Mercurial > repos > bgruening > openbabel
comparison modify/change_title_to_metadata_value.xml @ 0:527ecd2fc500 draft
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author | bgruening |
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date | Thu, 15 Aug 2013 03:25:06 -0400 |
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children | 125da3a296ca |
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-1:000000000000 | 0:527ecd2fc500 |
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1 <tool id="ctb_change_title" name="Change Title" version="0.0.1"> | |
2 <description>to meta-data value.</description> | |
3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism> | |
4 <requirements> | |
5 <requirement type="package" version="2.3.2">openbabel</requirement> | |
6 </requirements> | |
7 <command interpreter="python"> | |
8 ## The command is a Cheetah template which allows some Python based syntax. | |
9 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces | |
10 change_title_to_metadata_value.py | |
11 --infile "${infile}" | |
12 --key "${key}" | |
13 --outfile "${outfile}" | |
14 </command> | |
15 <inputs> | |
16 <param name="infile" type="data" format="sdf,mol2" label="Compound File" help="Specify a compound file in SD- or MOL2-format."/> | |
17 <param name="key" type="text" format="text" label="Compound Identifier encoded in the SDF file." help="Specify the key name of the SDF metadata, that contains the molecule identifier."/> | |
18 </inputs> | |
19 <outputs> | |
20 <data name="outfile" format_source="infile"/> | |
21 </outputs> | |
22 <tests> | |
23 <param name="infile" type="sdf" value="CID_3033.sdf"/> | |
24 <param name="key" value="PUBCHEM_SHAPE_VOLUME"/> | |
25 <data name="output" type="sdf" file="change_title_on_CID_3033.sdf"/> | |
26 </tests> | |
27 <help> | |
28 | |
29 .. class:: infomark | |
30 | |
31 **What this tool does** | |
32 | |
33 Changes the title of a molecule file to a metadata value of a given ID in the same molecule file. | |
34 | |
35 ----- | |
36 | |
37 .. class:: infomark | |
38 | |
39 **Input** | |
40 | |
41 `SD-file`_ with metadata including the given ID. | |
42 | |
43 .. _SD-file: http://en.wikipedia.org/wiki/Chemical_table_file | |
44 | |
45 ----- | |
46 | |
47 .. class:: infomark | |
48 | |
49 **Output** | |
50 | |
51 Same as input with changed title tag. | |
52 | |
53 ----- | |
54 | |
55 .. class:: infomark | |
56 | |
57 **Cite** | |
58 | |
59 `Open Babel`_ | |
60 | |
61 .. _Open Babel: http://openbabel.org/wiki/Main_Page | |
62 | |
63 </help> | |
64 </tool> |