Config File OverviewHardklör configuration files are in ASCII text format and can be used to set parameters and operate Hardklör in batch mode. There are two basic format structures: parameter lines and action lines. Parameter lines allow parameters to be set on a global level, i.e. you can set the parameter once and it will be applied to every data file being analyzed in your batch. Parameters are entered as one parameter per line and begin with a dash (
Example Config File #1
In this example, a batch analysis is being performed. There are a total of four analyses for three data files. Note the first two flags set indicate the locations of the Mercury and Hardklör data files. Setting these paths at the top of the config file allows the analysis to take place in the working directory instead of the directory where Hardklör is installed. Eight global parameters are set at the top of the config file. These parameters are set globally, and thus they are applied to all four analyses. Any parameters not specified use the default values. Below the parameters are three action lines specifying the input and output file names. The last line shows a second analysis being performed on the first data file. Notice that this line has a parameter specifying a different charge determination method than the previous analyses. This parameter value in the action line overrides the global parameter value.
Example Config File #2
In example #2, global parameters are set at the top of the config file and analysis is performed on
three data files. Then, about halfway down, three of the global parameters are set to new values. The last
three files being analyzed will still have
Example Config File #3
Example #3 is very similar to the previous examples, but the most distinguishing feature is that it emphasizes use of Hardklör's ability to differentiate peptides that are isotopically enriched from those that have the natural abundance of isotopes. Each file was presumably from a sample with a different enrichment level than the other samples. The first file is analyzed with 50% deuterium enrichment, the second file with 75% deuterium enrichment, and the third file with 90% deuterium enrichment.
Hardklör is Copyright ©2007 University of Washington. All rights reserved. Written by Michael R. Hoopmann, Michael J. MacCoss, in the Department of Genome Sciences at the University of Washington.