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comparison filter/ob_remDuplicates.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="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> 7 <command>
8 <![CDATA[
8 obabel 9 obabel
9 -i"${infile.ext}" 10 -i"${infile.ext}"
10 "${infile}" 11 "${infile}"
11 -ocopy 12 -ocopy
12 --unique "${descriptor}" 13 --unique "${descriptor}"
13 -O "${outfile}" 14 -O "${outfile}"
14 -e 15 -e
15 2>&#38;1 16 2>&1
17 ]]>
16 </command> 18 </command>
17 <inputs> 19 <inputs>
18 <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Molecular input file"/> 20 <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Molecular input file"/>
19 <param name="descriptor" type="select" label="Select descriptor for molecule comparison"> 21 <param name="descriptor" type="select" label="Select descriptor for molecule comparison">
20 <option value="inchi" checked="True">InChI (default)</option> 22 <option value="inchi" checked="True">InChI (default)</option>
31 <param name="descriptor" value="inchi" /> 33 <param name="descriptor" value="inchi" />
32 <output name="outfile" ftype="smi" file="ob_remDuplicates_on_2_mol.smi" /> 34 <output name="outfile" ftype="smi" file="ob_remDuplicates_on_2_mol.smi" />
33 </test> 35 </test>
34 </tests> 36 </tests>
35 <help> 37 <help>
38 <![CDATA[
36 39
37 .. class:: infomark 40 .. class:: infomark
38 41
39 **What this tool does** 42 **What this tool does**
40 43
62 65
63 ----- 66 -----
64 67
65 .. class:: infomark 68 .. class:: infomark
66 69
67 **Output** 70 **Output**
68 71
69 Same as input format. 72 Same as input format.
70 73
71 ----- 74 -----
72 75
80 83
81 `Open Babel`_ 84 `Open Babel`_
82 85
83 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page 86 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page
84 87
88 ]]>
85 </help> 89 </help>
86 </tool> 90 </tool>