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comparison chembl.xml @ 0:915e9be38994 draft

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planemo upload for repository https://github.com/chembl/chembl_webresource_client commit 2e3c3c2bd7ecdc9c2968a32f91e81136e0cb3835
author bgruening
date Mon, 05 Aug 2019 05:21:58 -0400
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children 6f8458d1cf46
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-1:000000000000 0:915e9be38994
1 <tool id="chembl" name="Search ChEMBL database" version="0.1.0">
2 <description>for compounds which are similar to a SMILES string</description>
3 <requirements>
4 <requirement type="package" version="0.9.31">chembl_webresource_client</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 python -W ignore '$__tool_directory__/chembl.py'
8 $input.format '$input.smiles'
9 -o $outfile
10 $search.type
11 #if $search.type == '-t':
12 $search.tanimoto
13 #end if
14 $drugs
15 $biotherapeutic
16 $natprod
17 $ro5
18 ]]></command>
19 <inputs>
20 <conditional name="input">
21 <param name='format' type='select' format='text' label="SMILES input type" help="Enter SMILES as either text or file.">
22 <option value='-i'>Text</option>
23 <option value='-f'>File</option>
24 </param>
25 <when value='-i'>
26 <param name="smiles" type="text" label="SMILES input" help="Enter SMILES for a compound.">
27 <validator type='length' min='5'/>
28 </param>
29 </when>
30 <when value='-f'>
31 <param name="smiles" type="data" format="smi" label="Input file" help="File containing a single compound in SMILES format. Note only the first line of the file will be read, if the file contains multiple compounds."/>
32 </when>
33 </conditional>
34
35 <conditional name="search">
36 <param name='type' type='select' format='text' label="Search type" help="Search for compounds are similar to the SMILES input, or which contain the SMILES input as a substructure">
37 <option value='-t'>Similarity</option>
38 <option value='-s'>Substructure</option>
39 </param>
40 <when value="-t">
41 <param type="integer" name="tanimoto" label="Tanimoto cutoff score" help="Score for similarity search. Minimum value is 70." value="70" min="70" max="100"/>
42 </when>
43 <when value="-s"/>
44 </conditional>
45
46 <param name="drugs" type="boolean" value="false" label="Filter to return only approved drugs" truevalue="-d" falsevalue=""/>
47 <param name="biotherapeutic" type="boolean" value="false" label="Filter to return only biotherapeutic molecules" truevalue="-b" falsevalue=""/>
48 <param name="natprod" type="boolean" value="false" label="Filter to return only natural products" truevalue="-n" falsevalue=""/>
49 <param name="ro5" type="boolean" value="false" label="Filter for Lipinski's Rule of Five" truevalue="-r" falsevalue=""/>
50 </inputs>
51 <outputs>
52 <data name="outfile" format="smi" />
53 </outputs>
54 <tests>
55 <test>
56 <param name="format" value="-f"/>
57 <param name="smiles" value="in1.smi"/>
58 <param name='type' value='-t' />
59 <param name='tanimoto' value='70' />
60 <output name="outfile" ftype="smi" file='out1.smi'/>
61 </test>
62 <test>
63 <param name="format" value="-f"/>
64 <param name="smiles" value="in1.smi"/>
65 <param name='type' value='-t' />
66 <param name='tanimoto' value='70' />
67 <param name='drugs' value='true'/>
68 <output name="outfile" ftype="smi" file='out2.smi'/>
69 </test>
70 <test>
71 <param name="format" value="-f"/>
72 <param name="smiles" value="in1.smi"/>
73 <param name='type' value='-s' />
74 <output name="outfile" ftype="smi" file='out3.smi'/>
75 </test>
76 <test>
77 <param name="format" value="-i"/>
78 <param name="smiles" value="C1CCCCC1"/>
79 <param name='type' value='-t' />
80 <param name='tanimoto' value='70' />
81 <output name="outfile" ftype="smi" file='out4.smi'/>
82 </test>
83 </tests>
84 <help><![CDATA[
85
86 Search the ChEMBL database for compounds which resemble a SMILES string. Two
87 search options are possible: similarity (searches for compounds which are
88 similar to the input within a specified Tanimoto cutoff) and substructure
89 (searches for compounds which contain the input substructure).
90
91 Results can be filtered for compounds which are 1) approved drugs 2) biotherapeutic
92 3) natural products and 4) fulfil all of the Lipinski rule of five criteria.
93
94 -----
95
96 .. class:: infomark
97
98 **Input**
99
100 A single molecule in SMILES format. This can be submitted either as text or as a
101 file containing the SMILES string on the first line. Note that if the file contains
102 multiple lines, only the SMILES string on the first line will be used for the search.
103
104 -----
105
106 .. class:: infomark
107
108 **Output**
109
110 A SMILES file with search results, each on a new line.
111
112 ]]></help>
113
114 <citations>
115 <citation type="doi">10.1093/nar/gkv352</citation>
116 <citation type="doi">arXiv:1607.00378v1</citation>
117 </citations>
118 </tool>