Mercurial > repos > bgruening > openbabel

annotate modify/change_title_to_metadata_value.xml @ 22:b4ba90dcfde0 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
ChemicalToolBoX update.
author Bjoern Gruening <bjoern.gruening@gmail.com>
date Tue, 23 Jul 2013 19:00:18 +0200
parents 3d3e7c1d0f49
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
6493d130f018 Uploaded
bgruening
parents:
diff changeset
1 <tool id="ctb_change_title" name="Change Title" version="0.0.1">
6493d130f018 Uploaded
bgruening
parents:
diff changeset
2 <description>to meta-data value.</description>
6493d130f018 Uploaded
bgruening
parents:
diff changeset
3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
6493d130f018 Uploaded
bgruening
parents:
diff changeset
4 <requirements>
15
ec87a42dccec ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents: 0
diff changeset
5 <requirement type="package" version="2.3.2">openbabel</requirement>
0
6493d130f018 Uploaded
bgruening
parents:
diff changeset
6 </requirements>
6493d130f018 Uploaded
bgruening
parents:
diff changeset
7 <command interpreter="python">
6493d130f018 Uploaded
bgruening
parents:
diff changeset
8 ## The command is a Cheetah template which allows some Python based syntax.
6493d130f018 Uploaded
bgruening
parents:
diff changeset
9 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
6493d130f018 Uploaded
bgruening
parents:
diff changeset
10 change_title_to_metadata_value.py
6493d130f018 Uploaded
bgruening
parents:
diff changeset
11 --infile "${infile}"
6493d130f018 Uploaded
bgruening
parents:
diff changeset
12 --key "${key}"
6493d130f018 Uploaded
bgruening
parents:
diff changeset
13 --outfile "${outfile}"
6493d130f018 Uploaded
bgruening
parents:
diff changeset
14 </command>
6493d130f018 Uploaded
bgruening
parents:
diff changeset
15 <inputs>
6493d130f018 Uploaded
bgruening
parents:
diff changeset
16 <param name="infile" type="data" format="sdf,mol2" label="Compound File" help="Specify a compound file in SD- or MOL2-format."/>
6493d130f018 Uploaded
bgruening
parents:
diff changeset
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."/>
6493d130f018 Uploaded
bgruening
parents:
diff changeset
18 </inputs>
6493d130f018 Uploaded
bgruening
parents:
diff changeset
19 <outputs>
6493d130f018 Uploaded
bgruening
parents:
diff changeset
20 <data name="outfile" format_source="infile"/>
6493d130f018 Uploaded
bgruening
parents:
diff changeset
21 </outputs>
6493d130f018 Uploaded
bgruening
parents:
diff changeset
22 <tests>
6493d130f018 Uploaded
bgruening
parents:
diff changeset
23 <param name="infile" type="sdf" value="CID_3033.sdf"/>
6493d130f018 Uploaded
bgruening
parents:
diff changeset
24 <param name="key" value="PUBCHEM_SHAPE_VOLUME"/>
6493d130f018 Uploaded
bgruening
parents:
diff changeset
25 <data name="output" type="sdf" file="change_title_on_CID_3033.sdf"/>
6493d130f018 Uploaded
bgruening
parents:
diff changeset
26 </tests>
6493d130f018 Uploaded
bgruening
parents:
diff changeset
27 <help>
6493d130f018 Uploaded
bgruening
parents:
diff changeset
28
6493d130f018 Uploaded
bgruening
parents:
diff changeset
29 .. class:: infomark
6493d130f018 Uploaded
bgruening
parents:
diff changeset
30
16
3d3e7c1d0f49 ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents: 15
diff changeset
31 **What this tool does**
0
6493d130f018 Uploaded
bgruening
parents:
diff changeset
32
16
3d3e7c1d0f49 ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents: 15
diff changeset
33 Changes the title of a molecule file to a metadata value of a given ID in the same molecule file.
3d3e7c1d0f49 ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents: 15
diff changeset
34
3d3e7c1d0f49 ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents: 15
diff changeset
35 -----
0
6493d130f018 Uploaded
bgruening
parents:
diff changeset
36
16
3d3e7c1d0f49 ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents: 15
diff changeset
37 .. class:: infomark
3d3e7c1d0f49 ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents: 15
diff changeset
38
3d3e7c1d0f49 ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents: 15
diff changeset
39 **Input**
0
6493d130f018 Uploaded
bgruening
parents:
diff changeset
40
16
3d3e7c1d0f49 ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents: 15
diff changeset
41 `SD-file`_ with metadata including the given ID.
0
6493d130f018 Uploaded
bgruening
parents:
diff changeset
42
16
3d3e7c1d0f49 ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents: 15
diff changeset
43 .. _SD-file: http://en.wikipedia.org/wiki/Chemical_table_file
0
6493d130f018 Uploaded
bgruening
parents:
diff changeset
44
6493d130f018 Uploaded
bgruening
parents:
diff changeset
45 -----
6493d130f018 Uploaded
bgruening
parents:
diff changeset
46
16
3d3e7c1d0f49 ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents: 15
diff changeset
47 .. class:: infomark
0
6493d130f018 Uploaded
bgruening
parents:
diff changeset
48
16
3d3e7c1d0f49 ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents: 15
diff changeset
49 **Output**
0
6493d130f018 Uploaded
bgruening
parents:
diff changeset
50
6493d130f018 Uploaded
bgruening
parents:
diff changeset
51 Same as input with changed title tag.
6493d130f018 Uploaded
bgruening
parents:
diff changeset
52
16
3d3e7c1d0f49 ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents: 15
diff changeset
53 -----
3d3e7c1d0f49 ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents: 15
diff changeset
54
3d3e7c1d0f49 ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents: 15
diff changeset
55 .. class:: infomark
0
6493d130f018 Uploaded
bgruening
parents:
diff changeset
56
16
3d3e7c1d0f49 ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents: 15
diff changeset
57 **Cite**
3d3e7c1d0f49 ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents: 15
diff changeset
58
3d3e7c1d0f49 ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents: 15
diff changeset
59 `Open Babel`_
3d3e7c1d0f49 ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents: 15
diff changeset
60
3d3e7c1d0f49 ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents: 15
diff changeset
61 .. _Open Babel: http://openbabel.org/wiki/Main_Page
0
6493d130f018 Uploaded
bgruening
parents:
diff changeset
62
6493d130f018 Uploaded
bgruening
parents:
diff changeset
63 </help>
6493d130f018 Uploaded
bgruening
parents:
diff changeset
64 </tool>