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October 20, 2016 22:29
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<?xml version="1.0"?>
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<process>
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<name>EXAMPLE</name>
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<version>1</version>
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<author>
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<name>John Doe</name>
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<email>john@doe.org</email>
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</author>
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<description>
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This file illustrates the basic specification of a process. The example analysis in this process counts - in a rather complicated way - the number
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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.
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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.
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</description>
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<inputs>
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<filetype>
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<identifier>input_file</identifier>
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<format>txt</format>
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<quantity>single</quantity>
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<comment>The input file can be of arbitrary length.</comment>
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</filetype>
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</inputs>
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<references>
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<filetype>
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<identifier>ref_file</identifier>
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<format>txt</format>
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<quantity>single</quantity>
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<comment>The reference file can be of arbitrary length.</comment>
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</filetype>
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</references>
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<outputs>
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<filetype>
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<identifier>result_file</identifier>
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<format>txt</format>
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<quantity>single</quantity>
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<comment>The result file contains only yes or no.</comment>
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</filetype>
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</outputs>
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<software>
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<tool>
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<name>grep</name>
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<version>2.12</version>
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<command_line><![CDATA[ grep {word1} {input_file} > temp_file ]]></command_line>
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<loop></loop>
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<comment>All lines having a match for the first word are saved to a temporary file.</comment>
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</tool>
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<tool>
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<name>grep</name>
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<version>2.12</version>
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<command_line><![CDATA[ grep {word2} temp_file > temp_file2 ]]></command_line>
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<loop></loop>
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<comment>All lines having a match for both words are saved to a temporary file.</comment>
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</tool>
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<tool>
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<name>wc, cut</name>
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<version>8.13, 8.13</version>
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<command_line><![CDATA[ wc -l temp_file2 | cut -d " " -f 1 > temp_file3 ]]></command_line>
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<loop></loop>
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<comment>wc outputs the number of lines and the corresponding filename; we reduce the output to just the number using cut</comment>
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</tool>
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<tool>
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<name>wc, cut, cat</name>
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<version>8.13, 8.13, 8.13</version>
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<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>
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<loop></loop>
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<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>
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</tool>
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</software>
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</process>