Example for external tools with gzip and gunzip
Created: 2011-05-18 09:22:50
Last updated: 2011-05-18 09:22:54
This workflow is self-contained. It has a fixed URL from which a text file is downloaded (output as Original_file). That file is gzipped (output as Compressed_File) and then gunzipped again (output as Decompressed_File).
The workflow wraps external tools from taverna.nordugrid.org and needs a beta version of Taverna 2.3 or later.
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Authors (1)
Steffen Moeller
Alan Williams |
Titles (1)
Example for external tools with gzip and gunzip |
Descriptions (1)
This workflow is self-contained. It has a fixed URL from which a text file is downloaded (output as Original_file). That file is gzipped (output as Compressed_File) and then gunzipped again (output as Decompressed_File).
The workflow wraps external tools from taverna.nordugrid.org and needs a beta version of Taverna 2.3 or later. |
Dependencies (0)
Processors (4)
Name |
Type |
Description |
Read_Text_File |
localworker |
ScriptBufferedReader getReader (String fileUrl) throws IOException {
InputStreamReader reader;
try {
reader = new FileReader(fileUrl);
}
catch (FileNotFoundException e) {
// try a real URL instead
URL url = new URL(fileUrl);
reader = new InputStreamReader (url.openStream());
}
return new BufferedReader(reader);
}
StringBuffer sb = new StringBuffer(4000);
BufferedReader in = getReader(fileurl);
String str;
String lineEnding = System.getProperty("line.separator");
while ((str = in.readLine()) != null) {
sb.append(str);
sb.append(lineEnding);
}
in.close();
filecontents = sb.toString();
|
GROMACS_MDP_FILE |
stringconstant |
Valuehttp://md.chem.rug.nl/~mdcourse/minim.mdp |
gzip |
externaltool |
|
gunzip |
externaltool |
|
Outputs (7)
Name |
Description |
Original_File |
Parameter file for GROMACS downloaded directly from http://md.chem.rug.nl/~mdcourse/minim.mdp
Any file would do for this example.
|
Compressed_File |
A particular text file compressed with gzip.
|
Decompressed_File |
The compressed file is uncompressed again.
|
gunzip_STDERR |
Empty if executing normally.
|
gunzip_STDOUT |
Always empty.
|
gzip_STDERR |
Empty if executing normally.
|
gzip_STDOUT |
Always empty.
|
Datalinks (10)
Source |
Sink |
GROMACS_MDP_FILE:value |
Read_Text_File:fileurl |
Read_Text_File:filecontents |
gzip:file_to_compress |
gzip:gzipped_file |
gunzip:gzipped_file |
Read_Text_File:filecontents |
Original_File |
gzip:gzipped_file |
Compressed_File |
gunzip:decompressed_file |
Decompressed_File |
gunzip:STDERR |
gunzip_STDERR |
gunzip:STDOUT |
gunzip_STDOUT |
gzip:STDERR |
gzip_STDERR |
gzip:STDOUT |
gzip_STDOUT |
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