# HG changeset patch
# User galaxyp
# Date 1445454797 14400
# Node ID 3fa49ed11f3dabda4987fcb8d2ad119a8f1cded7
# Parent 0c50fe88ebfc5a76cfe2b685048755d03876192e
Uploaded
diff -r 0c50fe88ebfc -r 3fa49ed11f3d peptide_shaker.xml
--- 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}"
diff -r 0c50fe88ebfc -r 3fa49ed11f3d searchgui.xml
--- 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 @@
+
@@ -787,6 +817,39 @@
+
+
+