Mercurial > repos > bgruening > padel

comparison PaDEL.xml @ 0:30c673b5b061 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/PaDEL commit dee96760dea60708d31899d4840191c1e67b5dc7"
author bgruening
date Tue, 20 Aug 2019 10:58:04 -0400
parents
children a84bcb007b09
comparison
equal deleted inserted replaced
-1:000000000000 0:30c673b5b061
1 <tool id="padel" name="PaDEL descriptor" version="2.21">
2 <description>calculator</description>
3 <requirements>
4 <requirement type="package" version="2.21">padel</requirement>
5 </requirements>
6 <command detect_errors="aggressive"><![CDATA[
7 ln -s '$input' ./molecule.${input.ext} &&
8
9 padel
10 $coordinate2d
11 $detectaromaticity
12 $removesalt
13 $standardizenitro
14 $convert3d
15 $retain3d
16 $coordinate3d
17 $fingerprint
18 -retainorder true
19 -file ./out.csv
20 -maxruntime 600000
21 -dir ./molecule.${input.ext}
22 &&
23
24 cat ./out.csv | tr "," "\\t" > '$descriptor'
25
26 ]]></command>
27 <inputs>
28 <param format="sdf,smi" name="input" type="data" label="SDF or SMILES file" optional= "false"/>
29
30 <param name="detectaromaticity" type="boolean" label="Detect aromaticity"
31 truevalue="-detectaromaticity" falsevalue="" checked="true" help="Remove existing aromaticity information in the molecule before calculation of descriptors."/>
32
33 <param name="removesalt" type="boolean" label="Remove salt"
34 truevalue="-removesalt" falsevalue="" checked="true" help="Remove salt from molecule(s). Choose No if you have already removed salt from the molecule yourself (recommended)."/>
35
36 <param name="standardizenitro" type="boolean" label="Standardize nitro groups"
37 truevalue="-standardizenitro" falsevalue="" checked="true" help="Standardize nitro groups to N(:O):O."/>
38
39 <param name="convert3d" type="boolean" label="Convert to 3D"
40 truevalue="-convert3d" falsevalue="" checked="false" help="Convert molecule to 3D representation."/>
41
42 <param name="coordinate2d" type="boolean" label="Calculate 2d descriptors"
43 truevalue="-2d" falsevalue="" checked="true" help="Calculate 1D and 2D descriptors."/>
44
45 <param name="retain3d" type="boolean" label="Retain 3D coordinates"
46 truevalue="-retain3d" falsevalue="" checked="false" help="Retain 3D coordinates when standardizing structure."/>
47
48 <param name="coordinate3d" type="boolean" label="Calculate 3d descriptors"
49 truevalue="-3d" falsevalue="" checked="false" help="Calculate 3D descriptors. To calculate 3D descriptors, the convert molecule to 3D option should be selected."/>
50
51 <param name="fingerprint" type="boolean" label="Calculate fingerprints"
52 truevalue="-fingerprints" falsevalue="" checked="true" help="Calculate molecular fingerprints."/>
53
54 </inputs>
55 <outputs>
56 <data format="csv" name="descriptor" label="PaDEL descriptor file for $input.name "/>
57 </outputs>
58 <tests>
59 <test>
60 <param name="input" value="test.sdf" ftype="sdf"/>
61 <param name="detectaromaticity" value="-detectaromaticity" />
62 <param name="removesalt" value="-removesalt" />
63 <param name="standardizenitro" value="-standardizenitro" />
64 <param name="convert3d" value="" />
65 <param name="retain3d" value="" />
66 <param name="maxruntime" value="600000" />
67 <param name="coordinate2d" value="-2d" />
68 <param name="coordinate3d" value="" />
69 <param name="fingerprint" value="" />
70 <param name="retainorder" value="-retainorder" />
71 <output name="descriptor">
72 <assert_contents>
73 <has_n_columns n="1445" />
74 <has_text text="3.735268" />
75 <has_text text="13.148254" />
76 <has_text text="0.38897" />
77 <has_text text="-0.00131" />
78 </assert_contents>
79 </output>
80 </test>
81 <test>
82 <param name="input" value="test.sdf" ftype="sdf"/>
83 <param name="detectaromaticity" value="-detectaromaticity" />
84 <param name="removesalt" value="-removesalt" />
85 <param name="standardizenitro" value="-standardizenitro" />
86 <param name="convert3d" value="" />
87 <param name="retain3d" value="" />
88 <param name="maxruntime" value="600000" />
89 <param name="coordinate2d" value="-2d" />
90 <param name="coordinate3d" value="" />
91 <param name="fingerprint" value="-fingerprints" />
92 <param name="retainorder" value="-retainorder" />
93 <output name="descriptor">
94 <assert_contents>
95 <has_n_columns n="2326" />
96 <has_text text="1.17828" />
97 <has_text text="2.77182" />
98 <has_text text="-1.06144" />
99 <has_text text="-5.91478" />
100 </assert_contents>
101 </output>
102 </test>
103 <test>
104 <param name="input" value="test.sdf" ftype="sdf"/>
105 <param name="detectaromaticity" value="" />
106 <param name="removesalt" value="-removesalt" />
107 <param name="standardizenitro" value="-standardizenitro" />
108 <param name="convert3d" value="" />
109 <param name="retain3d" value="" />
110 <param name="maxruntime" value="600000" />
111 <param name="coordinate2d" value="-2d" />
112 <param name="coordinate3d" value="" />
113 <param name="fingerprint" value="-fingerprints" />
114 <param name="retainorder" value="-retainorder" />
115 <output name="descriptor">
116 <assert_contents>
117 <has_n_columns n="2326" />
118 <has_text text="0.93896" />
119 <has_text text="2.85714" />
120 <has_text text="-33.59391" />
121 <has_text text="11.62754" />
122 </assert_contents>
123 </output>
124 </test>
125 </tests>
126 <help><![CDATA[
127
128 The PaDEL descriptor tool calculates different kinds of molecular descriptors and fingerprints, using the Chemistry Development Kit (CDK). Descriptors include atom type, electrotopological state descriptors, Crippen's logP and MR, extended topochemical atom (ETA) descriptors, McGowan volume, molecular linear free energy relation descriptors, ring counts, count of chemical substructures identified by Laggner, binary fingerprints and count of chemical substructures. For more details, please consult the cited publication.
129
130 -----
131
132 .. class:: infomark
133
134 **Input**
135
136 - SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file
137 - SMILES Format: http://www.molecular-networks.com/products/corina
138
139 -----
140
141 .. class:: infomark
142
143 **Output**
144 - Tabular file, where each descriptor (value) is shown in a separate column.
145
146 ]]></help>
147 <citations>
148 <citation type="bibtex">
149 @article{rdkit,
150 author = {Chun Wei Yap},
151 title = {PaDEL‐descriptor: An open source software to calculate molecular descriptors and fingerprints},
152 url ={https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.21707}
153 }</citation>
154 </citations>
155 </tool>