Added Cami Opal - A tool for evaluating taxonomic metagenome profilers

tools/cami_opal/cami_opal.xml

@@ -31,11 +31,6 @@
                 'inputs/${safe_identifier}'
             #end for
 
-            ## #for $input_file in $input_files:
-            ##    #set safe_identifier = re.sub('[^\w\-\.]', '_', $input_file.file.element_identifier)
-            ##    'inputs/${safe_identifier}'
-            ## #end for
-
             #set $sep = ''
             -l
             '
@@ -96,7 +91,7 @@
             label="Normalize samples" 
             help="Normalize the samples to compare them on the same scale."
             truevalue="-n" falsevalue="" />
-        <param argument="--filter" type="integer" value="0" optional="true"
+        <param argument="--filter" type="float" value="0" optional="true"
             label="Filter out predictions with the smallest relative abundances summing up to this percentage within a rank"
             help="This parameter allows you to filter out the predictions with the smallest relative abundances, such that their cumulative sum is equal to the specified percentage within a taxonomic rank. The value should be between 0 and 100."
             min="0" max="100" />
@@ -147,13 +142,13 @@
             <filter>html_output</filter>
         </data>
         <data name="result" format="tabular" from_work_dir="output/results.tsv" label="${tool.name} on ${on_string}: Results" />
-        <collection name="rank_output" type="list" label="${tool.name}: Rank tables" format="tabular" >
+        <collection name="rank_output" type="list" label="${tool.name}: Rank tables" >
             <filter>output_collections</filter>
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tsv" directory="output/by_rank"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tsv" directory="output/by_rank" format="tabular"/>
         </collection>
-        <collection name="tool_output" type="list" label="${tool.name}: Tool tables" format="tabular">
+        <collection name="tool_output" type="list" label="${tool.name}: Tool tables" >
             <filter>output_collections</filter>
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tsv" directory="output/by_tool/"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tsv" directory="output/by_tool/" format="tabular"/>
         </collection>
     </outputs>
     <tests>
@@ -194,7 +189,7 @@
             <param name="normalize" value="true"/>
             <param name="filter" value="5"/>
             <param name="plot_abundances" value="true"/>
-            <param name="desc" value="Detailed test description for OPAL"/>
+            <param name="desc" value="Test description for OPAL"/>
             <param name="ranks" value="superkingdom,species"/>
             <param name="metrics_plot_rel" value="w,l,c,p,f,t"/>
             <param name="metrics_plot_abs" value="c,p,b"/>
@@ -204,7 +199,7 @@
             <param name="output_collections" value="true"/>
             <output name="htmlreport" ftype="html">
                 <assert_contents>
-                    <has_text text="Detailed test description for OPAL" />
+                    <has_text text="Test description for OPAL" />
                 </assert_contents>
             </output>
             <output name="result" ftype="tabular">
@@ -224,7 +219,7 @@
             <param name="normalize" value="true"/>
             <param name="filter" value="5"/>
             <param name="plot_abundances" value="true"/>
-            <param name="desc" value="Detailed test description for OPAL"/>
+            <param name="desc" value="Test description for OPAL"/>
             <param name="ranks" value="superkingdom,species"/>
             <param name="metrics_plot_rel" value="w,l,c,p,f,t"/>
             <param name="metrics_plot_abs" value="c,p,b"/>
@@ -234,7 +229,7 @@
             <param name="output_collections" value="false"/>
             <output name="htmlreport" ftype="html">
                 <assert_contents>
-                    <has_text text="Detailed test description for OPAL" />
+                    <has_text text="Test description for OPAL" />
                 </assert_contents>
             </output>
             <output name="result" ftype="tabular">
@@ -246,6 +241,25 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- Test with normalization enabled -->
+        <test expect_num_outputs="1">
+            <param name="gold_standard_file" value="gs_test.profile" />
+            <param name="input_files" value="kraken_test.profile" />
+            <param name="normalize" value="true"/>
+            <param name="html_output" value="false"/>
+            <param name="output_collections" value="false"/>
+            <output name="result" ftype="tabular" file="normalized_k.tsv" lines_diff="30" />
+        </test>
+
+        <!-- Test with normalization disabled -->
+        <test expect_num_outputs="1">
+            <param name="gold_standard_file" value="gs_test.profile" />
+            <param name="input_files" value="kraken_test.profile" />
+            <param name="normalize" value="false"/>
+            <param name="html_output" value="false"/>
+            <param name="output_collections" value="false"/>
+            <output name="result" ftype="tabular" file="not_normalized_k.tsv" lines_diff="30" />
+        </test>
     </tests>    
     <help>
     <![CDATA[
@@ -269,10 +283,10 @@
         OPAL requires the following inputs:
 
         1. **Gold Standard File**
-            - This file is essential for the evaluation and should be in BIOM format.
+            - This file is essential for the evaluation and should be CAMI Profiling Bioboxes format.
 
         2. **Profiles Files**
-            - Multiple profile files are required for evaluation. These files should be in CAMI Profiling Bioboxes format or BIOM format. If your files are not in the required format, you can use the `profile2cami` tool to convert them to the CAMI Profiling format.
+            - Multiple profile files are required for evaluation. If your files are not in the required format, you can use the `profile2cami` tool to convert them to the CAMI Profiling format.
 
         **Outputs**
 

tools/cami_opal/macros.xml

@@ -5,7 +5,7 @@
             <yield/>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">1.0.12</token>
+    <token name="@TOOL_VERSION@">1.0.12-1</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.05</token>
     <xml name="citations">