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ADD: added supplemental material from Ox. DB publication - likewise, …
…the material was removed from the MPII-internal SVN
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,68 @@ | ||
| <?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> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,69 @@ | ||
| <?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> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,217 @@ | ||
|
|
||
| /* Design for top level elements */ | ||
|
|
||
| process { | ||
| margin: 25px; | ||
| background-color: white; | ||
| width: auto; | ||
| font-family: "Arial", sans-serif; | ||
| } | ||
|
|
||
| *:before { | ||
| font-weight: bold; | ||
| } | ||
|
|
||
| process>name:before { | ||
| content: "Process: "; | ||
| } | ||
|
|
||
| process>name { | ||
| display: block; | ||
| } | ||
|
|
||
| version:before { | ||
| content: "Version: "; | ||
| color: black; | ||
| } | ||
|
|
||
| process>version { | ||
| display: block; | ||
| font-weight: bold; | ||
| color: red; | ||
| } | ||
|
|
||
|
|
||
| author:before { | ||
| content: "Contact:"; | ||
| font-weight: bold; | ||
| } | ||
|
|
||
| author { | ||
| top: 10px; | ||
| display: block; | ||
| margin-bottom: 10px; | ||
| } | ||
|
|
||
| author>name { | ||
| display: block; | ||
| padding-left: 10px; | ||
| padding-top: 3px; | ||
| padding-bottom: 3px; | ||
| } | ||
|
|
||
| author>email { | ||
| display: block; | ||
| padding-left: 10px; | ||
| } | ||
|
|
||
| description:before { | ||
| content: "Process description: "; | ||
| font-weight: bold; | ||
| display: block; | ||
| } | ||
|
|
||
| description { | ||
| display: block; | ||
| border: 0px; | ||
| padding-bottom: 10px; | ||
| padding-top: 10px; | ||
| border-bottom-width: 2px; | ||
| border-top-width: 2px; | ||
| border-style: solid; | ||
| border-color: lightgrey; | ||
| } | ||
|
|
||
|
|
||
| inputs:before { | ||
| content: "Input files"; | ||
| font-weight: bold; | ||
| } | ||
|
|
||
| inputs { | ||
| margin-top: 10px; | ||
| display: block; | ||
| } | ||
|
|
||
| filetype:before { | ||
| content: "File"; | ||
| display: block; | ||
| } | ||
| filetype { | ||
| position: relative; | ||
| left: 20px; | ||
| display: block; | ||
| } | ||
|
|
||
| identifier:before { | ||
| content: "Identifier: "; | ||
| font-family: "Arial", sans-serif; | ||
| } | ||
|
|
||
| identifier, format, quantity, comment { | ||
| display: block; | ||
| position: relative; | ||
| left: 25px; | ||
| padding-bottom: 3px; | ||
| } | ||
|
|
||
| identifier, command_line { | ||
| font-family: "Courier New", Monospace; | ||
| } | ||
|
|
||
| format:before { | ||
| content: "File format: "; | ||
| } | ||
|
|
||
| quantity:before { | ||
| content: "Quantity: "; | ||
| } | ||
|
|
||
| comment:before { | ||
| content: "Comment: "; | ||
| } | ||
|
|
||
| references:before { | ||
| content: "Reference files"; | ||
| } | ||
|
|
||
| references { | ||
| margin-top: 10px; | ||
| display: block; | ||
| background-color: #F0F0F0; | ||
| padding-top: 10px; | ||
| padding-bottom: 10px; | ||
| } | ||
|
|
||
| outputs:before { | ||
| content: "Output files"; | ||
| font-weight: bold; | ||
| } | ||
| outputs { | ||
| margin-top: 10px; | ||
| margin-bottom: 10px; | ||
| display: block; | ||
| } | ||
| software:before { | ||
| content: "Process Steps"; | ||
| font-weight: bold; | ||
| display: block; | ||
| margin-bottom: 10px; | ||
| } | ||
|
|
||
| software { | ||
| display: block; | ||
| padding-top: 10px; | ||
| border: 0px; | ||
| border-top-width: 2px; | ||
| border-style: solid; | ||
| border-color: lightgrey; | ||
| counter-reset: subsection; | ||
| padding-bottom: 10px; | ||
| } | ||
|
|
||
| tool>name:before { | ||
| counter-increment: subsection; | ||
| content: "Step " counter(subsection) ": "; | ||
| } | ||
|
|
||
| tool>name { | ||
| position: relative; | ||
| margin-left: 15px; | ||
| padding: 5px; | ||
| border-style: solid; | ||
| border-width: 2px; | ||
| border-color: #47D147; | ||
| border-radius: 5px; | ||
| box-sizing: border-box; | ||
| text-align: center; | ||
| } | ||
|
|
||
| tool>version:before { | ||
| content: "Software version: "; | ||
| } | ||
|
|
||
| tool>version { | ||
| display: block; | ||
| margin-left: 25px; | ||
| margin-top: 10px; | ||
| padding-bottom: 3px; | ||
| } | ||
|
|
||
| command_line { | ||
| display: block; | ||
| position: relative; | ||
| left: 40px; | ||
| padding-top: 10px; | ||
| padding-bottom: 10px; | ||
| padding-left: 5px; | ||
| } | ||
|
|
||
| command_line:hover { | ||
| background-color: lightgrey; | ||
| } | ||
|
|
||
| loop:before { | ||
| content: "Loop: "; | ||
| } | ||
|
|
||
| loop { | ||
| display: block; | ||
| margin-left: 25px; | ||
| padding-bottom: 5px; | ||
|
|
||
| } | ||
|
|
||
| tool>comment { | ||
| margin-bottom: 15px; | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,20 @@ | ||
| [Description] | ||
| process EXAMPLEv1 | ||
| user jdoe | ||
| date 20150105 | ||
| analysis_id ex1_run_20150105 | ||
|
|
||
| [Inputs] | ||
| input_file pg218.txt | ||
|
|
||
| [References] | ||
| ref_file 38503-0.txt | ||
|
|
||
| [Outputs] | ||
| result_file res.txt | ||
|
|
||
| [Parameters] | ||
| word1 fines | ||
| word2 sunt | ||
|
|
||
| [Metrics] |
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