--- a/peptide_shaker.xml	Fri Jun 08 15:58:53 2018 -0400
+++ b/peptide_shaker.xml	Thu Jul 12 08:42:58 2018 -0400
@@ -1,12 +1,12 @@
-<tool id="peptide_shaker" name="Peptide Shaker" version="1.16.23.0">
+<tool id="peptide_shaker" name="Peptide Shaker" version="1.16.26">
     <description>
         Perform protein identification using various search engines based on results from SearchGUI
     </description>
     <macros>
-        <import>macros_basic.xml</import>
+        <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="1.16.23">peptide-shaker</requirement>
+        <requirement type="package" version="1.16.26">peptide-shaker</requirement>
     </requirements>
     <expand macro="stdio" />
     <command>
@@ -53,7 +53,34 @@
 
             -threads "\${GALAXY_SLOTS:-12}"
 
+            ##Optional processing parameters:
+            #if $processing_options.processing_options_selector == "yes"
+                -protein_fdr "${processing_options.protein_fdr}"
+                -peptide_fdr "${processing_options.peptide_fdr}"
+                -psm_fdr "${processing_options.psm_fdr}"
+                -ptm_score "${processing_options.ptm_score.ptm_score_selector}"
+                #if $processing_options.ptm_score.ptm_score_selector == 1
+                    -score_neutral_losses "${processing_options.ptm_score.neutral_losses}"
+                    #if str($processing_options.ptm_score.ptm_threshold) != ''
+                        -ptm_threshold "${processing_options.ptm_score.ptm_threshold}"
+                    #end if
+                #end if
+                -ptm_alignment "${processing_options.ptm_alignment}"
+                -ptm_sequence_matching_type "${processing_options.ptm_sequence_matching_type}"
+                -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}"
+            #end if
 
+           ##Optional filtering parameters:
+            #if $filtering_options.filtering_options_selector == "yes":
+                -import_peptide_length_min "${filtering_options.min_peptide_length}"
+                -import_peptide_length_max "${filtering_options.max_peptide_length}"
+                -import_precurosor_mz "${filtering_options.max_precursor_error}"
+                -import_precurosor_mz_ppm "${filtering_options.max_precursor_error_type}"
+                ##-max_xtandem_e "${filtering_options.max_xtandem_e}"
+                ##-max_omssa_e "${filtering_options.max_omssa_e}"
+                ##-max_mascot_e "${filtering_options.max_mascot_e}"
+                -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}"
+            #end if
 
         2>> $temp_stderr)
 
@@ -177,8 +204,63 @@
                 <filter type="add_value" value="@SEARCHGUI_MAJOR_VERSION@" />
             </options>
         </param>
-
-
+        <conditional name="processing_options">
+            <param name="processing_options_selector" type="select" label="Specify Advanced PeptideShaker Processing Options">
+                <option value="no" selected="True">Default Processing Options</option>
+                <option value="yes">Advanced Processing Options</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
+                <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
+                <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
+                <param name="protein_fraction_mw_confidence" value="95.0" type="float" label="Minimum confidence required for a protein in the fraction MW plot"
+                    help="default 95%: '95.0'" />
+                <conditional name="ptm_score">
+                    <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization">
+                        <option value="0" selected="True">A-score</option>
+                        <option value="1">PhosphoRS</option>
+                        <option value="2">None</option>
+                    </param>
+                    <when value="0" />
+                    <when value="1">
+                        <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" />
+                        <param name="ptm_threshold" label="The threshold to use for the PTM scores" optional="true" value="" type="float"
+                            help="Automatic mode will be used if not set" />
+                    </when>
+                    <when value="2" />
+                </conditional>
+                <param name="ptm_sequence_matching_type" type="select" label="The PTM to peptide sequence matching type">
+                     <option value="0">Character Sequence</option>
+                     <option value="1" selected="true">Amino Acids</option>
+                     <option value="2">Indistinguishable Amino Acids</option>
+                </param>
+                <param name="ptm_alignment" label="Align peptide ambiguously localized PTMs on confident sites" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
+                <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} -->
+            </when>
+        </conditional>
+        <conditional name="filtering_options">
+            <param name="filtering_options_selector" type="select" label="Specify Advanced Filtering Options"
+                help="Filter based on peptide lengths, precursor mass error, E value errors from X! Tandem and OMSSA, and include/exclude unknown PTM’s">
+                <option value="no" selected="True">Default Filtering Options</option>
+                <option value="yes">Advanced Filtering Options</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <param name="min_peptide_length" type="integer" label="Minimum Peptide Length" value="6" />
+                <param name="max_peptide_length" type="integer" label="Maximum Peptide Length" value="30" />
+                <param name="max_precursor_error" type="float" label="Maximum Precursor Error" value="10"
+                    help="Next option specifies units (Da or ppm)" />
+                <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select">
+                    <option value="1">ppm</option>
+                    <option value="0">Daltons</option>
+                </param>
+                <!--param name="max_xtandem_e" label="Maximum X! Tandem e-value" value="100" type="float" help="" /-->
+                <!--param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" /-->
+                <!--param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="" /-->
+                <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />
+            </when>
+        </conditional>
         <conditional name="contact_options">
             <param name="contact_options_selector" type="select" label="Specify Contact Information for mzIdendML"
                 help="Create a Galaxy workflow to save these values">
@@ -273,11 +355,11 @@
     </outputs>
     <tests>
         <test>
-            <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
+            <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>
             <param name="processing_options_selector" value="no"/>
             <param name="filtering_options_selector" value="no"/>
             <param name="outputs" value="zip,3"/>
-            <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="3000" />
+            <output name="output_zip" file="peptide_shaker_modifications_result1.zip" ftype="zip" compare="sim_size" delta="3000" />
             <output name="output_psm">
                 <assert_contents>
                     <has_text text="cds.comp41779_c0_seq1" />
@@ -285,7 +367,7 @@
             </output>
         </test>
         <test>
-            <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
+            <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>
             <param name="processing_options_selector" value="no"/>
             <param name="filtering_options_selector" value="yes"/>
             <param name="min_peptide_length" value="1"/>
@@ -339,11 +421,11 @@
             </output>
         </test>
         <test>
-            <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
+            <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>
             <param name="processing_options_selector" value="no"/>
             <param name="filtering_options_selector" value="no"/>
             <param name="outputs" value="3,cps"/>
-            <output name="output_cps" file="peptide_shaker_result1.cpsx" ftype="peptideshaker_archive" compare="sim_size" delta="3000"/>
+            <output name="output_cps" file="peptide_shaker_modifications_result1.cpsx" ftype="peptideshaker_archive" compare="sim_size" delta="3000"/>
             <output name="output_psm">
                 <assert_contents>
                     <has_text text="cds.comp41779_c0_seq1" />
@@ -354,10 +436,9 @@
     <help>
 **What it does**
 
-Combines search results given by SearchGUI after running multiple search engines (X! Tandem, OMSSA and MS-GF+) on any number of MGF peak lists.
+Runs multiple search engines (X! Tandem, OMSSA and MS-GF+) on any number of MGF peak lists using the SearchGUI application and combines the results.
 
 http://compomics.github.io/projects/peptide-shaker.html
-
 http://compomics.github.io/projects/searchgui.html
 
 ----