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comparison silicos_qed.xml @ 0:5ccd3a432785 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/qed commit 4379e712f76f2bb12ee2cc270dd8a0e806df2cd6
author bgruening
date Tue, 23 May 2017 03:57:14 -0400
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-1:000000000000 0:5ccd3a432785
1 <tool id="ctb_silicos_qed" name="Drug-likeness" version="0.1">
2 <description>quantitative estimation (QED)</description>
3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
4 <requirements>
5 <requirement type="package" version="2015.09.2">rdkit</requirement>
6 </requirements>
7 <command detect_errors="aggressive">
8 <![CDATA[
9 python '$__tool_directory__/qed.py'
10 -i '${infile}'
11 --method '${method}'
12 --iformat ${infile.ext}
13 -o '${outfile}'
14 $header
15 ]]>
16 </command>
17 <inputs>
18 <param format="smi,sdf" name="infile" type="data" label="Molecule data in SD- or SMILES-format" help="Dataset missing? See TIP below"/>
19 <param name="method" type="select" label="Method">
20 <option value="max">Max weight (QEDw,max)</option>
21 <option value="mean">Mean weight (QEDw,mo)</option>
22 <option value="unweighted">unweighted (QEDw,u)</option>
23 </param>
24 <param name="header" type="boolean" label="Include the descriptor name as header" truevalue="--header" falsevalue="" checked="false" />
25 </inputs>
26 <outputs>
27 <data format="tabular" name="outfile" />
28 </outputs>
29 <tests>
30 <!--
31 Test a tabular input with the first line being a comment without a # character to start
32 -->
33 <test>
34 <param name="infile" value="qed_test.smi" ftype="smi"/>
35 <param name="method" value="max"/>
36 <param name="header" value="True"/>
37 <output name="outfile" file="qed_test_max.tab" ftype="tabular"/>
38 </test>
39 <test>
40 <param name="infile" value="qed_test.smi" ftype="smi"/>
41 <param name="method" value="mean"/>
42 <param name="header" value="True"/>
43 <output name="outfile" file="qed_test_mean.tab" ftype="tabular"/>
44 </test>
45 <test>
46 <param name="infile" value="qed_test.smi" ftype="smi" />
47 <param name="method" value="unweighted"/>
48 <param name="header" value="True"/>
49 <output name="outfile" file="qed_test_unweighted.tab" ftype="tabular" />
50 </test>
51 </tests>
52 <help>
53 <![CDATA[
54
55 .. class:: infomark
56
57 **What this tool does**
58
59 Estimates the drug-likeness of molecules and reports a score. Comes with three applicable varieties (QED\ :sub:`w,mo`\ , QED\ :sub:`w,max`\ , QED\ :sub:`w,u` ).
60
61 -----
62
63 .. class:: warningmark
64
65 **HINT**
66
67 - All invalid, blank and comment lines are skipped when performing computations. The number of skipped lines is displayed in the resulting history item.
68
69 - QED\ :sub:`w,max` using the set of weights that give maximal information content
70
71 - QED\ :sub:`w,mo` using the mean weights of the optimal 1,000 weight combinations that give the highest information content
72
73 - QED\ :sub:`w,u` with all weights as unity, hence unweighted.
74
75 -----
76
77 .. class:: infomark
78
79 **Input**
80
81
82 | - `SD-Format`_
83 | - `SMILES Format`_
84
85 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
86 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
87
88 -----
89
90 .. class:: infomark
91
92 **Output**
93
94 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
95 | MW | ALOGP | HBA | HBD | PSA | ROTB | AROM | ALERTS | QED | NAME | Ro5 |
96 +========+=======+=====+=====+========+======+======+========+=======+================+=====+
97 | 286.34 | 1.092 | 6 | 3 | 101.88 | 4 | 2 | 1 | 0.737 | Abacavir | 0 |
98 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
99 | 181.21 | 0.481 | 4 | 2 | 83.47 | 5 | 0 | 2 | 0.487 | Acamprosate | 0 |
100 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
101 | 336.43 | 2.365 | 5 | 3 | 87.66 | 11 | 1 | 1 | 0.540 | Acebutolol | 0 |
102 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
103 | 151.16 | 1.351 | 2 | 2 | 49.33 | 2 | 1 | 1 | 0.633 | Acetaminophen | 0 |
104 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
105 | 222.25 | 0.225 | 5 | 2 | 115.04 | 3 | 1 | 1 | 0.727 | Acetazolamide | 0 |
106 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
107 | 324.40 | 3.291 | 4 | 2 | 92.34 | 6 | 1 | 1 | 0.772 | Acetohexamide | 0 |
108 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
109 | 411.57 | 3.492 | 6 | 1 | 47.02 | 7 | 2 | 1 | 0.688 | Acetophenazine | 0 |
110 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
111 | 329.37 | 3.327 | 4 | 1 | 39.72 | 4 | 2 | 0 | 0.917 | Paroxetine | 0 |
112 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
113 | 270.21 | 3.146 | 3 | 1 | 55.13 | 4 | 2 | 0 | 0.915 | Leflunomide | 0 |
114 +--------+-------+-----+-----+--------+------+------+--------+-------+----------------+-----+
115
116
117
118 ]]>
119 </help>
120 <citations>
121 <citation type="doi">10.1038/nchem.1243</citation>
122 </citations>
123 </tool>