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comparison filter/ob_remIons.xml @ 2:125da3a296ca draft default tip

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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="50000" shared_inputs="" merge_outputs="outfile"></parallelism> 3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="50000" 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_remIons.py 9 ob_remIons.py
9 -i "${infile}" 10 -i "${infile}"
10 -iformat "${infile.ext}" 11 -iformat "${infile.ext}"
11 -o "${outfile}" 12 -o "${outfile}"
13 ]]>
12 </command> 14 </command>
13 <inputs> 15 <inputs>
14 <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Select input file with multiple molecules"/> 16 <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Select input file with multiple molecules"/>
15 </inputs> 17 </inputs>
16 <outputs> 18 <outputs>
21 <param name="infile" ftype="smi" value="2_mol.smi"/> 23 <param name="infile" ftype="smi" value="2_mol.smi"/>
22 <output name="outfile" ftype="smi" file="obrmions_on_2_mol.smi" /> 24 <output name="outfile" ftype="smi" file="obrmions_on_2_mol.smi" />
23 </test> 25 </test>
24 </tests> 26 </tests>
25 <help> 27 <help>
28 <![CDATA[
26 29
27 .. class:: infomark 30 .. class:: infomark
28 31
29 **What this tool does** 32 **What this tool does**
30 33
35 .. class:: warningmark 38 .. class:: warningmark
36 39
37 **Hint** 40 **Hint**
38 41
39 | Only the **largest fragment** on every molecule is extracted. 42 | Only the **largest fragment** on every molecule is extracted.
40 | 43 |
41 | Only molecules with more than 5 heavy atoms are parsed. 44 | Only molecules with more than 5 heavy atoms are parsed.
42 45
43 ----- 46 -----
44 47
45 .. class:: infomark 48 .. class:: infomark
56 59
57 `Open Babel`_ 60 `Open Babel`_
58 61
59 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page 62 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page
60 63
64 ]]>
61 </help> 65 </help>
62 </tool> 66 </tool>