Mercurial > repos > recetox > msmetaenhancer

changeset 15:560053b805d2 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit a57d984a9850c1faa44b6948981eb1303881ba9c
author recetox
date Thu, 14 Aug 2025 12:44:57 +0000
parents 646ef66527da
children
files msmetaenhancer.xml test-data/msme_sample.tsv test-data/msme_sample_out.tabular test-data/sample_out.msp
diffstat 4 files changed, 52 insertions(+), 50 deletions(-) [+]
line wrap: on
line diff
--- 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"/>
--- a/test-data/msme_sample.tsv	Thu May 29 11:21:26 2025 +0000
+++ b/test-data/msme_sample.tsv	Thu Aug 14 12:44:57 2025 +0000
@@ -1,4 +1,4 @@
-comment	name	id	num_peaks	casno	formula	mw
+comment	compound_name	id	num_peaks	casno	formula	mw
 NIST MS# 245692, Seq# M1	Hydrogen	1	2	1333740	H2	2
 NIST MS# 61316, Seq# M2	Deuterium	2	2	7782390	D2	4
 Any=100 ; NIST MS# 61313, Seq# M64	Methane	3	6	74828	CH4	16
--- a/test-data/msme_sample_out.tabular	Thu May 29 11:21:26 2025 +0000
+++ b/test-data/msme_sample_out.tabular	Thu Aug 14 12:44:57 2025 +0000
@@ -1,7 +1,7 @@
-comment	name	id	num_peaks	casno	formula	mw
-NIST MS# 245692, Seq# M1	Hydrogen	1	2	1333-74-0	H2	2
-NIST MS# 61316, Seq# M2	Deuterium	2	2	7782-39-0	D2	4
-Any=100 ; NIST MS# 61313, Seq# M64	Methane	3	6	74-82-8	CH4	16
-Any=100 ; NIST MS# 18807, Seq# R26	Methane	4	6	74-82-8	CH4	16
-Any=100 ; NIST MS# 18809, Seq# R27	Methane	5	6	74-82-8	CH4	16
-Any=100 ; NIST MS# 423924, Seq# R28	Methane	6	6	74-82-8	CH4	16
+comment	compound_name	id	num_peaks	casno	formula	mw	inchi
+NIST MS# 245692, Seq# M1	Hydrogen	1	2	1333-74-0	H2	2	InChI=1S/H2/h1H
+NIST MS# 61316, Seq# M2	Deuterium	2	2	7782-39-0	D2	4	InChI=1S/H2/h1H/i1+1D
+Any=100 ; NIST MS# 61313, Seq# M64	Methane	3	6	74-82-8	CH4	16	InChI=1S/CH4/h1H4
+Any=100 ; NIST MS# 18807, Seq# R26	Methane	4	6	74-82-8	CH4	16	InChI=1S/CH4/h1H4
+Any=100 ; NIST MS# 18809, Seq# R27	Methane	5	6	74-82-8	CH4	16	InChI=1S/CH4/h1H4
+Any=100 ; NIST MS# 423924, Seq# R28	Methane	6	6	74-82-8	CH4	16	InChI=1S/CH4/h1H4
--- a/test-data/sample_out.msp	Thu May 29 11:21:26 2025 +0000
+++ b/test-data/sample_out.msp	Thu Aug 14 12:44:57 2025 +0000
@@ -5,7 +5,6 @@
 COMMENT: NIST MS# 245692, Seq# M1
 NOMINAL_MASS: 2
 INCHI: InChI=1S/H2/h1H
-CANONICAL_SMILES: [HH]
 NUM PEAKS: 2
 1.0	20.98
 2.0	999.0
@@ -17,7 +16,6 @@
 COMMENT: NIST MS# 61316, Seq# M2
 NOMINAL_MASS: 4
 INCHI: InChI=1S/H2/h1H/i1+1D
-CANONICAL_SMILES: [HH]
 NUM PEAKS: 2
 2.0	14.99
 4.0	999.0
@@ -29,7 +27,6 @@
 COMMENT: Any=100 ; NIST MS# 61313, Seq# M64
 NOMINAL_MASS: 16
 INCHI: InChI=1S/CH4/h1H4
-CANONICAL_SMILES: C
 NUM PEAKS: 6
 12.0	37.97
 13.0	105.9
@@ -45,7 +42,6 @@
 COMMENT: Any=100 ; NIST MS# 18807, Seq# R26
 NOMINAL_MASS: 16
 INCHI: InChI=1S/CH4/h1H4
-CANONICAL_SMILES: C
 NUM PEAKS: 6
 12.0	25.98
 13.0	85.92
@@ -61,7 +57,6 @@
 COMMENT: Any=100 ; NIST MS# 18809, Seq# R27
 NOMINAL_MASS: 16
 INCHI: InChI=1S/CH4/h1H4
-CANONICAL_SMILES: C
 NUM PEAKS: 6
 12.0	7.99
 13.0	28.97
@@ -77,7 +72,6 @@
 COMMENT: Any=100 ; NIST MS# 423924, Seq# R28
 NOMINAL_MASS: 16
 INCHI: InChI=1S/CH4/h1H4
-CANONICAL_SMILES: C
 NUM PEAKS: 6
 12.0	25.98
 13.0	74.93