Mercurial > repos > bgruening > openbabel_change_title
comparison change_title_to_metadata_value.xml @ 7:9c15e92bed39 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author | bgruening |
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date | Tue, 07 May 2019 13:34:42 -0400 |
parents | fd7097abe45a |
children | eed751918a20 |
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6:3bf4dcc945f9 | 7:9c15e92bed39 |
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1 <tool id="openbabel_change_title" name="Change Title" version="@VERSION@.0"> | 1 <tool id="openbabel_change_title" name="Change title" version="@VERSION@.0"> |
2 <description>to meta-data value.</description> | 2 <description>to metadata value.</description> |
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 <macros> | 4 <macros> |
5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
6 </macros> | 6 </macros> |
7 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
12 --key '${key}' | 12 --key '${key}' |
13 --outfile '${outfile}' | 13 --outfile '${outfile}' |
14 ]]> | 14 ]]> |
15 </command> | 15 </command> |
16 <inputs> | 16 <inputs> |
17 <param name="infile" type="data" format="sdf,mol2" label="Compound File" help="Specify a compound file in SD- or MOL2-format."/> | 17 <param name="infile" type="data" format="sdf,mol2" label="Compound file" help="Specify a compound file in SDF or MOL2 format."/> |
18 <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 <param name="key" type="text" format="text" label="Compound identifier encoded in the SD-file." help="Specify the key name of the SDF metadata which contains the molecule identifier (e.g. 'PUBCHEM_SHAPE_VOLUME')"/> |
19 </inputs> | 19 </inputs> |
20 <outputs> | 20 <outputs> |
21 <expand macro="output_like_input"/> | 21 <expand macro="output_like_input"/> |
22 </outputs> | 22 </outputs> |
23 <tests> | 23 <tests> |
32 | 32 |
33 .. class:: infomark | 33 .. class:: infomark |
34 | 34 |
35 **What this tool does** | 35 **What this tool does** |
36 | 36 |
37 Changes the title of a molecule file to a metadata value of a given ID in the same molecule file. | 37 Reassigns the title of a molecule file (SDF or MOL2) to a metadata value of a given ID in the same molecule file. For example, if the metadata identifier chosen is PUBCHEM_SHAPE_VOLUME, then the title of the file (in the first line) will be replaced by the variable listed under PUBCHEM_SHAPE_VOLUME. |
38 | 38 |
39 ----- | 39 ----- |
40 | 40 |
41 .. class:: infomark | 41 .. class:: infomark |
42 | 42 |
50 | 50 |
51 .. class:: infomark | 51 .. class:: infomark |
52 | 52 |
53 **Output** | 53 **Output** |
54 | 54 |
55 Same as input with changed title tag. | 55 Same as input, with changed title tag. |
56 | 56 |
57 | 57 |
58 ]]> | 58 ]]> |
59 </help> | 59 </help> |
60 <expand macro="citations"/> | 60 <expand macro="citations"/> |