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comp-metadata/publication/supp_file_1_process_raw.xml
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<?xml version="1.0"?> | |
<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> |