|
0
|
1 <tool id="bg_mol2gspan" name="Molecule to gSpan" version="0.1">
|
|
|
2 <description>converter</description>
|
|
|
3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10" shared_inputs="" merge_outputs="outfile"></parallelism>
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="2.3.2">openbabel</requirement>
|
|
|
6 <requirement type="set_environment">MOL2GSPAN_SCRIPT_PATH</requirement>
|
|
|
7 </requirements>
|
|
|
8 <command>
|
|
|
9
|
|
|
10 #if $infile.ext == 'sdf':
|
|
|
11 python \$MOL2GSPAN_SCRIPT_PATH/mol2gspan.py --infile $infile --outfile $outfile
|
|
|
12
|
|
|
13 #else:
|
|
|
14 obabel -i $infile.ext -o sdf $infile ---errorlevel 1 | python \$MOL2GSPAN_SCRIPT_PATH/mol2gspan.py --infile - --outfile $outfile
|
|
|
15
|
|
|
16 #end if
|
|
|
17
|
|
|
18 </command>
|
|
|
19 <inputs>
|
|
|
20 <param format="smi,sdf,mol,inchi,mol2" name="infile" type="data"
|
|
|
21 label="Input molecules" help=""/>
|
|
|
22 </inputs>
|
|
|
23 <outputs>
|
|
|
24 <data format="gspan" name="outfile" label="gSpan from ${on_string}"/>
|
|
|
25 </outputs>
|
|
|
26 <tests>
|
|
|
27 <test>
|
|
|
28 <param name="infile" value="3_molceuls.sdf" />
|
|
|
29 <output name="outfile" file="3_molecules.gspan" />
|
|
|
30 </test>
|
|
|
31 </tests>
|
|
|
32 <help>
|
|
|
33
|
|
|
34 .. class:: infomark
|
|
|
35
|
|
|
36 **What it does**
|
|
|
37
|
|
|
38 That converter will convert arbitratry molecule files to the gSpan format.
|
|
|
39
|
|
|
40 </help>
|
|
|
41 </tool>
|
