format>
			<quantity>single</quantity>
			<comment>The input file can be of arbitrary length.</comment>
		</filetype>
	</inputs>
	<references>
		<filetype>
			<identifier>ref_file</identifier>
			<format>txt</format>
			<quantity>single</quantity>
			<comment>The reference file can be of arbitrary length.</comment>
		</filetype>
	</references>
	<outputs>
		<filetype>
			<identifier>result_file</identifier>
			<format>txt</format>
			<quantity>single</quantity>
			<comment>The result file contains only yes or no.</comment>
		</filetype>
	</outputs>
	<software>
		<tool>
			<name>grep</name>
			<version>2.12</version>
			<command_line><![CDATA[ grep {word1} {input_file} > temp_file ]]></command_line>
            <loop></loop>
			<comment>All lines having a match for the first word are saved to a temporary file.</comment>
		</tool>
		<tool>
			<name>grep</name>
			<version>2.12</version>
			<command_line><![CDATA[ grep {word2} temp_file > temp_file2 ]]></command_line>
            <loop></loop>
			<comment>All lines having a match for both words are saved to a temporary file.</comment>
		</tool>
		<tool>
			<name>wc, cut</name>
			<version>8.13, 8.13</version>
			<command_line><![CDATA[ wc -l temp_file2 | cut -d " " -f 1 > temp_file3 ]]></command_line>
            <loop></loop>
			<comment>wc outputs the number of lines and the corresponding filename; we reduce the output to just the number using cut</comment>
		</tool>
		<tool>
			<name>wc, cut, cat</name>
			<version>8.13, 8.13, 8.13</version>
			<command_line><![CDATA[ if [ `cat temp_file3` -eq `wc -l {ref_file} | cut -d " " -f 1` ]; then echo "yes" > {result_file}; else echo "no" > {result_file}; fi; ]]></command_line>
            <loop></loop>
			<comment>Since this command line contains some bash syntax, the process author should state the precise version of the shell environment: GNU bash ver. 4.2.37</comment>
		</tool>
	</software>
</process>