# HG changeset patch
# User recetox
# Date 1644927964 0
# Node ID 4ae5b466a805a1d35e7522867b6920b9ec81b56d
# Parent  4c328e0e59ab46664e5f681fd3886a212aa3a6ae
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit f09a5b3ee451d78dc025baee5eccb099f71be2b4"

diff -r 4c328e0e59ab -r 4ae5b466a805 macros.xml
--- a/macros.xml	Fri Jan 28 16:23:58 2022 +0000
+++ b/macros.xml	Tue Feb 15 12:26:04 2022 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.1.2</token>
+    <token name="@TOOL_VERSION@">0.1.3</token>
 
     <xml name="creator">
         <creator>
@@ -32,26 +32,29 @@
     </token>
 
     <xml name="job_options">
+        <option value="inchi canonical_smiles PubChem">PubChem: inchi -> canonical_smiles</option>
         <option value="inchi formula PubChem">PubChem: inchi -> formula</option>
         <option value="inchi inchikey PubChem">PubChem: inchi -> inchikey</option>
+        <option value="inchi isomeric_smiles PubChem">PubChem: inchi -> isomeric_smiles</option>
         <option value="inchi iupac_name PubChem">PubChem: inchi -> iupac_name</option>
-        <option value="inchi smiles PubChem">PubChem: inchi -> smiles</option>
+        <option value="name canonical_smiles PubChem">PubChem: name -> canonical_smiles</option>
         <option value="name formula PubChem">PubChem: name -> formula</option>
         <option value="name inchi PubChem">PubChem: name -> inchi</option>
         <option value="name inchikey PubChem">PubChem: name -> inchikey</option>
+        <option value="name isomeric_smiles PubChem">PubChem: name -> isomeric_smiles</option>
         <option value="name iupac_name PubChem">PubChem: name -> iupac_name</option>
-        <option value="name smiles PubChem">PubChem: name -> smiles</option>
+        <option value="casno inchikey CTS">CTS: casno -> inchikey</option>
+        <option value="inchikey inchi CTS">CTS: inchikey -> inchi</option>
+        <option value="inchikey iupac_name CTS">CTS: inchikey -> iupac_name</option>
+        <option value="inchikey name CTS">CTS: inchikey -> name</option>
+        <option value="name inchikey CTS">CTS: name -> inchikey</option>
         <option value="casno smiles CIR">CIR: casno -> smiles</option>
+        <option value="inchi smiles CIR">CIR: inchi -> smiles</option>
         <option value="inchikey casno CIR">CIR: inchikey -> casno</option>
         <option value="inchikey formula CIR">CIR: inchikey -> formula</option>
         <option value="inchikey inchi CIR">CIR: inchikey -> inchi</option>
         <option value="inchikey smiles CIR">CIR: inchikey -> smiles</option>
         <option value="smiles inchikey CIR">CIR: smiles -> inchikey</option>
-        <option value="casno inchikey CTS">CTS: casno -> inchikey</option>
-        <option value="inchikey inchi CTS">CTS: inchikey -> inchi</option>
-        <option value="inchikey iupac_name CTS">CTS: inchikey -> iupac_name</option>
-        <option value="inchikey name CTS">CTS: inchikey -> name</option>
-        <option value="name inchikey CTS">CTS: name -> inchikey</option>
         <option value="inchikey casno NLM">NLM: inchikey -> casno</option>
         <option value="inchikey formula NLM">NLM: inchikey -> formula</option>
         <option value="inchikey name NLM">NLM: inchikey -> name</option>
diff -r 4c328e0e59ab -r 4ae5b466a805 msmetaenhancer.xml
--- a/msmetaenhancer.xml	Fri Jan 28 16:23:58 2022 +0000
+++ b/msmetaenhancer.xml	Tue Feb 15 12:26:04 2022 +0000
@@ -19,6 +19,9 @@
             python3 ${__tool_directory__}/msmetaenhancer_wrapper.py \
             --input_file "$input_file" \
             --output_file "$output_file" \
+            #if $options.output_log:
+            --log_file "$log_file"\
+            #end if
             #if len($ordered_jobs) != 0:
                 #set ordered_jobs = ",".join([str($job.ordered_jobs_select) for $job in $ordered_jobs]) + ","
             #else:
@@ -46,10 +49,18 @@
         <param name="jobs" type="select" label="Other conversions" multiple="true" optional="true">
             <expand macro="job_options" />
         </param>
+
+        <section name="options" title="Options">
+            <param label="Save the log file" name="output_log" type="boolean" truevalue="TRUE" falsevalue="FALSE"
+                   checked="false" help="Preserve a log with details about the annotation process."/>
+        </section>
     </inputs>
 
     <outputs>
         <data label="MSMetaEnhancer on ${on_string}" name="output_file" format="msp" />
+        <data label="Log of MSMetaEnhancer on ${on_string}" name="log_file" format="txt">
+           <filter>options['output_log']</filter>
+       </data>
     </outputs>
 
     <tests>
diff -r 4c328e0e59ab -r 4ae5b466a805 msmetaenhancer_wrapper.py
--- a/msmetaenhancer_wrapper.py	Fri Jan 28 16:23:58 2022 +0000
+++ b/msmetaenhancer_wrapper.py	Tue Feb 15 12:26:04 2022 +0000
@@ -11,9 +11,10 @@
     parser.add_argument("--input_file", type=str, help="Path to query spectra file in MSP format.")
     parser.add_argument("--output_file", type=str, help="Path to output spectra file.")
     parser.add_argument("--jobs", type=str, help="Sequence of conversion jobs to be used.")
+    parser.add_argument("--log_file", type=str, help="Path to log with details of the annotation process.")
     args = parser.parse_args()
 
-    app = Application()
+    app = Application(log_file=args.log_file)
 
     # import .msp file
     app.load_spectra(args.input_file, file_format='msp')
diff -r 4c328e0e59ab -r 4ae5b466a805 test-data/sample_out.msp
--- a/test-data/sample_out.msp	Fri Jan 28 16:23:58 2022 +0000
+++ b/test-data/sample_out.msp	Tue Feb 15 12:26:04 2022 +0000
@@ -4,13 +4,15 @@
 CASNO: 1333-74-0
 ID: 1
 COMMENT: NIST MS# 245692, Seq# M1
-INCHIKEY: UFHFLCQGNIYNRP-UHFFFAOYSA-N
+CANONICAL_SMILES: [HH]
 INCHI: InChI=1S/H2/h1H
-IUPAC_NAME: hydrogen monohydride
+INCHIKEY: UFHFLCQGNIYNRP-UHFFFAOYSA-N
+ISOMERIC_SMILES: [HH]
+IUPAC_NAME: molecular hydrogen
 SMILES: [H][H]
 NUM PEAKS: 2
-1.0	20.98
-2.0	999.0
+1.0         20.98
+2.0         999.0
 
 NAME: Deuterium
 FORMULA: D2
@@ -18,12 +20,14 @@
 CASNO: 7782-39-0
 ID: 2
 COMMENT: NIST MS# 61316, Seq# M2
+CANONICAL_SMILES: [HH]
+INCHI: InChI=1S/H2/h1H/i1+1D
 INCHIKEY: UFHFLCQGNIYNRP-VVKOMZTBSA-N
-INCHI: InChI=1S/H2/h1H/i1+1D
+ISOMERIC_SMILES: [2H][2H]
 SMILES: [2H][2H]
 NUM PEAKS: 2
-2.0	14.99
-4.0	999.0
+2.0         14.99
+4.0         999.0
 
 NAME: Methane
 FORMULA: CH4
@@ -31,16 +35,16 @@
 CASNO: 74-82-8
 ID: 3
 COMMENT: Any=100 ; NIST MS# 61313, Seq# M64
+INCHI: InChI=1S/CH4/h1H4
 INCHIKEY: VNWKTOKETHGBQD-UHFFFAOYSA-N
-INCHI: InChI=1S/CH4/h1H4
 IUPAC_NAME: methane
 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
 
 NAME: Methane
 FORMULA: CH4
@@ -48,16 +52,16 @@
 CASNO: 74-82-8
 ID: 4
 COMMENT: Any=100 ; NIST MS# 18807, Seq# R26
+INCHI: InChI=1S/CH4/h1H4
 INCHIKEY: VNWKTOKETHGBQD-UHFFFAOYSA-N
-INCHI: InChI=1S/CH4/h1H4
 IUPAC_NAME: methane
 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
 
 NAME: Methane
 FORMULA: CH4
@@ -65,16 +69,16 @@
 CASNO: 74-82-8
 ID: 5
 COMMENT: Any=100 ; NIST MS# 18809, Seq# R27
+INCHI: InChI=1S/CH4/h1H4
 INCHIKEY: VNWKTOKETHGBQD-UHFFFAOYSA-N
-INCHI: InChI=1S/CH4/h1H4
 IUPAC_NAME: methane
 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
 
 NAME: Methane
 FORMULA: CH4
@@ -82,14 +86,14 @@
 CASNO: 74-82-8
 ID: 6
 COMMENT: Any=100 ; NIST MS# 423924, Seq# R28
+INCHI: InChI=1S/CH4/h1H4
 INCHIKEY: VNWKTOKETHGBQD-UHFFFAOYSA-N
-INCHI: InChI=1S/CH4/h1H4
 IUPAC_NAME: methane
 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