Mercurial > repos > recetox > msmetaenhancer

changeset 14:646ef66527da draft default tip

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 187cd20cfa1502639fa2678dbcd69d2f3158d436
author recetox
date Thu, 29 May 2025 11:21:26 +0000
parents b5467dead5b1
children
files macros.xml msmetaenhancer.xml msmetaenhancer_wrapper.py test-data/msme_sample.tsv test-data/msme_sample_out.tabular test-data/sample_out.msp
diffstat 6 files changed, 76 insertions(+), 50 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Fri May 31 07:51:40 2024 +0000
+++ b/macros.xml	Thu May 29 11:21:26 2025 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.4.0</token>
+    <token name="@TOOL_VERSION@">0.4.1</token>
 
     <xml name="creator">
         <creator>
--- a/msmetaenhancer.xml	Fri May 31 07:51:40 2024 +0000
+++ b/msmetaenhancer.xml	Thu May 29 11:21:26 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy1"  profile="21.09">
+<tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy0"  profile="21.09">
     <description>annotate MS data</description>
 
     <macros>
@@ -26,7 +26,11 @@
         <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" \
@@ -48,7 +52,7 @@
     </configfiles>
 
     <inputs>
-        <param label="Input spectra dataset" name="input_file" type="data" format="msp,mgf,json,csv,tsv,xlsx" />
+        <param label="Input spectra dataset" name="input_file" type="data" format="msp,mgf,json,csv,tabular,xlsx" />
 
         <repeat name="ordered_jobs" title="Ordered conversions">
             <param name="ordered_jobs_select" type="select" label="Available conversions" multiple="false" optional="true">
@@ -80,13 +84,11 @@
     </inputs>
 
     <outputs>
-        <data label="MSMetaEnhancer on ${on_string}" name="output_file" format="msp">
+        <data label="MSMetaEnhancer on ${on_string}" name="output_file" format_source="input_file">
             <change_format>
-                <when input="input_file.ext" value="mgf" format="mgf" />
-                <when input="input_file.ext" value="json" format="json" />
-                <when input="input_file.ext" value="csv" format="tsv" />
-                <when input="input_file.ext" value="tsv" format="tsv" />
-                <when input="input_file.ext" value="xlsx" format="xlsx" />
+                <when input="input_file.ext" value="csv" format="tabular" />
+                <when input="input_file.ext" value="tsv" format="tabular" />
+                <when input="input_file.ext" value="xlsx" format="tabular" />
             </change_format>
         </data>    
         <data label="Log of MSMetaEnhancer on ${on_string}" name="log_file" format="txt">
@@ -100,6 +102,16 @@
             <param name="jobs" value="compound_name inchi PubChem,inchi canonical_smiles PubChem"/>
             <output name="output_file" file="sample_out.msp" ftype="msp"/>
         </test>
+        <test expect_num_outputs="2">
+            <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">
+            <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"/>
+        </test>
     </tests>
 
     <help>
--- a/msmetaenhancer_wrapper.py	Fri May 31 07:51:40 2024 +0000
+++ b/msmetaenhancer_wrapper.py	Thu May 29 11:21:26 2025 +0000
@@ -56,7 +56,7 @@
     if args.file_format == 'xlsx':
         handle_xlsx_file(app, args.output_file)
     else:
-        if args.file_format == 'csv':
+        if args.file_format in ['csv', 'tsv', 'tabular']:
             app.save_data(args.output_file, file_format="tsv")
         else:
             app.save_data(args.output_file, file_format=args.file_format)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/msme_sample.tsv	Thu May 29 11:21:26 2025 +0000
@@ -0,0 +1,7 @@
+comment	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
+Any=100 ; NIST MS# 18807, Seq# R26	Methane	4	6	74828	CH4	16
+Any=100 ; NIST MS# 18809, Seq# R27	Methane	5	6	74828	CH4	16
+Any=100 ; NIST MS# 423924, Seq# R28	Methane	6	6	74828	CH4	16
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/msme_sample_out.tabular	Thu May 29 11:21:26 2025 +0000
@@ -0,0 +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
--- a/test-data/sample_out.msp	Fri May 31 07:51:40 2024 +0000
+++ b/test-data/sample_out.msp	Thu May 29 11:21:26 2025 +0000
@@ -1,88 +1,88 @@
+COMPOUND_NAME: Hydrogen
 FORMULA: H2
-MW: 2
 CASNO: 1333-74-0
 ID: 1
 COMMENT: NIST MS# 245692, Seq# M1
-COMPOUND_NAME: Hydrogen
+NOMINAL_MASS: 2
 INCHI: InChI=1S/H2/h1H
 CANONICAL_SMILES: [HH]
 NUM PEAKS: 2
-1.0         20.98
-2.0         999.0
+1.0	20.98
+2.0	999.0
 
+COMPOUND_NAME: Deuterium
 FORMULA: D2
-MW: 4
 CASNO: 7782-39-0
 ID: 2
 COMMENT: NIST MS# 61316, Seq# M2
-COMPOUND_NAME: Deuterium
+NOMINAL_MASS: 4
 INCHI: InChI=1S/H2/h1H/i1+1D
 CANONICAL_SMILES: [HH]
 NUM PEAKS: 2
-2.0         14.99
-4.0         999.0
+2.0	14.99
+4.0	999.0
 
+COMPOUND_NAME: Methane
 FORMULA: CH4
-MW: 16
 CASNO: 74-82-8
 ID: 3
 COMMENT: Any=100 ; NIST MS# 61313, Seq# M64
-COMPOUND_NAME: Methane
+NOMINAL_MASS: 16
 INCHI: InChI=1S/CH4/h1H4
 CANONICAL_SMILES: C
 NUM PEAKS: 6
-12.0        37.97
-13.0        105.9
-14.0        203.82
-15.0        886.2
-16.0        999.0
-17.0        15.99
+12.0	37.97
+13.0	105.9
+14.0	203.82
+15.0	886.2
+16.0	999.0
+17.0	15.99
 
+COMPOUND_NAME: Methane
 FORMULA: CH4
-MW: 16
 CASNO: 74-82-8
 ID: 4
 COMMENT: Any=100 ; NIST MS# 18807, Seq# R26
-COMPOUND_NAME: Methane
+NOMINAL_MASS: 16
 INCHI: InChI=1S/CH4/h1H4
 CANONICAL_SMILES: C
 NUM PEAKS: 6
-12.0        25.98
-13.0        85.92
-14.0        170.85
-15.0        855.23
-16.0        999.0
-17.0        10.99
+12.0	25.98
+13.0	85.92
+14.0	170.85
+15.0	855.23
+16.0	999.0
+17.0	10.99
 
+COMPOUND_NAME: Methane
 FORMULA: CH4
-MW: 16
 CASNO: 74-82-8
 ID: 5
 COMMENT: Any=100 ; NIST MS# 18809, Seq# R27
-COMPOUND_NAME: Methane
+NOMINAL_MASS: 16
 INCHI: InChI=1S/CH4/h1H4
 CANONICAL_SMILES: C
 NUM PEAKS: 6
-12.0        7.99
-13.0        28.97
-14.0        74.93
-15.0        753.32
-16.0        999.0
-17.0        11.99
+12.0	7.99
+13.0	28.97
+14.0	74.93
+15.0	753.32
+16.0	999.0
+17.0	11.99
 
+COMPOUND_NAME: Methane
 FORMULA: CH4
-MW: 16
 CASNO: 74-82-8
 ID: 6
 COMMENT: Any=100 ; NIST MS# 423924, Seq# R28
-COMPOUND_NAME: Methane
+NOMINAL_MASS: 16
 INCHI: InChI=1S/CH4/h1H4
 CANONICAL_SMILES: C
 NUM PEAKS: 6
-12.0        25.98
-13.0        74.93
-14.0        152.86
-15.0        829.25
-16.0        999.0
-17.0        10.99
+12.0	25.98
+13.0	74.93
+14.0	152.86
+15.0	829.25
+16.0	999.0
+17.0	10.99