# HG changeset patch
# User galaxyp
# Date 1465567051 14400
# Node ID 2f8e9d0351a81ce19bd0c0f820018feb8e52496a
# Parent  c353378140caba24e356be90ba2616cbeebb0d49
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty

diff -r c353378140ca -r 2f8e9d0351a8 macros.xml
--- a/macros.xml	Sun Feb 21 11:17:39 2016 -0500
+++ b/macros.xml	Fri Jun 10 09:57:31 2016 -0400
@@ -26,7 +26,7 @@
             -ri $reverse_ion
     </token>
     <token name="@SEARCHGUI_MAJOR_VERSION@">2</token>
-    <token name="@SEARCHGUI_VERSION@">2.1</token>
+    <token name="@SEARCHGUI_VERSION@">2.9</token>
     <xml name="general_options">
         <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"
             help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
@@ -50,13 +50,13 @@
             <option value="Trypsin + CNBr">Trypsin + CNBr</option>
             <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option>
             <option value="Trypsin, no P rule">Trypsin, no P rule</option>
-            <option value="whole protein">whole protein</option>
+            <option value="Whole Protein">Whole Protein</option> 
             <option value="Asp-N">Asp-N</option>
             <option value="Glu-C">Glu-C</option>
             <option value="Asp-N + Glu-C">Asp-N + Glu-C</option>
             <option value="Top-Down">Top-Down</option>
             <option value="Semi-Tryptic">Semi-Tryptic</option>
-            <option value="No enzyme">No enzyme</option>
+            <option value="Unspecific">Unspecific (No enzyme)</option> <!-- note: cleaves at every residue! -->
             <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option>
             <option value="Asp-N (DE)">Asp-N (DE)</option>
             <option value="Glu-C (DE)">Glu-C (DE)</option>
@@ -64,6 +64,13 @@
             <option value="Thermolysin, no P rule">Thermolysin, no P rule</option>
             <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option>
             <option value="Semi-Glu-C">Semi-Glu-C</option>
+            <option value="LysargiNase">LysargiNase</option>
+            <option value="Semi-LysargiNase">Semi-LysargiNase</option>
+            <option value="Trypsin + Glu-C">Trypsin + Glu-C</option>
+            <option value="Semi-Arg-C">Semi-Arg-C</option>
+            <option value="Semi-Glu-C (DE)">Semi-Glu-C (DE)</option>
+            <option value="Arg-N">Arg-N</option>
+            <option value="Semi-Arg-N">Semi-Arg-N</option>
         </param>
         <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
             help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
diff -r c353378140ca -r 2f8e9d0351a8 peptide_shaker.xml
--- a/peptide_shaker.xml	Sun Feb 21 11:17:39 2016 -0500
+++ b/peptide_shaker.xml	Fri Jun 10 09:57:31 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="peptide_shaker" name="Peptide Shaker" version="1.1.1">
+<tool id="peptide_shaker" name="Peptide Shaker" version="1.11.0">
     <description>
         Perform protein identification using various search engines based on results from SearchGUI
     </description>
@@ -6,7 +6,7 @@
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="1.1">peptide_shaker</requirement>
+        <requirement type="package" version="1.11">peptide_shaker</requirement>
     </requirements>
     <expand macro="stdio" />
     <command>
@@ -47,9 +47,9 @@
 
             ##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}"
+                -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}"
@@ -58,14 +58,15 @@
                     #end if
                 #end if
                 -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}"
+                -ptm_alignment "${processing_options.ptm_alignment}"
             #end if
 
            ##Optional filtering parameters:
             #if $filtering_options.filtering_options_selector == "yes":
-                -min_peptide_length "${filtering_options.min_peptide_length}"
-                -max_peptide_length "${filtering_options.max_peptide_length}"
-                -max_precursor_error "${filtering_options.max_precursor_error}"
-                -max_precursor_error_type "${filtering_options.max_precursor_error_type}"
+                -import_peptide_length_min "${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}"
@@ -170,7 +171,6 @@
             <options options_filter_attribute="metadata.searchgui_major_version" >
                 <filter type="add_value" value="@SEARCHGUI_MAJOR_VERSION@" />
             </options>
-            <validator type="expression" message="This version of PeptideShaker will only work with SearchGUI version: @SEARCHGUI_MAJOR_VERSION@ .">value is not None and value.metadata.searchgui_major_version == "@SEARCHGUI_MAJOR_VERSION@"</validator>
         </param>
 
         <conditional name="species_type">
@@ -477,6 +477,7 @@
                             help="Automatic mode will be used if not set" />
                     </when>
                 </conditional>
+                <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>
@@ -493,8 +494,8 @@
                 <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="0">ppm</option>
-                    <option value="1">Daltons</option>
+                    <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="" /-->
diff -r c353378140ca -r 2f8e9d0351a8 searchgui.xml
--- a/searchgui.xml	Sun Feb 21 11:17:39 2016 -0500
+++ b/searchgui.xml	Fri Jun 10 09:57:31 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.1">
+<tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.0">
     <description>
         Perform protein identification using various search engines and prepare results for input to Peptide Shaker
     </description>
@@ -56,6 +56,7 @@
             @GENERAL_PARAMETERS@
 
             -db input_database.fasta
+            $use_gene_mapping
 
             #if $xtandem.xtandem_advanced == "yes"
 
@@ -85,6 +86,8 @@
                     -xtandem_refine_pot ${xtandem.xtandem_refine.xtandem_refine_evalue}
                     
                 #end if
+            #else 
+                -xtandem_output_spectra 1
             #end if
 
             #if $omssa.omssa_advanced == "yes"
@@ -94,7 +97,7 @@
                 -omssa_estimate_charge ${omssa.estimate_charge}
 
                 -omssa_memory ${omssa.omssa_memory}
-                -omssa_isotopes ${omssa.omssa_isotopes} 
+                ## -omssa_isotopes ${omssa.omssa_isotopes} 
                 -omssa_neutron ${omssa.omssa_neutron} 
                 -omssa_low_intensity "${omssa.omssa_low_intensity}" 
                 -omssa_high_intensity ${omssa.omssa_high_intensity} 
@@ -143,6 +146,7 @@
                 -msgf_isotope_high ${msgf.msgf_isotope_high} 
             #end if
             
+            #* Not working in tests
             #if $ms_amanda.ms_amanda_advanced == "yes"
                  -ms_amanda_decoy ${ms_amanda.ms_amanda_decoy}
                  -ms_amanda_max_evalue ${ms_amanda.ms_amanda_max_evalue}
@@ -150,7 +154,9 @@
                  -ms_amanda_max_rank ${ms_amanda.ms_amanda_max_rank} 
                  -ms_amanda_mono ${ms_amanda.ms_amanda_mono}
             #end if
+            *#
             
+            #* Not working in tests
             #if $myrimatch.myrimatch_advanced == "yes"
                 -myrimatch_min_pep_length ${myrimatch.myrimatch_min_pep_length}
                 -myrimatch_max_pep_length ${myrimatch.myrimatch_max_pep_length}
@@ -170,8 +176,9 @@
                 -myrimatch_num_batches ${myrimatch.myrimatch_num_batches}
                 -myrimatch_max_peak ${myrimatch.myrimatch_max_peak}                    
             #end if
+            *#
 
-            #*
+            #* Not working in tests
             #if $andromeda.andromeda_advanced == "yes"
                 -andromeda_max_pep_mass ${andromeda.andromeda_max_pep_mass}
                 -andromeda_max_comb ${andromeda.andromeda_max_comb}
@@ -191,7 +198,8 @@
                 -andromeda_max_psms ${andromeda.andromeda_max_psms}
             #end if
             *#
-
+ 
+            #* Not working in tests
             #if $tide.tide_advanced == "yes"
                 -tide_num_ptms ${tide.tide_num_ptms}
                 -tide_num_ptms_per_type ${tide.tide_num_ptms_per_type}
@@ -230,6 +238,7 @@
                 -tide_export_pin ${tide.tide_export_pin}
                 -tide_remove_temp ${tide.tide_remove_temp}
             #end if
+            *#
 
             #if $comet.comet_advanced == "yes"
 
@@ -293,7 +302,7 @@
 
             ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created
             ## the tree is generated afterwards in PeptideShaker
-            -protein_index 0
+            ## -protein_index 0
 
             ##-makeblastdb_folder \$BLAST_ROOT_DIR
 
@@ -360,9 +369,7 @@
 
         &&
 
-        (zip -u searchgui_out.zip searchgui.properties 2>> $temp_stderr)
-
-        &&
+        (zip -u searchgui_out.zip searchgui.properties 2>> $temp_stderr);
 
         exit_code_for_galaxy=\$?;
         cat $temp_stderr 2>&1;
@@ -378,6 +385,10 @@
             label="Create a concatenated target/decoy database before running PeptideShaker"
             help="Selecting this option will help PeptideShaker calculate FDR values" />
 
+        <param name="use_gene_mapping" type="boolean" truevalue="-useGeneMapping 1" falsevalue="-useGeneMapping 0" checked="false"
+            label="gene mappings will be used and saved along with the project (UniProt databases only)"
+            help="This should only be enabled for UniProt databaases" />
+
         <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)"
             help="Select appropriate MGF dataset(s) from history" />
 
@@ -385,12 +396,16 @@
         <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
             <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help>
             <option value="X!Tandem" selected="True">X!Tandem</option>
-            <option value="MyriMatch">MyriMatch</option>
-            <option value="MS_Amanda">MS_Amanda</option> 
+            <!-- Not working in tests
+            <option value="MyriMatch">MyriMatch</option> 
+            <option value="MS_Amanda">MS_Amanda</option>
+            -->
             <option value="MSGF" selected="True">MS-GF+</option>
             <option value="OMSSA" selected="True">OMSSA</option>
             <option value="Comet">Comet</option>
+            <!-- Not working in tests
             <option value="Tide">Tide</option>
+            -->
             <!-- Windows only
             <option value="Andromeda">Andromeda</option>
             -->
@@ -461,7 +476,7 @@
                 <param name="xtandem_output_sequences" help="Controls output of sequence information"
                     label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" />
                 <param name="xtandem_output_spectra" help="Controls output of spectrum information"
-                    label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="false" />
+                    label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" />
                 <!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="text" help="Path to a spectrum data file for use by skyline." -->
                     
                 <conditional name="xtandem_refine"><!-- -xtandem_refine -->
@@ -642,6 +657,7 @@
         </conditional>
 
           <!-- MS-AMANDA ADVANCED PARAMETERS  -->
+        <!-- Not working in tests
         <conditional name="ms_amanda">
             <param name="ms_amanda_advanced" type="select" label="MS Amanda Options">
                 <option value="yes">Advanced</option>
@@ -660,9 +676,11 @@
                     label="MS Amanda: Use Monoisotopic Mass Values" help="MS Amanda use monoisotopic mass values" />
             </when>
         </conditional>
+        -->
 
 
         <!-- TIDE ADVANCED PARAMETERS -->
+        <!-- Not working in tests
         <conditional name="tide">
             <param name="tide_advanced" type="select" label="TIDE Options">
                 <option value="yes">Advanced</option>
@@ -766,8 +784,10 @@
                     label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done"/>
             </when>
         </conditional>
+        -->
 
         <!-- MyriMatch ADVANCED PARAMETERS -->
+        <!-- Not working in tests
         <conditional name="myrimatch">
             <param name="myrimatch_advanced" type="select" label="MyriMatch Options">
                 <option value="yes">Advanced</option>
@@ -816,6 +836,7 @@
                     label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" />
             </when>
         </conditional>
+        -->
 
         <!-- Andromeda ADVANCED PARAMETERS -->
         <!-- Windows only
diff -r c353378140ca -r 2f8e9d0351a8 searchgui_mods.loc.sample
--- a/searchgui_mods.loc.sample	Sun Feb 21 11:17:39 2016 -0500
+++ b/searchgui_mods.loc.sample	Fri Jun 10 09:57:31 2016 -0400
@@ -23,13 +23,13 @@
 Didehydro of T
 Diiodination of Y
 Dimethylation of K
-Dimethylation of K 2H(4)
 Dimethylation of K 2H(6)
+Dimethylation of K 2H(6) 13C(2)
 Dimethylation of R
+Dimethylation of peptide N-term
+Dimethylation of peptide N-term 2H(4)
 Dimethylation of peptide N-term 2H(6)
 Dimethylation of peptide N-term 2H(6) 13C(2)
-Dimethylation of peptide N-term K
-Dimethylation of peptide N-term K 2H(4)
 Dioxidation of M
 Dioxidation of W
 Farnesylation of C
@@ -63,6 +63,7 @@
 ICPL6 of K
 ICPL6 of peptide N-term
 Isoleucine 13C(6) 15N(1)
+Label of K 2H(4)
 Leucine 13C(6) 15N(1)
 Lipoyl of K
 Lysine 13C(6)
diff -r c353378140ca -r 2f8e9d0351a8 tool_dependencies.xml
--- a/tool_dependencies.xml	Sun Feb 21 11:17:39 2016 -0500
+++ b/tool_dependencies.xml	Fri Jun 10 09:57:31 2016 -0400
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="searchgui" version="2.1">
-        <repository changeset_revision="996169901942" name="package_searchgui_2_1" owner="galaxyp" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="searchgui" version="2.9">
+        <repository changeset_revision="ad67fd4127ae" name="package_searchgui_2_9" owner="galaxyp" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="peptide_shaker" version="1.1">
-        <repository changeset_revision="a639559a8e83" name="package_peptideshaker_1_1" owner="galaxyp" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="peptide_shaker" version="1.11">
+        <repository changeset_revision="7c812d11f172" name="package_peptideshaker_1_11" owner="galaxyp" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>