# HG changeset patch
# User bgruening
# Date 1399622531 14400
# Node ID b9f2cedab007fe9fe46ea1054d124174285c1049
# Parent  e5bdaa2ac9c709c1b742efa1894db642808eecb4
Uploaded

diff -r e5bdaa2ac9c7 -r b9f2cedab007 peptide_shaker.xml
--- a/peptide_shaker.xml	Wed May 07 00:47:14 2014 -0400
+++ b/peptide_shaker.xml	Fri May 09 04:02:11 2014 -0400
@@ -11,9 +11,12 @@
         <exit_code range="1:" level="fatal" description="Job Failed" />
     </stdio>
     <command>
+
         #from datetime import datetime
         #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
         #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
+        #set $temp_stderr = 'macs2_stderr'
+
         mkdir output;
         mkdir output_reports;
         cwd=`pwd`;
@@ -39,7 +42,7 @@
         ## generate IdentificationParameters for SearchGUI ##
         #####################################################
 
-        java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.IdentificationParametersCLI
+        (java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.IdentificationParametersCLI
             -out SEARCHGUI_IdentificationParameters.parameters
             -prec_ppm "${precursor_ion_tol_units}"
             -prec_tol "${precursor_ion_tol}"
@@ -62,8 +65,23 @@
 
             #if $advanced.advanced_type_selector == "advanced":
 
-                ##if $advanced.xtandem.xtandem_selector == "yes"
-                ##end if
+                #if $advanced.xtandem.xtandem_selector == "yes"
+
+                    -xtandem_npeaks ${advanced.xtandem.xtandem_npeaks}
+                    -xtandem_min_peaks ${advanced.xtandem.xtandem_min_peaks}
+                    -xtandem_min_frag_mz ${advanced.xtandem.xtandem_min_frag_mz}
+                    -xtandem_min_prec_mass ${advanced.xtandem.xtandem_min_prec_mass}
+                    -xtandem_noise_suppr ${advanced.xtandem.xtandem_noise_suppr}
+
+                    #if $advanced.xtandem.xtandem_refine.xtandem_refine_selector == "yes"
+                        -xtandem_refine 1
+                        -xtandem_refine_unc ${advanced.xtandem.xtandem_refine.xtandem_refine_unc}
+                        -xtandem_refine_semi ${advanced.xtandem.xtandem_refine.xtandem_refine_semi}
+                        -xtandem_refine_p_mut ${advanced.xtandem.xtandem_refine.xtandem_refine_p_mut}
+                        -xtandem_refine_snaps ${advanced.xtandem.xtandem_refine.xtandem_refine_snaps}
+                        -xtandem_refine_spec_synt ${advanced.xtandem.xtandem_refine.xtandem_refine_spec_synt}
+                    #end if
+                #end if
 
                 #if $advanced.omssa.omssa_selector == "yes"
                     -omssa_hitlist_length ${advanced.omssa.hitlist_length}
@@ -72,19 +90,26 @@
                     -omssa_estimate_charge ${advanced.omssa.estimate_charge}
                 #end if
 
-                ##if $advanced.msgf.msgf_selector == "yes"
-                ##end if
+                #if $advanced.msgf.msgf_selector == "yes"
+                    -msgf_decoy ${advanced.msgf.msgf_decoy}
+                    -msgf_min_pep_length ${advanced.msgf.msgf_min_pep_length}
+                    -msgf_max_pep_length ${advanced.msgf.msgf_max_pep_length}
+                    -msgf_termini ${advanced.msgf.msgf_termini}
+                    -msgf_num_ptms ${advanced.msgf.msgf_num_ptms}
+                #end if
 
                 ##if $advanced.ms_amanda.ms_amanda_selector == "yes"
                 ##end if
 
             #end if
-        ;
+
+        2> $temp_stderr)
+        &amp;&amp;
 
         ################
         ## Search CLI ##
         ################
-        java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI
+        (java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI
             -temp_folder `pwd`
             -spectrum_files \$cwd
             -output_folder \$cwd/output
@@ -128,12 +153,13 @@
                 #end if
 
             #end if
-        ;
+        2>> $temp_stderr)
+        &amp;&amp;
 
         #########################################################
         ## generate IdentificationParameters for PeptideShaker ##
         #########################################################
-        java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.IdentificationParametersCLI
+        (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.IdentificationParametersCLI
             -out PEPTIDESHAKER_IdentificationParameters.parameters
             -prec_ppm "${precursor_ion_tol_units}"
             -prec_tol "${precursor_ion_tol}"
@@ -153,12 +179,14 @@
             -fi $forward_ion
             -ri $reverse_ion
             -db input_database.fasta
-        ;
+
+        2>> $temp_stderr)
+        &amp;&amp;
 
         ######################
         ## PeptideShakerCLI ##
         ######################
-        java -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}'
@@ -200,12 +228,14 @@
                 -max_mascot_e "${filtering_options.max_mascot_e}"
                 -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}"
             #end if
-        ;
+
+        2>> $temp_stderr)
+        &amp;&amp;
 
         ##################################
         ## PeptideShaker Report options ##
         ##################################
-        java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.ReportCLI
+        (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.ReportCLI
             -temp_folder `pwd`
             -in \$cwd/peptide_shaker_output.cps
             -out_reports \$cwd/output_reports
@@ -216,7 +246,9 @@
             #else:
                 -reports #echo str($outputs)#
             #end if
-        ;
+
+        2>> $temp_stderr)
+        &amp;&amp;
 
         #if '0' in str($outputs).split(','):
             find \$cwd/output_reports -name '*Certificate*' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
@@ -239,8 +271,10 @@
             ;
         #end if
 
-        ## the following line is needed. Otherwise, Galaxy will strip away the ';'
-        echo 'Finished!';
+        exit_code_for_galaxy=\$?;
+        cat $temp_stderr 2&gt;&amp;1;
+        (exit \$exit_code_for_galaxy)
+
     </command>
     <inputs>
         <param format="fasta" name="input_database" type="data" label="Protein Database"
@@ -567,7 +601,30 @@
                     </param>
                     <when value="no" />
                     <when value="yes">
-                    </when>
+
+
+                            <param name="xtandem_npeaks" label="X!Tandem: Total Peaks" type="integer" value="50" help="Maximum number of peaks to be used from a spectrum"/>
+                            <param name="xtandem_min_peaks" label="X!Tandem: Min Peaks" type="integer" value="15" help="Minimum number of peaks required for a spectrum to be considered"/>
+                            <param name="xtandem_min_frag_mz" label="X!Tandem: Min Frag m/z" type="integer" value="200" help="Fragment mass peaks with m/z less than this value will be discarded"/>
+                            <param name="xtandem_min_prec_mass" label="X!Tandem: Min Precursor Mass" type="integer" value="200" help="Minimum mass of 1+ mass of parent ion to be considered"/>
+                            <param name="xtandem_noise_suppr" label="X!Tandem: Noise Suppression" type="boolean" checked="true" truevalue="1" falsevalue="0" help="Use noise suppression"/>
+
+
+                            <conditional name="xtandem_refine"><!-- -xtandem_refine -->
+                                <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement">
+                                    <option value="no" selected="True">Don't refine</option>
+                                    <option value="yes" >Use refinement</option>
+                                </param>
+                                <when value="no"/>
+                                <when value="yes">
+                                    <param name="xtandem_refine_unc" label="X!Tandem: Unanticipated cleavage, refinement" type="boolean" truevalue="1" falsevalue="0" help="Allow for unanticipated cleavage during refinement"/>
+                                    <param name="xtandem_refine_semi" label="X!Tandem: Cleavage semi, refinement" type="boolean" truevalue="1" falsevalue="0" help="Search for semi-tryptic peptides during refinement"/>
+                                    <param name="xtandem_refine_p_mut" label="X!Tandem: Point mutations, refinement" type="boolean" truevalue="1" falsevalue="0" help="Allow for point mutations during refinement"/>
+                                    <param name="xtandem_refine_snaps" label="X!Tandem: snAPs, refinement" type="boolean" truevalue="1" falsevalue="0" help="Search for known single amino acid polymorphisms during refinement"/>
+                                    <param name="xtandem_refine_spec_synt" label="X!Tandem: Spectrum synthesis, refinement" type="boolean" truevalue="1" falsevalue="0" help="Use spectrum synthesis scoring"/>
+                                </when>
+                            </conditional>
+                        </when>
                 </conditional>
 
                 <conditional name="omssa">
@@ -591,6 +648,15 @@
                     </param>
                     <when value="no" />
                     <when value="yes">
+                        <param name="msgf_decoy" label="MS-GF+: Search Decoys" type="boolean" truevalue="1" falsevalue="0" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/>
+                        <param name="msgf_min_pep_length" label="MS-GF+: Minimum Peptide Length" type="integer" value="6" help="Minimum length for a peptide to be considered"/>
+                        <param name="msgf_max_pep_length" label="MS-GF+: Maximum Peptide Length" type="integer" value="30" help="Maximum length for a peptide to be considered"/>
+                        <param name="msgf_termini" label="MS-GF+: Number of tolerable termini" type="select" format="text" help="Searches will take much longer if selecting a value other than 2">
+                            <option value="0">0 (ie non-specific cleavage)</option>
+                            <option value="1">1 (ie semi-tryptic cleavage)</option>
+                            <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option>
+                        </param>
+                        <param name="msgf_num_ptms" label="MS-GF+: Max PTMs per peptide" type="integer" value="2"/>
                     </when>
                 </conditional>
 
@@ -694,6 +760,9 @@
             <param name="min_charge" value="1"/>
             <param name="max_charge" value="3"/>
             <param name="advanced_type_selector" value="advanced"/>
+            <param name="species_type_selector" value="no_species_type"/>
+            <param name="processing_options_selector" value="no"/>
+            <param name="filtering_options_selector" value="no"/>
             <param name="xtandem_selector" value="yes"/>
             <param name="omssa_selector" value="no"/>
             <param name="msgf_selector" value="yes"/>