Mercurial > repos > bgruening > ctb_im_screen

comparison screen.xml @ 0:2c11d1f9e00b draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
author bgruening
date Tue, 21 Jul 2020 05:22:46 -0400
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-1:000000000000 0:2c11d1f9e00b
1 <tool id="ctb_im_screen" name="Screen" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <description>a compound against a library using RDKit</description>
3 <macros>
4 <import>macros.xml</import>
5 <token name="@GALAXY_VERSION@">0</token>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[
9 screen
10 #if $comparator.comparator_opts == 'str':
11 --qsmiles '${comparator.input}'
12 #else:
13 --qmolfile ${comparator.input}
14 #end if
15
16 -i '$infile'
17 -if sdf
18 #if $comparator.comparator_opts == 'mol'
19 --isMol
20 #end if
21 #if $fragment_opts
22 -f '$fragment_opts'
23 #end if
24 --simmin '$sim_min'
25 --simmax '$sim_max'
26 -d '$descriptor_opts'
27 -m '$metric_opts'
28 #if $hac_min != ''
29 --hacmin '$hac_min'
30 #end if
31 #if $hac_max != ''
32 --hacmax '$hac_max'
33 #end if
34 #if $mw_min != ''
35 --mwmin '$mw_min'
36 #end if
37 #if $mw_max != ''
38 --mwmax '$mw_max'
39 #end if
40 --meta
41 -o outp &>> $logfile && ## the script does not exit 0
42 cat outp_metrics.txt &>> $logfile &&
43 gzip -d outp.sdf.gz
44 ]]></command>
45 <inputs>
46 <conditional name="comparator">
47 <param name='comparator_opts' type='select' label="Input type" help="Enter SMILES string or Mol file.">
48 <option value='file'>Mol/SDF file</option>
49 <option value='str'>SMILES string</option>
50 </param>
51 <when value='str'>
52 <param name="input" type="text" label="SMILES input" help="Enter SMILES for a compound.">
53 <validator type='length' min='5'/>
54 </param>
55 </when>
56 <when value='file'>
57 <param name="input" type="data" format="sdf,mol" label="Input" help="Input file in mol/sdf format"/>
58 </when>
59 </conditional>
60 <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF or JSON format, for comparison"/>
61 <param name="sim_min" type="float" label="Similarity lower cutoff" value="0.7" min="0" max="1" help="(1.0 means identical)"/>
62 <param name="sim_max" type="float" label="Similarity upper cutoff" value="1.0" min="0" max="1" help="(1.0 means identical)"/>
63 <param name="descriptor_opts" type="select" label="Type of descriptor or fingerprint" help="Default is rdkit">
64 <option value="rdkit" selected="true">rdkit</option>
65 <option value="maccs">maccs</option>
66 <option value="morgan2">morgan2</option>
67 <option value="morgan3">morgan3</option>
68 </param>
69 <param name="metric_opts" type="select" label="Similarity metric" help="Default is the Tanimoto coefficient">
70 <option value="tanimoto" selected="true">tanimoto</option>
71 <option value="asymmetric">asymmetric</option>
72 <option value="braunblanquet">braunblanquet</option>
73 <option value="cosine">cosine</option>
74 <option value="dice">dice</option>
75 <option value="kulczynski">kulczynski</option>
76 <option value="mcconnaughey">mcconnaughey</option>
77 <option value="rogotgoldberg">rogotgoldberg</option>
78 <option value="russel">russel</option>
79 <option value="sokal">sokal</option>
80 </param>
81 <param name="fragment_opts" type="select" optional="true" label="Find single fragment" help="Find single fragment if more than one (hac = biggest by heavy atom count, mw = biggest by mol weight )">
82 <option value="hac">Biggest by heavy atom count</option>
83 <option value="mw">Biggest by molecular weight</option>
84 </param>
85 <param name="hac_min" type="integer" optional="true" label="Minimum heavy atom count" help="Minimum number of heavy atoms for a candidate to pass screening"/>
86 <param name="hac_max" type="integer" optional="true" label="Maximum heavy atom count" help="Maximum number of heavy atoms for a candidate to pass screening"/>
87 <param name="mw_min" type="float" optional="true" label="Minimum molecular weight" help="Minimum molecular weight for a candidate to pass screening"/>
88 <param name="mw_max" type="float" optional="true" label="Maximum molecular weight" help="Maximum molecular weight for a candidate to pass screening"/>
89 </inputs>
90
91 <expand macro="outputs" />
92
93 <tests>
94 <test>
95 <param name='comparator_opts' value="str"/>
96 <param name="input" value="C1N=C(C2=CC=CC=C2)C2=CC=CC=C2C2=C1C=NC(NC1=CC=CC=C1)=N2"/>
97 <param name="infile" value="dhfr_3d.sdf" ftype="sdf"/>
98 <param name="descriptor_opts" value="rdkit" />
99 <param name="metric_opts" value="tanimoto" />
100 <param name="sim_min" value="0.45" />
101 <param name="sim_max" value="1.0" />
102 <output name="outfile" ftype='sdf' file="screen_output1.sdf"/>
103 </test>
104 <test>
105 <param name='comparator_opts' value="file"/>
106 <param name="input" value="pyrimethamine.mol" ftype="mol"/>
107 <param name="infile" value="dhfr_3d.sdf" ftype="sdf"/>
108 <param name="descriptor_opts" value="rdkit" />
109 <param name="metric_opts" value="tanimoto" />
110 <param name="sim_min" value="0.7" />
111 <param name="sim_max" value="0.8" />
112 <output name="outfile" ftype='sdf' file="screen_output2.sdf"/>
113 </test>
114 </tests>
115 <help><![CDATA[
116
117 .. class:: infomark
118
119 **What this tool does**
120
121 Screen a library against a compound, filtering by fingerprint similarity and a number of other properties.
122
123 .. class:: infomark
124
125 **Input**
126
127 | - Compound library in `SDF Format`_
128 | - Compound to screen against in `SMILES`_ or `SDF Format`_
129 | - Type of fingerprint
130 | - Required molecular weight and heavy atom count
131
132 .. _SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file
133 .. _SMILES: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
134
135 -----
136
137 .. class:: infomark
138
139 **Output**
140
141 SD-file of screened compounds, with new 'Similarity' property.
142
143 ]]></help>
144 <expand macro="citations" />
145 </tool>