Mercurial > repos > recetox > assign_ri_from_comment

changeset 2:97ccdb1ba47c draft default tip

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/riassigner commit 722ce0aee0a49d5bd76f261d949945adf69aae90
author recetox
date Tue, 07 May 2024 12:25:38 +0000
parents 7226eba9c09d
children
files macros.xml riassigner_from_comment.xml test-data/nist_ei_ms_3mols_input.msp test-data/nist_ei_ms_3mols_output.msp
diffstat 4 files changed, 140 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Tue Apr 16 11:30:39 2024 +0000
+++ b/macros.xml	Tue May 07 12:25:38 2024 +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>
             <person
--- a/riassigner_from_comment.xml	Tue Apr 16 11:30:39 2024 +0000
+++ b/riassigner_from_comment.xml	Tue May 07 12:25:38 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="riassigner_from_comment" name="RIAssigner init from comment" version="@TOOL_VERSION@+galaxy5" profile="21.09">
+<tool id="riassigner_from_comment" name="RIAssigner init from comment" version="@TOOL_VERSION@+galaxy0" profile="21.09">
     <description>Assign different retention indices from unstructured comment metadata</description>
     <macros>
         <import>macros.xml</import>
@@ -72,6 +72,10 @@
             <param name="input" value="nist_ei_ms_2mols_input.msp" ftype="msp"/>
             <output name="output" file="nist_ei_ms_2mols_output.msp" ftype="msp"/>
         </test>
+        <test>
+            <param name="input" value="nist_ei_ms_3mols_input.msp" ftype="msp"/>
+            <output name="output" file="nist_ei_ms_3mols_output.msp" ftype="msp"/>
+        </test>
     </tests>
 
     <help><![CDATA[
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nist_ei_ms_3mols_input.msp	Tue May 07 12:25:38 2024 +0000
@@ -0,0 +1,66 @@
+NAME: Water
+FORMULA: H2O
+MW: 18
+CASNO: 7732185
+ID: 9
+COMMENT: SemiStdNP=317 StdNP=323/4/2 StdPolar=1053/14/2 ; NIST MS# 7, Seq# M67
+NUM PEAKS: 5
+STDINCHI: InChI=1S/H2O/h1H2
+SMILES: O
+16.0	8.99
+17.0	211.81
+18.0	999.0
+19.0	5.0
+20.0	3.0
+
+NAME: Methyl Alcohol
+FORMULA: CH4O
+MW: 32
+CASNO: 67561
+ID: 32
+COMMENT: SemiStdNP=354/16/10 StdNP=379/7/34 StdPolar=903/8/35 ; NIST MS# 229809, Seq# M1806
+NUM PEAKS: 16
+STDINCHI: InChI=1S/CH4O/c1-2/h2H,1H3
+SMILES: CO
+2.0	3.0
+12.0	2.0
+13.0	5.99
+14.0	15.99
+15.0	122.89
+16.0	1.0
+17.0	3.0
+18.0	6.99
+19.0	1.0
+28.0	44.96
+29.0	444.6
+30.0	63.94
+31.0	999.0
+32.0	742.33
+33.0	10.99
+34.0	1.0
+
+FORMULA: C2H6
+COMMENT: Any=200 ; NIST MS# 23, Seq# M168 |RI:220|
+INCHI: InChI=1S/C2H6/c1-2/h1-2H3
+SMILES: CC
+IONMODE: positive
+COMPOUND_NAME: Ethane
+RETENTION_INDEX: 220.0
+RETENTION_TIME: None
+ADDUCT: [M]+
+PRECURSORMZ: 29.99945142009076
+NUM PEAKS: 14
+2.0         2.0
+12.0        4.0
+13.0        9.99
+14.0        29.97
+15.0        43.96
+16.0        1.0
+24.0        5.0
+25.0        34.97
+26.0        231.79
+27.0        331.7
+28.0        999.0
+29.0        214.81
+30.0        261.76
+31.0        5.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nist_ei_ms_3mols_output.msp	Tue May 07 12:25:38 2024 +0000
@@ -0,0 +1,68 @@
+FORMULA: H2O
+CASNO: 7732185
+ID: 9
+COMMENT: SemiStdNP=317 StdNP=323/4/2 StdPolar=1053/14/2 ; NIST MS# 7, Seq# M67
+SMILES: O
+COMPOUND_NAME: Water
+NOMINAL_MASS: 18
+INCHI: InChI=1S/H2O/h1H2
+RETENTION_INDEX: 317
+NUM PEAKS: 5
+16.0        8.99
+17.0        211.81
+18.0        999.0
+19.0        5.0
+20.0        3.0
+
+FORMULA: CH4O
+CASNO: 67561
+ID: 32
+COMMENT: SemiStdNP=354/16/10 StdNP=379/7/34 StdPolar=903/8/35 ; NIST MS# 229809, Seq# M1806
+SMILES: CO
+COMPOUND_NAME: Methyl Alcohol
+NOMINAL_MASS: 32
+INCHI: InChI=1S/CH4O/c1-2/h2H,1H3
+RETENTION_INDEX: 354
+NUM PEAKS: 16
+2.0         3.0
+12.0        2.0
+13.0        5.99
+14.0        15.99
+15.0        122.89
+16.0        1.0
+17.0        3.0
+18.0        6.99
+19.0        1.0
+28.0        44.96
+29.0        444.6
+30.0        63.94
+31.0        999.0
+32.0        742.33
+33.0        10.99
+34.0        1.0
+
+FORMULA: C2H6
+COMMENT: Any=200 ; NIST MS# 23, Seq# M168 |RI:220|
+INCHI: InChI=1S/C2H6/c1-2/h1-2H3
+SMILES: CC
+IONMODE: positive
+COMPOUND_NAME: Ethane
+RETENTION_TIME: None
+ADDUCT: [M]+
+PRECURSOR_MZ: 29.99945142009076
+NUM PEAKS: 14
+2.0         2.0
+12.0        4.0
+13.0        9.99
+14.0        29.97
+15.0        43.96
+16.0        1.0
+24.0        5.0
+25.0        34.97
+26.0        231.79
+27.0        331.7
+28.0        999.0
+29.0        214.81
+30.0        261.76
+31.0        5.0
+