Mercurial > repos > bgruening > openbabel
annotate modify/change_title_to_metadata_value.xml @ 15:ec87a42dccec
ChemicalToolBoX update.
| author | Bjoern Gruening <bjoern.gruening@gmail.com> |
|---|---|
| date | Sat, 01 Jun 2013 20:02:50 +0200 |
| parents | 6493d130f018 |
| children | 3d3e7c1d0f49 |
| rev | line source |
|---|---|
| 0 | 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> | |
|
15
ec87a42dccec
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
0
diff
changeset
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5 <requirement type="package" version="2.3.2">openbabel</requirement> |
| 0 | 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 **Hint** | |
| 32 | |
| 33 To convert the output, use the pencil icon next to the history entry. | |
| 34 | |
| 35 ------ | |
| 36 | |
| 37 **What it does** | |
| 38 | |
| 39 Change the title from a molecule file to metadata value of a given-id of the same molecule file. | |
| 40 | |
| 41 ----- | |
| 42 | |
| 43 **Input format** | |
| 44 | |
| 45 SDF with metadata including the given key. | |
| 46 | |
| 47 **Output format** | |
| 48 | |
| 49 Same as input with changed title tag. | |
| 50 | |
| 51 **References** | |
| 52 | |
| 53 | |
| 54 </help> | |
| 55 </tool> |