diff searchgui.xml @ 39:f63401dd6cbb draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8

--- 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**