diff msmetaenhancer.xml @ 15:560053b805d2 draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit a57d984a9850c1faa44b6948981eb1303881ba9c

--- a/msmetaenhancer.xml	Thu May 29 11:21:26 2025 +0000
+++ b/msmetaenhancer.xml	Thu Aug 14 12:44:57 2025 +0000
@@ -1,5 +1,5 @@
-<tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy0"  profile="21.09">
-    <description>annotate MS data</description>
+<tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy2" profile="23.0">
+    <description>collect and convert chemical identifiers in tables or MS libraries</description>
 
     <macros>
         <import>macros.xml</import>
@@ -13,8 +13,35 @@
         <requirement type="package" version="@TOOL_VERSION@">msmetaenhancer</requirement>
     </requirements>
 
-    <command detect_errors="exit_code"><![CDATA[
-        sh ${msmetaenhancer_python_cli}
+    <required_files>
+        <include path="msmetaenhancer_wrapper.py"/>
+    </required_files>
+
+    <command detect_errors="aggressive"><![CDATA[
+        python3 '${__tool_directory__}/msmetaenhancer_wrapper.py'
+        --input_file '$input_file'
+        #if $input_file.ext == "tabular":
+        --file_format 'tsv'
+        #else
+        --file_format '$input_file.ext'
+        #end if
+        --output_file '$output_file'
+        #if $options.logging.output_log == "TRUE":
+        --log_file '$log_file'
+        --log_level '$options.logging.log_level'
+        #end if
+        #if len($ordered_jobs) != 0:
+            #set ordered_jobs = ",".join([str($job.ordered_jobs_select) for $job in $ordered_jobs]) + ","
+        #else:
+            #set ordered_jobs = ""
+        #end if
+        #if $jobs != 'None':
+            #set random_jobs = str($jobs)
+        #else:
+            #set random_jobs = ""
+        #end if
+        #set all_jobs = str($ordered_jobs) + str($random_jobs)
+        --jobs '$all_jobs'
     ]]> </command>
 
     <environment_variables>
@@ -22,35 +49,6 @@
         <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable>
     </environment_variables>
 
-    <configfiles>
-        <configfile name="msmetaenhancer_python_cli">
-            python3 ${__tool_directory__}/msmetaenhancer_wrapper.py \
-            --input_file "$input_file" \
-            #if $input_file.ext == "tabular":
-            --file_format "tsv" \
-            #else
-            --file_format "$input_file.ext" \
-            #end if
-            --output_file "$output_file" \
-            #if $options.logging.output_log == "TRUE":
-            --log_file "$log_file" \
-            --log_level "$options.logging.log_level" \
-            #end if
-            #if len($ordered_jobs) != 0:
-                #set ordered_jobs = ",".join([str($job.ordered_jobs_select) for $job in $ordered_jobs]) + ","
-            #else:
-                #set ordered_jobs = ""
-            #end if
-            #if $jobs != 'None':
-                #set random_jobs = str($jobs)
-            #else:
-                #set random_jobs = ""
-            #end if
-            #set all_jobs = str($ordered_jobs) + str($random_jobs)
-            --jobs "$all_jobs"
-        </configfile>
-    </configfiles>
-
     <inputs>
         <param label="Input spectra dataset" name="input_file" type="data" format="msp,mgf,json,csv,tabular,xlsx" />
 
@@ -92,7 +90,7 @@
             </change_format>
         </data>    
         <data label="Log of MSMetaEnhancer on ${on_string}" name="log_file" format="txt">
-           <filter>options['logging']['output_log']</filter>
+           <filter>options['logging']['output_log'] == 'TRUE'</filter>
        </data>
     </outputs>
 
@@ -100,14 +98,24 @@
         <test expect_num_outputs="2">
             <param name="input_file" value="sample.msp" ftype="msp" />
             <param name="jobs" value="compound_name inchi PubChem,inchi canonical_smiles PubChem"/>
+            <section name="options">
+                <conditional name="logging">
+                    <param name="output_log" value="TRUE"/>
+                </conditional>
+            </section>
             <output name="output_file" file="sample_out.msp" ftype="msp"/>
+            <output name="log_file" ftype="txt">
+                <assert_contents>
+                    <has_text text=""/>
+                </assert_contents>
+            </output>
         </test>
-        <test expect_num_outputs="2">
+        <test expect_num_outputs="1">
             <param name="input_file" value="msme_sample.tsv" ftype="tsv" />
             <param name="jobs" value="compound_name inchi PubChem,inchi canonical_smiles PubChem"/>
             <output name="output_file" file="msme_sample_out.tabular" ftype="tabular"/>
         </test>
-        <test expect_num_outputs="2">
+        <test expect_num_outputs="1">
             <param name="input_file" value="msme_sample.tsv" ftype="tabular" />
             <param name="jobs" value="compound_name inchi PubChem,inchi canonical_smiles PubChem"/>
             <output name="output_file" file="msme_sample_out.tabular" ftype="tabular"/>