# HG changeset patch
# User bgruening
# Date 1605040325 0
# Node ID 4e3b2049a4d301464714f63bbcd8883571e0d85e
# Parent  3153b6f3087c89ecbeb7fa3180d997a7376ac995
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 327c29cc43f56d7067ab9fa51323ea31951db98b"

diff -r 3153b6f3087c -r 4e3b2049a4d3 macros.xml
--- a/macros.xml	Mon Oct 19 14:43:01 2020 +0000
+++ b/macros.xml	Tue Nov 10 20:32:05 2020 +0000
@@ -4,7 +4,7 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">openbabel</requirement>
-            <requirement type="package" version="3">python</requirement>
+            <requirement type="package" version="3.6">python</requirement>
             <yield />
         </requirements>
     </xml>
diff -r 3153b6f3087c -r 4e3b2049a4d3 ob_remIons.py
--- a/ob_remIons.py	Mon Oct 19 14:43:01 2020 +0000
+++ b/ob_remIons.py	Tue Nov 10 20:32:05 2020 +0000
@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+
 """
     Input: molecular input file.
     Output: Molecule file with removed ions and fragments.
@@ -15,20 +16,24 @@
     parser.add_argument('-iformat', default='sdf', help='input file format')
     parser.add_argument('-i', '--input', required=True, help='input file name')
     parser.add_argument('-o', '--output', required=True, help='output file name')
+    parser.add_argument('-idx', default=False, action='store_true', help='should output be an indexed text table? works only for inchi/smiles, otherwise is ignored')
     return parser.parse_args()
 
 
 def remove_ions(args):
-    outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True)
-    for mol in pybel.readfile(args.iformat, args.input):
-        if mol.OBMol.NumHvyAtoms() > 5:
-            mol.OBMol.StripSalts(0)
-            if 'inchi' in mol.data:
-                del mol.data['inchi']  # remove inchi cache so modified mol is saved
-            # Check if new small fragments have been created and remove them
+    with open(args.output, 'w') as outfile:
+        for index, mol in enumerate(pybel.readfile(args.iformat, args.input)):
             if mol.OBMol.NumHvyAtoms() > 5:
-                outfile.write(mol)
-    outfile.close()
+                mol.OBMol.StripSalts(0)
+                if 'inchi' in mol.data:
+                    del mol.data['inchi']  # remove inchi cache so modified mol is saved
+
+            mol = mol.write(args.iformat) if mol.OBMol.NumHvyAtoms() > 5 else '\n'
+
+            if args.idx and args.iformat in ['inchi', 'smi']:
+                outfile.write(f'{index}\t{mol}')
+            elif mol != '\n':
+                outfile.write(f'{mol}')
 
 
 def __main__():
diff -r 3153b6f3087c -r 4e3b2049a4d3 ob_remIons.xml
--- a/ob_remIons.xml	Mon Oct 19 14:43:01 2020 +0000
+++ b/ob_remIons.xml	Tue Nov 10 20:32:05 2020 +0000
@@ -3,7 +3,7 @@
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="50000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">1</token>
+        <token name="@GALAXY_VERSION@">2</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="aggressive">
@@ -12,10 +12,12 @@
       -i '${infile}'
       -iformat '${infile.ext}'
       -o '${outfile}'
+      $index
 ]]>
     </command>
     <inputs>
         <expand macro="infile_all_types"/>
+        <param name="index" type="boolean" checked="false" truevalue="-idx" falsevalue="" label="Output indexed tab-separated table?" help="Add an index column to the output file. This option will work only when input format is InChI or SMILES, otherwise it will be ignored." />
     </inputs>
     <outputs>
         <expand macro="output_like_input"/>
@@ -29,6 +31,11 @@
             <param name="infile" ftype="inchi" value="na-sal.inchi"/>
             <output name="outfile" ftype="inchi" file="na-sal_obrmions.inchi" />
         </test>
+        <test>
+            <param name="infile" ftype="inchi" value="multiple.inchi"/>
+            <param name="index" value="true"/>
+            <output name="outfile" ftype="inchi" file="multiple_obrmions.inchi" />
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r 3153b6f3087c -r 4e3b2049a4d3 test-data/multiple.inchi
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple.inchi	Tue Nov 10 20:32:05 2020 +0000
@@ -0,0 +1,3 @@
+InChI=1S/C2H5ClO/c3-1-2-4/h4H,1-2H2
+InChI=1S/C18H29NO3/c1-14(2)19-11-17(20)13-22-18-7-5-15(6-8-18)9-10-21-12-16-3-4-16/h5-8,14,16-17,19-20H,3-4,9-13H2,1-2H3
+InChI=1S/C13H22NO3PS/c1-6-16-18(15,14-10(2)3)17-12-7-8-13(19-5)11(4)9-12/h7-10H,6H2,1-5H3,(H,14,15)
diff -r 3153b6f3087c -r 4e3b2049a4d3 test-data/multiple_obrmions.inchi
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/multiple_obrmions.inchi	Tue Nov 10 20:32:05 2020 +0000
@@ -0,0 +1,3 @@
+0	
+1	InChI=1S/C18H29NO3/c1-14(2)19-11-17(20)13-22-18-7-5-15(6-8-18)9-10-21-12-16-3-4-16/h5-8,14,16-17,19-20H,3-4,9-13H2,1-2H3
+2	InChI=1S/C13H22NO3PS/c1-6-16-18(15,14-10(2)3)17-12-7-8-13(19-5)11(4)9-12/h7-10H,6H2,1-5H3,(H,14,15)