Mercurial > repos > tomnl > metfrag

changeset 7:0b3816a7a14b draft

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planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit 6dc5d494a84dd572f277dcd1c979e6edfb40383d
author tomnl
date Thu, 05 Sep 2019 06:48:28 -0400
parents ceb9bd68f6bc
children 9a3019c609d9
files config.ini metfrag.py metfrag.xml
diffstat 3 files changed, 24 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/config.ini	Thu Sep 05 06:48:28 2019 -0400
@@ -0,0 +1,9 @@
+[MetChem]
+LocalMetChemDatabase: metchem
+LocalMetChemDatabasePortNumber: 5432
+LocalMetChemDatabaseUser: metchem
+LocalMetChemDatabasePassword: metchem
+
+
+
+
--- a/metfrag.py	Fri Aug 02 11:51:17 2019 -0400
+++ b/metfrag.py	Thu Sep 05 06:48:28 2019 -0400
@@ -5,8 +5,7 @@
 import sys
 import six
 import re
-import random
-import string
+import ConfigParser
 import shutil
 import glob
 import tempfile
@@ -60,6 +59,11 @@
 args = parser.parse_args()
 print(args)
 
+
+config = ConfigParser.ConfigParser()
+config.read(os.path.join(os.path.dirname(os.path.abspath(__file__)), 'config.ini'))
+
+
 if os.stat(args.input_pth).st_size == 0:
     print('Input file empty')
     exit()
@@ -154,11 +158,11 @@
     if args.MetFragDatabaseType == "LocalCSV":
         paramd["LocalDatabasePath"] = args.LocalDatabasePath
     elif args.MetFragDatabaseType == "MetChem":
-        paramd["LocalMetChemDatabase"] = "metchem"
-        paramd["LocalMetChemDatabasePortNumber"] = 5432
+        paramd["LocalMetChemDatabase"] = config.get('MetChem', 'LocalMetChemDatabase')
+        paramd["LocalMetChemDatabasePortNumber"] = config.get('MetChem', 'LocalMetChemDatabasePortNumber')
         paramd["LocalMetChemDatabaseServerIp"] = args.LocalMetChemDatabaseServerIp
-        paramd["LocalMetChemDatabaseUser"] = "metchemro"
-        paramd["LocalMetChemDatabasePassword"] = "metchemro"
+        paramd["LocalMetChemDatabaseUser"] = config.get('MetChem', 'LocalMetChemDatabaseUser')
+        paramd["LocalMetChemDatabasePassword"] = config.get('MetChem', 'LocalMetChemDatabasePassword')
 
     paramd["FragmentPeakMatchAbsoluteMassDeviation"] = args.FragmentPeakMatchAbsoluteMassDeviation
     paramd["FragmentPeakMatchRelativeMassDeviation"] = args.FragmentPeakMatchRelativeMassDeviation
--- a/metfrag.xml	Fri Aug 02 11:51:17 2019 -0400
+++ b/metfrag.xml	Thu Sep 05 06:48:28 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="metfrag" name="MetFrag" version="2.4.5+galaxy0.1.11">
+<tool id="metfrag" name="MetFrag" version="2.4.5+galaxy0.1.12">
     <description> </description>
     <requirements>
         <requirement type="package" version="2.4.5">metfrag</requirement>
@@ -63,6 +63,10 @@
             --score_thrshld $PostProcessFilter.score_thrshld
             --pctexplpeak_thrshld $PostProcessFilter.pctexplpeak_thrshld
 
+
+
+
+
     ]]></command>
     <inputs>