Mercurial > repos > galaxyp > peptideshaker
changeset 15:3fa49ed11f3d draft
Uploaded
author | galaxyp |
---|---|
date | Wed, 21 Oct 2015 15:13:17 -0400 |
parents | 0c50fe88ebfc |
children | c353378140ca |
files | peptide_shaker.xml searchgui.xml |
diffstat | 2 files changed, 67 insertions(+), 4 deletions(-) [+] |
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--- a/peptide_shaker.xml Mon Oct 19 16:57:46 2015 -0400 +++ b/peptide_shaker.xml Wed Oct 21 15:13:17 2015 -0400 @@ -33,7 +33,7 @@ -sample '$samp_str' -replicate 1 -identification_files \$cwd/searchgui_input.zip - -out \$cwd/peptideshaker_output.cps + -out \$cwd/peptideshaker_output.cpsx -zip \$cwd/peptideshaker_output.zip -threads "\${GALAXY_SLOTS:-12}"
--- a/searchgui.xml Mon Oct 19 16:57:46 2015 -0400 +++ b/searchgui.xml Wed Oct 21 15:13:17 2015 -0400 @@ -22,7 +22,7 @@ cwd=`pwd`; export HOME=\$cwd; - # Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present + ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present echo "searchgui.version=@SEARCHGUI_VERSION@" >> searchgui.properties; cp -r "\${SEARCHGUI_JAR_PATH%/*}" bin; @@ -51,7 +51,7 @@ ##################################################### (java -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.IdentificationParametersCLI - -out SEARCHGUI_IdentificationParameters.parameters + -out SEARCHGUI_IdentificationParameters.par @GENERAL_PARAMETERS@ @@ -171,6 +171,27 @@ -myrimatch_max_peak ${myrimatch.myrimatch_max_peak} #end if + #* + #if $andromeda.andromeda_advanced == "yes" + -andromeda_max_pep_mass ${andromeda.andromeda_max_pep_mass} + -andromeda_max_comb ${andromeda.andromeda_max_comb} + -andromeda_top_peaks ${andromeda.andromeda_top_peaks} + -andromeda_top_peaks_window ${andromeda.andromeda_top_peaks_window} + -andromeda_incl_water ${andromeda.andromeda_incl_water} + -andromeda_incl_ammonia ${andromeda.andromeda_incl_ammonia} + -andromeda_neutral_losses ${andromeda.andromeda_neutral_losses} + -andromeda_fragment_all ${andromeda.andromeda_fragment_all} + -andromeda_emp_correction ${andromeda.andromeda_emp_correction} + -andromeda_higher_charge ${andromeda.andromeda_higher_charge} + -andromeda_equal_il ${andromeda.andromeda_equal_il} + -andromeda_frag_method ${andromeda.andromeda_frag_method} + -andromeda_max_mods ${andromeda.andromeda_max_mods} + -andromeda_min_pep_length ${andromeda.andromeda_min_pep_length} + -andromeda_max_pep_length ${andromeda.andromeda_max_pep_length} + -andromeda_max_psms ${andromeda.andromeda_max_psms} + #end if + *# + #if $tide.tide_advanced == "yes" -tide_num_ptms ${tide.tide_num_ptms} -tide_num_ptms_per_type ${tide.tide_num_ptms_per_type} @@ -259,7 +280,7 @@ -temp_folder `pwd` -spectrum_files \$cwd -output_folder \$cwd/output - -id_params SEARCHGUI_IdentificationParameters.parameters + -id_params SEARCHGUI_IdentificationParameters.par -threads "\${GALAXY_SLOTS:-12}" @@ -319,6 +340,12 @@ -ms_amanda 0 #end if + #if 'Andromeda' in $engines_list: + -andromeda 1 + #else + -andromeda 0 + #end if + ## single zip file -output_option 0 @@ -364,6 +391,9 @@ <option value="OMSSA" selected="True">OMSSA</option> <option value="Comet">Comet</option> <option value="Tide">Tide</option> + <!-- Windows only + <option value="Andromeda">Andromeda</option> + --> <validator type="no_options" message="Please select at least one output file" /> </param> @@ -787,6 +817,39 @@ </when> </conditional> + <!-- Andromeda ADVANCED PARAMETERS --> + <!-- Windows only + <conditional name="andromeda"> + <param name="andromeda_advanced" type="select" label="Andromeda Options"> + <option value="yes">Advanced</option> + <option value="no" selected="True">Default</option> + </param> + <when value="no" /> + <when value="yes"> + <param name="andromeda_max_pep_mass" type="float" value="4600.0" label="Andromeda maximum peptide mass, default is: 4600.0" /> + <param name="andromeda_max_comb" type="integer" value="250" label="Andromeda maximum combinations, default is: 250" /> + <param name="andromeda_top_peaks" type="integer" value="8" label="Andromeda number of top peaks, default is: 8" /> + <param name="andromeda_top_peaks_window" type="integer" value="100" label="Andromeda top peaks window width, default is: 100" /> + <param name="andromeda_incl_water" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for water losses, default is: true" /> + <param name="andromeda_incl_ammonia" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for ammonina losses, default is: true" /> + <param name="andromeda_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda neutral losses are sequence dependent, default is: true" /> + <param name="andromeda_fragment_all" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda fragment all option, default is: false" /> + <param name="andromeda_emp_correction" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda emperical correction, default is: true" /> + <param name="andromeda_higher_charge" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda higher charge option, default is: true" /> + <param name="andromeda_equal_il" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda whether I and L should be considered indistinguishable, default is: false" /> + <param name="andromeda_frag_method" type="select" value="" label="Andromeda fragmentation method, (HCD, CID or EDT), default is: CID." > + <option value="CID" selected="true">CID</option> + <option value="HCD">HCD</option> + <option value="EDT">EDT</option> + </param> + <param name="andromeda_max_mods" type="integer" value="5" label="Andromeda maximum number of modifications, default is: 5" /> + <param name="andromeda_min_pep_length" type="integer" value="8" label="Andromeda minimum peptide length when using no enzyme, default is: 8" /> + <param name="andromeda_max_pep_length" type="integer" value="25" label="Andromeda maximum peptide length when using no enzyme, default is: 25" /> + <param name="andromeda_max_psms" type="integer" value="10" label="Andromeda maximum number of spectrum matches spectrum, default is: 10" /> + </when> + </conditional> + --> + <!-- Comet ADVANCED PARAMETERS --> <conditional name="comet"> <param name="comet_advanced" type="select" label="Comet Options">