# HG changeset patch
# User galaxyp
# Date 1531311245 14400
# Node ID f63401dd6cbb53f73b27c488636d5876051932fe
# Parent  263440bb190043b42dd2b8c2fa407a172ecde1e7
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8

diff -r 263440bb1900 -r f63401dd6cbb macros.xml
--- a/macros.xml	Mon Apr 30 04:41:10 2018 -0400
+++ b/macros.xml	Wed Jul 11 08:14:05 2018 -0400
@@ -49,7 +49,7 @@
 
     </token>
     <token name="@SEARCHGUI_MAJOR_VERSION@">3</token>
-    <token name="@SEARCHGUI_VERSION@">3.2.24</token>
+    <token name="@SEARCHGUI_VERSION@">3.3.3</token>
     <xml name="general_options">
 
         <section name="protein_digest_options" expanded="false" title="Protein Digestion Options">
diff -r 263440bb1900 -r f63401dd6cbb peptide_shaker.xml
--- a/peptide_shaker.xml	Mon Apr 30 04:41:10 2018 -0400
+++ b/peptide_shaker.xml	Wed Jul 11 08:14:05 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="peptide_shaker" name="Peptide Shaker" version="1.16.20">
+<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>
@@ -6,7 +6,7 @@
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="1.16.20">peptide-shaker</requirement>
+        <requirement type="package" version="1.16.26">peptide-shaker</requirement>
     </requirements>
     <expand macro="stdio" />
     <command>
@@ -355,11 +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" />
@@ -367,7 +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"/>
@@ -421,11 +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" />
diff -r 263440bb1900 -r f63401dd6cbb searchgui.xml
--- a/searchgui.xml	Mon Apr 30 04:41:10 2018 -0400
+++ b/searchgui.xml	Wed Jul 11 08:14:05 2018 -0400
@@ -1092,8 +1092,6 @@
             <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
             <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
             <param name="precursor_ion_tol" value="100"/>
-            <param name="fixed_modifications" value="carbamidomethyl c"/>
-            <param name="variable_modifications" value="oxidation of m"/>
             <param name="min_charge" value="1"/>
             <param name="max_charge" value="3"/>
             <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
@@ -1106,13 +1104,42 @@
             <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
             <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
             <param name="precursor_ion_tol" value="100"/>
+            <param name="min_charge" value="1"/>
+            <param name="max_charge" value="3"/>
+            <param name="engines" value="MS_Amanda"/>
+            <output name="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
+        </test>
+
+        <!-- Test that specifying non-default search engines works using modifications -->
+        <!--
+        <test>
+            <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
+            <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
+            <param name="precursor_ion_tol" value="100"/>
+            <param name="fixed_modifications" value="carbamidomethyl c"/>
+            <param name="variable_modifications" value="oxidation of m"/>
+            <param name="min_charge" value="1"/>
+            <param name="max_charge" value="3"/>
+            <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
+            <param name="xtandem.xtandem_advanced" value="yes"/>
+            <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/>
+            <output name="output" file="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
+        </test>
+        -->
+        <!-- Test that search works with MSAmanda - with modifications -->
+        <!--
+        <test>
+            <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
+            <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
+            <param name="precursor_ion_tol" value="100"/>
             <param name="fixed_modifications" value="carbamidomethyl c"/>
             <param name="variable_modifications" value="oxidation of m"/>
             <param name="min_charge" value="1"/>
             <param name="max_charge" value="3"/>
             <param name="engines" value="MS_Amanda"/>
-            <output name="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
+            <output name="output" file="tiny_searchgui_modifications_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
         </test>
+        -->
     </tests>
     <help>
 **What it does**
diff -r 263440bb1900 -r f63401dd6cbb test-data/peptide_shaker_modifications_result1.cpsx
Binary file test-data/peptide_shaker_modifications_result1.cpsx has changed
diff -r 263440bb1900 -r f63401dd6cbb test-data/peptide_shaker_modifications_result1.zip
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diff -r 263440bb1900 -r f63401dd6cbb test-data/peptide_shaker_result1.cpsx
Binary file test-data/peptide_shaker_result1.cpsx has changed
diff -r 263440bb1900 -r f63401dd6cbb test-data/peptide_shaker_result1.zip
Binary file test-data/peptide_shaker_result1.zip has changed
diff -r 263440bb1900 -r f63401dd6cbb test-data/tiny_searchgui_modifications_result1.zip
Binary file test-data/tiny_searchgui_modifications_result1.zip has changed
diff -r 263440bb1900 -r f63401dd6cbb test-data/tiny_searchgui_modifications_result_amandaonly.zip
Binary file test-data/tiny_searchgui_modifications_result_amandaonly.zip has changed
diff -r 263440bb1900 -r f63401dd6cbb test-data/tiny_searchgui_result1.zip
Binary file test-data/tiny_searchgui_result1.zip has changed
diff -r 263440bb1900 -r f63401dd6cbb test-data/tiny_searchgui_result_amandaonly.zip
Binary file test-data/tiny_searchgui_result_amandaonly.zip has changed