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comparison ob_genProp.xml @ 0:df6d948e95ba draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
author bgruening
date Sat, 20 May 2017 08:38:38 -0400
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-1:000000000000 0:df6d948e95ba
1 <tool id="openbabel_genProp" name="Compute physico-chemical properties" version="@VERSION@.0">
2 <description>for a set of molecules</description>
3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command detect_errors="aggressive">
9 <![CDATA[
10 python '$__tool_directory__/ob_genProp.py'
11 -i '${infile}'
12 --iformat '${infile.ext}'
13 --oformat '${output_opts.output_format_types}'
14 #if $output_opts.header.value:
15 --header $output_opts.header
16 #end if
17 -o '${outfile}'
18 ]]>
19 </command>
20 <inputs>
21 <expand macro="infile_all_types"/>
22 <conditional name="output_opts">
23 <param name="output_format_types" type="select" label="Specify output format file">
24 <option value="table">Tabular format</option>
25 <option value="sdf" selected="True">sdf</option>
26 </param>
27 <when value="table">
28 <param name="header" type="boolean" checked="False" label="Print the headers of the table as the first row of the table"/>
29 </when>
30 <when value="sdf">
31 <param name="header" type="hidden"/>
32 </when>
33 </conditional>
34 </inputs>
35 <outputs>
36 <data format="tabular" name="outfile" label="${tool.name} on ${on_string}">
37 <change_format>
38 <when input="output_opts.output_format_types" value="sdf" format="sdf"/>
39 </change_format>
40 </data>
41 </outputs>
42 <tests>
43 <test>
44 <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
45 <param name="output_format_types" value="sdf" />
46 <output name="outfile" ftype="sdf" file="ob_genprop_on_CID2244.sdf" lines_diff="2" />
47 </test>
48 <test>
49 <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
50 <param name="output_format_types" value="table" />
51 <param name="header" value="true" />
52 <output name="outfile" ftype="tabular" file="ob_genprop_on_CID2244.tabular" />
53 </test>
54 </tests>
55 <help>
56 <![CDATA[
57
58 .. class:: infomark
59
60 **What this tool does**
61
62 Computes several physico-chemical properties for a set of molecules.
63
64 The following physico-chemical properties and descriptors are computed for each molecule:
65
66 - number of hydrogen-bond donor and acceptor groups
67
68 - number of rotatable bonds
69
70 - logP
71
72 - number of rings
73
74 - number of heavy atoms
75
76 - molecular weight
77
78 - total Polar Surface Area
79
80 - molecular refractivity
81
82 - Canonical SMILES
83
84 - InChI string
85
86 - InChI-Key
87
88 - Spectrophores(TM)
89
90 -----
91
92 .. class:: infomark
93
94 **Input**
95
96 - SDF_
97 - MOL2_
98
99 .. _SDF: http://en.wikipedia.org/wiki/Chemical_table_file
100 .. _MOL2: http://www.tripos.com/index.php?family=modules,SimplePage,Mol2_File_Format2009
101
102 3D coordinates of the molecules have to be provided.
103
104 -----
105
106 .. class:: warningmark
107
108 **Hint** the generation of Spectrophores(TM) requires the previous addition of explicit hydrogen atoms and the proper definition of 3D coordinates. The user is directed towards the corresponding tools if accurate Spectrophores(TM) descriptors are required.
109
110 -----
111
112 .. class:: infomark
113
114 **Output**
115
116 Either a SD-file containing several computed physico-chemical properties stored as metadata or a tabular file with the metadata stored in columns.
117
118 -----
119
120 .. class:: infomark
121
122 **Cite**
123
124 N M O'Boyle, C Morley and G R Hutchison - `Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`_
125
126 Silicos_ - |Spectrophores (TM)| is a registered tool implemented in the open-source OpenBabel.
127
128 .. |Spectrophores (TM)| unicode:: Spectrophores U+2122
129
130 `Open Babel`_
131
132 .. _Open Babel: http://openbabel.org/wiki/Main_Page
133 .. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://www.biomedcentral.com/content/pdf/1752-153X-2-5.pdf
134 .. _Silicos: http://openbabel.org/docs/dev/Fingerprints/spectrophore.html
135
136
137 ]]>
138 </help>
139 <expand macro="citations">
140 <citation type="doi">10.1186/1752-153X-2-5</citation>
141 </expand>
142 </tool>