Mercurial > repos > bgruening > peptideshaker
changeset 10:5a74b76d48fc draft
Uploaded
| author | iracooke |
|---|---|
| date | Tue, 06 May 2014 15:45:35 -0400 |
| parents | e6b36f17cea1 |
| children | e5bdaa2ac9c7 |
| files | peptide_shaker.xml |
| diffstat | 1 files changed, 1 insertions(+), 5 deletions(-) [+] |
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--- a/peptide_shaker.xml Mon May 05 03:44:02 2014 -0400 +++ b/peptide_shaker.xml Tue May 06 15:45:35 2014 -0400 @@ -158,7 +158,7 @@ ###################### ## PeptideShakerCLI ## ###################### - java -Xmx${java_heapsize}m -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI + java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI -temp_folder `pwd` -experiment '${exp_str}' -sample '${samp_str}' @@ -300,9 +300,6 @@ <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting" help="(-mgf_spectrum_count)"/> - <param name="java_heapsize" type="integer" value="2000" label="Java Memory Limit in mb for PeptideShaker" - help="Increase this value if you encounter out of memory errors"/> - <conditional name="species_type"> <param name="species_type_selector" type="select" optional="true" label="The species type to use for the gene annotation" help="(-species_type)"> @@ -692,7 +689,6 @@ <param name="input_database" value="tinydb.fasta"/> <param name="peak_lists" value="tinyspectra.mgf"/> <param name="precursor_ion_tol" value="100"/> - <param name="java_heapsize" value="1500"/> <param name="fixed_modifications" value="carbamidomethyl c"/> <param name="variable_modifications" value="oxidation of m"/> <param name="min_charge" value="1"/>