--- a/ramclustr.xml	Wed Jul 28 08:42:02 2021 +0000
+++ b/ramclustr.xml	Thu Aug 19 07:17:15 2021 +0000
@@ -1,12 +1,16 @@
-<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy1">
+<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy0">
     <macros>
         <import>ramclustr_macros.xml</import>
     </macros>
-
+    <creator>
+        <organization
+            url="https://www.recetox.muni.cz/"
+            name="RECETOX MUNI" />
+    </creator>
     <requirements>
-        <container type="docker">recetox/ramclustr:1.1.0-recetox0</container>
+        <requirement type="package" version="@TOOL_VERSION@">r-ramclustr</requirement>
+        <requirement type="package" version="3.14.0">bioconductor-xcms</requirement>
     </requirements>
-
     <command detect_errors="aggressive"><![CDATA[
         Rscript
             -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
@@ -56,7 +60,6 @@
             -e 'store_output(x, "$result", "$method_metadata", $filetype.required.merge_msp, "$spec_abundance")'
     ]]>
     </command>
-
     <inputs>
         <conditional name="filetype">
             <param name="type_choice" type="select" label="Choose input format:">
@@ -86,70 +89,50 @@
     </outputs>
 
     <tests>
-        <test>
+        <test><!-- TEST 1 -->
             <param name="type_choice" value="xcms"/>
-            <param name="input_xcms" value="xcmsObj_1.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
-            <output name="result" file="ramclustObj_xcms_1.rdata" ftype="RData" compare="sim_size" delta="100"/>
+            <param name="input_xcms" value="test1_xcmsObj_1.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
+            <output name="result" file="test1_ramclustObj_xcms_1.rdata" ftype="RData" compare="sim_size" delta="200"/>
             <output_collection name="mass_spectra" type="list">
-                <element name="fill" file="fill_xcms_1.msp" ftype="msp" checksum="md5$d53ed06d6f888a88ff321f833e29bb47"/>
+                <element name="fill" file="test1_fill_xcms_1.msp" ftype="msp"/>
             </output_collection>
-            <output name="method_metadata" file="metadata_xcms_1.txt" ftype="txt" checksum="md5$81db28b08860988e3966f585b0f44b0f"/>
-            <output name="spec_abundance" file="spec_abundance_xcms_1.csv" ftype="csv" compare="sim_size" delta="100"/>
+            <output name="method_metadata" file="test1_metadata_xcms_1.txt" ftype="txt"/>
+            <output name="spec_abundance" file="test1_spec_abundance_xcms_1.csv" ftype="csv" compare="sim_size" delta="100"/>
         </test>
-        <test>
+        <test><!-- TEST 2 -->
             <param name="type_choice" value="xcms"/>
-            <param name="input_xcms" value="xcmsObj_2.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
-            <param name="batch_order_qc" value="sample_metadata_xcms_2.csv" ftype="csv" />
-            <output name="result" file="ramclustObj_xcms_2.rdata" ftype="RData" compare="sim_size" delta="200"/>
+            <param name="input_xcms" value="test2_xcmsObj_2.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
+            <param name="batch_order_qc" value="test2_sample_metadata_xcms_2.csv" ftype="csv" />
+            <output name="result" file="test2_ramclustObj_xcms_2.rdata" ftype="RData" compare="sim_size" delta="200"/>
             <output_collection name="mass_spectra" type="list">
-                <element name="fill" file="fill_xcms_2.msp" ftype="msp" lines_diff="10"/>
+                <element name="fill" file="test2_fill_xcms_2.msp" ftype="msp" compare="diff" lines_diff="10"/>
             </output_collection>
-            <output name="method_metadata" file="metadata_xcms_2.txt" ftype="txt" checksum="md5$286e4aa53c38c99e92202584d7407406"/>
-            <output name="spec_abundance" file="spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/>
+            <output name="method_metadata" file="test2_metadata_xcms_2.txt" ftype="txt"/>
+            <output name="spec_abundance" file="test2_spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/>
         </test>
-        <test>
+        <test><!-- TEST 3 -->
             <param name="type_choice" value="csv"/>
-            <param name="ms" value="csv_test-input_1_2.csv" ftype="csv"/>
-            <param name="sample_name_column" value="1"/>
-            <param name="feature_delimiter" value="_"/>
-            <param name="retention_time_column" value="2"/>
+            <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/>
             <param name="st" value="5.0"/>
-            <param name="sr" value="0.5"/>
-            <param name="deepSplit" value="False"/>
             <param name="blocksize" value="1000"/>
             <param name="mult" value="1"/>
-            <param name="hmax" value="0.3"/>
-            <param name="collapse" value="True"/>
-            <param name="usePheno" value="True"/>
-            <param name="normalize" value="none"/>
-            <param name="qc_inj_range" value="20"/>
-            <param name="minModuleSize" value="2"/>
-            <param name="linkage" value="average"/>
-            <param name="mzdec" value="3"/>
-            <param name="cor_method" value="pearson"/>
-            <param name="rt_only_low_n" value="True"/>
-            <param name="replace_zeros" value="True"/>
-            <param name="Merge MSP Files" value="True"/>
             <param name="maxt" value="1"/>
-            <output name="result" file="ramclustObj_csv_1.rdata"/>
-            <output name="spec_abundance" file="spec_abundance_csv_1.csv" ftype="csv"/>
-            <output name="method_metadata" file="metadata_csv_1.txt" ftype="txt"/>
+            <output name="result" file="test3_ramclustObj_csv_1.rdata" ftype="RData" compare="sim_size" delta="200"/>
+            <output name="spec_abundance" file="test3_spec_abundance_csv_1.csv" ftype="csv"/>
+            <output name="method_metadata" file="test3_metadata_csv_1.txt" ftype="txt"/>
             <output_collection name="mass_spectra" type="list">
-                <element name="fill" file="spectra_csv_1.msp" ftype="msp"/>
+                <element name="fill" file="test3_spectra_csv_1.msp" ftype="msp"/>
             </output_collection>
         </test>
-        <test>
+        <test><!-- TEST 4 -->
             <param name="type_choice" value="csv"/>
-            <param name="ms" value="csv_test-input_1_2.csv" ftype="csv"/>
-            <param name="sample_name_column" value="1"/>
-            <param name="feature_delimiter" value="_"/>
-            <param name="retention_time_column" value="2"/>
-            <param name="batch_order_qc" value="sample_metadata_csv_2.csv" ftype="csv" />
-            <output name="result" file="ramclustObj_csv_2.rdata"/>
-            <output name="spec_abundance" file="spec_abundance_csv_2.csv" ftype="csv"/>
-            <output name="method_metadata" file="metadata_csv_2.txt" ftype="txt"/>
+            <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/>
+            <param name="batch_order_qc" value="test4_sample_metadata_csv_2.csv" ftype="csv" />
+            <output name="result" file="test4_ramclustObj_csv_2.rdata" ftype="RData" compare="sim_size" delta="200"/>
+            <output name="spec_abundance" file="test4_spec_abundance_csv_2.csv" ftype="csv"/>
+            <output name="method_metadata" file="test4_metadata_csv_2.txt" ftype="txt"/>
             <output_collection name="mass_spectra" type="list">
-                <element name="fill" file="spectra_csv_2.msp" ftype="msp" lines_diff="10"/>
+                <element name="fill" file="test4_spectra_csv_2.msp" ftype="msp" lines_diff="10"/>
             </output_collection>
         </test>
     </tests>