Mercurial > repos > bgruening > sdf_to_tab

comparison sdf_to_tab.xml @ 0:06828e0cc8a7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
author bgruening
date Wed, 16 Oct 2019 07:26:19 -0400
parents
children 40ff81f67f5e
comparison
equal deleted inserted replaced
-1:000000000000 0:06828e0cc8a7
1 <tool id="sdf_to_tab" name="Extract values from an SD-file" version="@VERSION@">
2 <macros>
3 <token name="@VERSION@">2019.03.1</token>
4 </macros>
5 <description>into a tabular file using RDKit</description>
6 <requirements>
7 <requirement type="package" version="@VERSION@">rdkit</requirement>
8 </requirements>
9 <command detect_errors="exit_code">
10 <![CDATA[
11 python '$__tool_directory__/sdf_to_tab.py'
12 -i '${infile}'
13 -o '${outfile}'
14 -p '$props'
15 $header
16 $smiles
17 $name
18 ]]>
19 </command>
20 <inputs>
21 <param name="infile" format="sdf" type="data" label="Input SD-file"/>
22 <param name="header" type="boolean" label="Include the property name as header"
23 truevalue="--header" falsevalue="" checked="false" />
24 <param name="smiles" type="boolean" label="Include SMILES as column in output"
25 truevalue="--smiles" falsevalue="" checked="false" />
26 <param name="name" type="boolean" label="Include molecule name as column in output"
27 truevalue="--name" falsevalue="" checked="false" />
28 <param name="props" type="text" optional="true" label="Properties to extract from the SD-file" help="Separated with a comma, e.g. RMSD_UB,RMSD_LB,SCORE. To extract values for all properties in the file, leave the field blank."/>
29 </inputs>
30 <outputs>
31 <data format="tabular" name="outfile" />
32 </outputs>
33 <tests>
34 <test>
35 <param name="infile" ftype='sdf' value="CID_3037.sdf" />
36 <param name="header" value="True" />
37 <param name="props" value="" />
38 <param name="name" value="True" />
39 <output name="outfile" ftype='tabular' file="CID_3037.tab" />
40
41 </test>
42 <test>
43 <param name="infile" ftype='sdf' value="ligand.sdf" />
44 <param name="header" value="True" />
45 <param name="props" value="RMSD_UB,RMSD_LB,SCORE" />
46 <param name="smiles" value="True" />
47 <output name="outfile" ftype='tabular' file="ligand.tab" />
48 </test>
49 </tests>
50 <help>
51 <![CDATA[
52
53 .. class:: infomark
54
55 **What this tool does**
56
57 Structure-data (SD-) files may contain values for various properties saved under each of the records. These are indicated using angled brackets, as in the following extract::
58
59 > <TORSDO>
60 F 3
61
62 > <SCORE>
63 -4.9
64
65 > <RMSD_LB>
66 0.000
67
68 > <RMSD_UB>
69 0.000
70
71 This tool extracts properties for all molecules saved within an input SD-file, using RDKit, and saves them to tabular format.
72
73
74 -----
75
76 .. class:: infomark
77
78 **Input**
79
80 An SD-file. The properties to be extracted can also be specified, separated with a comma; for example, SCORE,RMSD_LB,RMSD_UB.
81
82 If the field is left blank, all properties found in the SD-file will be saved, excluding properties with values that contain newline or tab characters, which would disrupt the tabular format.
83
84 -----
85
86 .. class:: infomark
87
88 **Output**
89
90 Tabular file, where each property is shown in a separate column, with compounds found in the SD-file listed in each row::
91
92 Name RMSD_LB RMSD_UB SCORE
93 pose1 0.0 0.0 -4.9
94 pose2 0.118 2.246 -4.9
95 pose3 2.96 5.795 -4.9
96 pose4 2.958 5.379 -4.8
97 pose5 2.763 5.379 -4.5
98 pose6 3.106 4.85 -4.4
99 pose7 2.847 5.816 -4.4
100 pose8 3.964 5.892 -4.3
101 pose9 3.971 6.363 -4.3
102
103 ]]>
104 </help>
105 <citations>
106 <citation type="bibtex">
107 @article{rdkit,
108 author = {Greg Landrum and others},
109 title = {RDKit: Open-source cheminformatics},
110 url ={http://www.rdkit.org}
111 }</citation>
112 </citations>
113 </tool>