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author bgruening
date Wed, 15 Jul 2015 12:13:08 -0400
parents 527ecd2fc500
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1:b52872a1755a 2:125da3a296ca
3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism> 3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2.3.2">openbabel</requirement> 5 <requirement type="package" version="2.3.2">openbabel</requirement>
6 </requirements> 6 </requirements>
7 <command interpreter="python"> 7 <command interpreter="python">
8 <![CDATA[
8 ob_addh.py 9 ob_addh.py
9 -i "${infile}" 10 -i "${infile}"
10 --iformat "${infile.ext}" 11 --iformat "${infile.ext}"
11 -o "${outfile}" 12 -o "${outfile}"
12 $polar 13 $polar
13 --pH "${pH_value}" 14 --pH "${pH_value}"
15 ]]>
14 </command> 16 </command>
15 <inputs> 17 <inputs>
16 <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi" label="Select input file"/> 18 <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi" label="Select input file"/>
17 <param name="polar" type="boolean" truevalue="--polar" falsevalue="" label="Add hydrogens to polar atoms only"/> 19 <param name="polar" type="boolean" truevalue="--polar" falsevalue="" label="Add hydrogens to polar atoms only"/>
18 <param name="pH_value" type="float" size="4" value="7.4" label="Specify pH value"/> 20 <param name="pH_value" type="float" size="4" value="7.4" label="Specify pH value"/>
27 <param name="pH_value" value="7.4" /> 29 <param name="pH_value" value="7.4" />
28 <output name="outfile" file="CID_2244_addh.can" ftype="can" /> 30 <output name="outfile" file="CID_2244_addh.can" ftype="can" />
29 </test> 31 </test>
30 </tests> 32 </tests>
31 <help> 33 <help>
34 <![CDATA[
32 35
33 .. class:: infomark 36 .. class:: infomark
34 37
35 **What this tool does** 38 **What this tool does**
36 39
53 56
54 ----- 57 -----
55 58
56 .. class:: warningmark 59 .. class:: warningmark
57 60
58 **Hint** 61 **Hint**
59 62
60 To avoid possible crashes, only molecules with more than five heavy atoms are parsed. 63 To avoid possible crashes, only molecules with more than five heavy atoms are parsed.
61 64
62 ----- 65 -----
63 66
64 .. class:: infomark 67 .. class:: infomark
65 68
66 **Output** 69 **Output**
67 70
68 Same output format as the input format. 71 Same output format as the input format.
69 72
70 ----- 73 -----
71 74
79 82
80 N M O'Boyle, C Morley and G R Hutchison - `Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`_ 83 N M O'Boyle, C Morley and G R Hutchison - `Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`_
81 84
82 .. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://www.biomedcentral.com/content/pdf/1752-153X-2-5.pdf 85 .. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://www.biomedcentral.com/content/pdf/1752-153X-2-5.pdf
83 86
87 ]]>
84 </help> 88 </help>
85 </tool> 89 </tool>