# HG changeset patch
# User recetox
# Date 1701422601 0
# Node ID ae66b58846cdee38abe31a43a67974eef3cd4662
# Parent  d1f44632f206479edcb191c97ceeab48653445b5
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit ad60bf881a8fd00546909c76d65ea3c6b65a4fe9

diff -r d1f44632f206 -r ae66b58846cd macros.xml
--- a/macros.xml	Sat Oct 21 12:31:00 2023 +0000
+++ b/macros.xml	Fri Dec 01 09:23:21 2023 +0000
@@ -2,7 +2,7 @@
     <token name="@TOOL_VERSION@">v3.5.2</token>
     <xml name="requirements">
         <requirements>
-            <container type="docker">recetox/recetox-msfinder:v3.5.2-rcx0</container>
+            <container type="docker">recetox/recetox-msfinder:v3.5.2-rcx1</container>
         </requirements>
     </xml>
     <xml name="creator">
@@ -54,7 +54,10 @@
         <param name="SiCheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="SiCheck" />
     </xml>  -->
     <xml name="output">
-        <data name="annotated_data" format="msp" />
+        <collection type="list" format="txt" name="output" label="${tool.name} on ${on_string}">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.smi" directory="output" ext="smi" />
+            <discover_datasets  pattern="(?P&lt;designation&gt;.+)\.msp" directory="output" ext="msp" />
+        </collection>
     </xml>
 
     <token name="@HELP@"><![CDATA[
diff -r d1f44632f206 -r ae66b58846cd recetox_msfinder.xml
--- a/recetox_msfinder.xml	Sat Oct 21 12:31:00 2023 +0000
+++ b/recetox_msfinder.xml	Fri Dec 01 09:23:21 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="recetox_msfinder" name="RECETOX MsFinder" version="@TOOL_VERSION@+galaxy2">
+<tool id="recetox_msfinder" name="RECETOX MsFinder" version="@TOOL_VERSION@+galaxy3">
     <description>Annotation of fragment peaks in mass spectral libraries.</description>
     <macros>
         <import>macros.xml</import>
@@ -9,8 +9,11 @@
     <expand macro="requirements" />
     <command>
         <![CDATA[
-        sh ${write_param} &&
-        mono /MsFinder/MsFinder/bin/Debug/MsfinderConsoleApp.exe annotate -i "$input_data" -m 'MSFINDER.INI' -o "$annotated_data"        
+        mkdir output;
+        sh ${write_param};
+        mono /MsFinder/MsFinder/bin/Debug/MsfinderConsoleApp.exe annotate -i "$input_data" -m 'MSFINDER.INI' -o 'output/result.msp';
+        [ -s output/result.msp ] || rm output/result.msp;
+
     ]]>
     </command>
 
@@ -52,9 +55,16 @@
     <tests>
         <test>
             <param name="input_data" value="test.msp" ftype="msp" />
-            <output name="annotated_data" file="out.msp" lines_diff="16	" /> 
+            <output_collection name="output" type="list">
+                <element name="result" file="out.msp" lines_diff="16"/>
+            </output_collection>
             <!-- This is set to 16 since msfinder sometimes places double bonds between certain atoms and sometimes not - there are 16 such cases in this file. -->
-
+        </test>
+        <test>
+            <param name="input_data" value="test_log.msp" ftype="msp" />
+            <output_collection name="output" type="list">
+                <element name="log_smiles" file="log_smiles.smi" />
+            </output_collection>
         </test>
     </tests>
 
diff -r d1f44632f206 -r ae66b58846cd test-data/log_smiles.smi
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/log_smiles.smi	Fri Dec 01 09:23:21 2023 +0000
@@ -0,0 +1,1 @@
+Cl[Si]1Oc2ccccc2O1.[C-]#[O+].[C-]#[O+].[CH]1C=CC=C1.[Fe]
diff -r d1f44632f206 -r ae66b58846cd test-data/test_log.msp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_log.msp	Fri Dec 01 09:23:21 2023 +0000
@@ -0,0 +1,37 @@
+FORMULA: C13H9ClFeO4Si
+COMMENT: SpectrumID: 1519953; Source: C4-1998-38-3; Class: Benzenoids; CASRN not real!
+NAME: ((.eta.5-Cyclopentadienylironbiscarbonyl)(1,2-phenylenedioxysilyl)chloride complex
+INCHI: InChI=1S/C6H4ClO2Si.C5H5.2CO.Fe/c7-10-8-5-3-1-2-4-6(5)9-10;1-2-4-5-3-1;2*1-2;/h1-4H;1-5H;;;
+SMILES: Cl[Si]1Oc2ccccc2O1.[C-]#[O+].[C-]#[O+].[CH]1C=CC=C1.[Fe]
+NUM PEAKS: 3
+292.0       999.0
+314.0       118.89
+348.0       734.24
+
+FORMULA: C13H14O
+COMMENT: SpectrumID: 1752764; Source: A1-13-956/SMS7-13; DOI: 10.1021/ol1029996; QI: 383; Class: Benzene and substituted derivatives; CASRN not real! |RI:1588|
+NAME: ((1R*,2R*)-1-Methyl-2-phenylethynylcyclopropyl)methanol
+RETENTIONINDEX: 1588.0
+INCHI: InChI=1S/C13H14O/c1-13(10-14)9-12(13)8-7-11-5-3-2-4-6-11/h2-6,12,14H,9-10H2,1H3/t12-,13-/m0/s1
+SMILES: C[C@@]1(CO)C[C@@H]1C#Cc1ccccc1
+NUM PEAKS: 20
+51.0        89.92
+63.0        89.92
+77.0        179.84
+88.0        39.96
+89.0        59.95
+91.0        49.95
+102.0       149.86
+113.0       49.95
+115.0       229.79
+127.0       139.87
+128.0       999.0
+129.0       199.82
+144.0       99.91
+155.0       119.89
+156.0       14.89
+157.0       1.1
+158.0       0.1
+186.0       39.96
+187.0       5.89
+188.0       0.5
\ No newline at end of file