Mercurial > repos > bgruening > peptideshaker
changeset 7:3b058d96e8a7 draft
Added functional test
author | iracooke |
---|---|
date | Mon, 05 May 2014 03:38:17 -0400 |
parents | f62545ff7fa0 |
children | 4748cc855cdb |
files | peptide_shaker.xml |
diffstat | 1 files changed, 25 insertions(+), 3 deletions(-) [+] |
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--- a/peptide_shaker.xml Sun May 04 03:20:54 2014 -0400 +++ b/peptide_shaker.xml Mon May 05 03:38:17 2014 -0400 @@ -158,7 +158,7 @@ ###################### ## PeptideShakerCLI ## ###################### - java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI + java -Xmx${java_heapsize}m -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI -temp_folder `pwd` -experiment '${exp_str}' -sample '${samp_str}' @@ -300,6 +300,9 @@ <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)"> @@ -596,8 +599,8 @@ <conditional name="ms_amanda"> <param name="ms_amanda_selector" type="select" label="Run MS Amanda search"> - <option value="yes" selected="True">Search with MSGF</option> - <option value="no">No MS Amanda search</option> + <option value="yes">Search with MS Amanda</option> + <option value="no" selected="True">No MS Amanda search</option> </param> <when value="no" /> <when value="yes"> @@ -684,6 +687,25 @@ <filter>'1' in outputs</filter> </data> </outputs> + <tests> + <test> + <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"/> + <param name="max_charge" value="3"/> + <param name="advanced_type_selector" value="advanced"/> + <param name="xtandem_selector" value="yes"/> + <param name="omssa_selector" value="no"/> + <param name="msgf_selector" value="yes"/> + <param name="ms_amanda_selector" value="no"/> + + <output name="output" file="tinyoutput.cps" compare="sim_size" delta="600" /> + </test> + </tests> <help> **What it does**