diff searchgui.xml @ 59:943a34df6047 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588"

--- a/searchgui.xml	Sat Apr 10 15:57:17 2021 +0000
+++ b/searchgui.xml	Fri May 21 19:13:14 2021 +0000
@@ -65,6 +65,7 @@
         echo 'running search gui' &&
         searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI
             --exec_dir="\$cwd/${bin_dir}"
+            -use_log_folder 0
             -spectrum_files \$cwd
             -fasta_file "\$cwd/input_fasta_file.fasta"
             -output_folder \$cwd/output
@@ -173,12 +174,14 @@
         <param format="fasta" name="input_fasta_file" type="data" label="Fasta file" help="For postprocessing with PeptideShaker the sequences must have UniProt style headers and contain decoy sequences (see help)."/>
 
         <param name="peak_lists_files" format="mgf,mzml" type="data" multiple="true" label="Input Peak Lists"
-            help="Select appropriate MGF/MZML dataset(s) from history" />
+            help="Select appropriate MGF/MZML dataset(s) from history.
+               Remember to choose only .mzML files when using MetaMorpheus." />
 
         <!-- Search Engine Selection -->
         <section name="search_engines_options" expanded="true" title="Search Engine Options">
             <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. OMSSA may not work into isolated environments like containers.</help>
+                <help>Comet and Tide shouldn't both be selected since they use a similar algoritm. OMSSA may not work into isolated environments like containers. 
+                    MetaMorpheus only produce results when using mzML format.</help>
                 <option value="X!Tandem" selected="True">X!Tandem</option>
                 <option value="MSGF" selected="True">MS-GF+</option>
                 <option value="OMSSA">OMSSA</option>
@@ -186,8 +189,7 @@
                 <option value="Tide">Tide</option>
                 <option value="MyriMatch">MyriMatch</option>
                 <option value="MS_Amanda">MS_Amanda</option>
-                <!-- TODO: MetaMorpheus Waiting for support for dotnet in bioconda package -->
-                <!-- <option value="MetaMorpheus">MetaMorpheus</option> -->
+                <option value="MetaMorpheus">MetaMorpheus</option>
                 <!-- Windows only
                 <option value="Andromeda">Andromeda</option>
                 -->
@@ -239,6 +241,21 @@
             <param name="engines" value="X!Tandem,MSGF,MyriMatch,Comet"/>
             <output name="searchgui_results" file="searchgui_tiny_result_default_4engines.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
         </test>
+        
+        
+        <!-- Test that search works with MetaMorpheus with default parameters works-->
+        <!-- Test data has been taken from metamorpheus galaxy tool -->
+        <test>
+            <param name="peak_lists_files" value="searchgui_smallCalibratible_Yeast.mzML"/>
+            <param name="input_parameters_file" value="Identification_Parameters_default.par"/>
+            <param name="input_fasta_file" value="searchgui_smallYeast.fasta" ftype="fasta" />
+            <param name="engines" value="MetaMorpheus"/>
+            <output name="searchgui_results" ftype="searchgui_archive">
+                <assert_contents>
+                    <has_size value="798597" delta="10000"/>
+                </assert_contents>
+            </output>
+        </test>
 
         <!-- Test that search works with MSAmanda with default parameters works-->
         <test>
@@ -324,7 +341,7 @@
 
 Default:     X! Tandem and MS-GF+ are executed.
 
-Optional:     MyriMatch, MS-Amanda, OMSSA (it may not work into isolated environments like containers), Comet, Tide, DirecTag and Novor can be executed.
+Optional:     MyriMatch, MS-Amanda, MetaMorpheus, OMSSA (it may not work into isolated environments like containers), Comet, Tide, DirecTag and Novor can be executed.
 
 **Input FASTA**