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comparison mol2fps.xml @ 38:02e03ac072cf draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:19:01 -0400
parents 73b8c87779ae
children 0a1c281e9224
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37:ea7557bd4635 38:02e03ac072cf
1 <tool id="ctb_chemfp_mol2fps" name="Molecules to Fingerprints" version="0.3.0"> 1 <tool id="ctb_chemfp_mol2fps" name="Molecule to fingerprint" version="1.5">
2 <description>with different fingerprint types</description> 2 <description>conversion to several different fingerprint formats</description>
3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" merge_outputs="outfile"></parallelism--> 3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" merge_outputs="outfile"></parallelism-->
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.1p1">chemfp</requirement> 5 <requirement type="package" version="1.5">chemfp</requirement>
6 <requirement type="package" version="2016.03.3">rdkit</requirement> 6 <requirement type="package" version="2018.09.3">rdkit</requirement>
7 <requirement type="package" version="2.4.1">openbabel</requirement> 7 <requirement type="package" version="2.4.1">openbabel</requirement>
8 </requirements> 8 </requirements>
9 <command> 9 <command>
10 <![CDATA[ 10 <![CDATA[
11 #set $fptype = $fp_opts.fp_opts_selector 11
12 12 #if $fp_opts.fp_opts_selector in ['--FP2', '--FP3', '--FP4', '--MACCS']:
13 #if $fptype in ['--FP2', '--FP3', '--FP4', '--MACCS']:
14 ## Open Babel fingerprints 13 ## Open Babel fingerprints
15 ob2fps $fptype --in '${infile.ext}' '${infile}' -o '${outfile}' 14 ob2fps $fp_opts.fp_opts_selector --in '${infile.ext}' '${infile}' -o '${outfile}' --out 'fps'
16 #else: 15 #else:
17 ## RDKit fingerprints 16 ## RDKit fingerprints
18 rdkit2fps --in '${infile.ext}' '${infile}' -o '${outfile}' 17 rdkit2fps --in '${infile.ext}' '${infile}' -o '${outfile}' --out 'fps'
19 #if $fp_opts.fp_opts_selector == "--RDK": 18 #if $fp_opts.fp_opts_selector == "--RDK":
20 --RDK 19 --RDK
21 --fpSize $fp_opts.fpSize 20 --fpSize $fp_opts.fpSize
22 --minPath $fp_opts.minPath 21 --minPath $fp_opts.minPath
23 --maxPath $fp_opts.maxPath 22 --maxPath $fp_opts.maxPath
33 --radius $fp_opts.radius 32 --radius $fp_opts.radius
34 $fp_opts.useFeatures 33 $fp_opts.useFeatures
35 $fp_opts.useChirality 34 $fp_opts.useChirality
36 $fp_opts.useBondTypes 35 $fp_opts.useBondTypes
37 #elif $fp_opts.fp_opts_selector == "--pairs": 36 #elif $fp_opts.fp_opts_selector == "--pairs":
38 --paris 37 --pairs
39 --fpSize $fp_opts.fpSize 38 --fpSize $fp_opts.fpSize
40 --minLength $fp_opts.minLength 39 --minLength $fp_opts.minLength
41 --maxLength $fp_opts.maxLength 40 --maxLength $fp_opts.maxLength
42 #elif $fp_opts.fp_opts_selector == "--maccs166": 41 #elif $fp_opts.fp_opts_selector == "--maccs166":
43 --maccs166 42 --maccs166
47 #end if 46 #end if
48 --errors report 2>&1 47 --errors report 2>&1
49 ]]> 48 ]]>
50 </command> 49 </command>
51 <inputs> 50 <inputs>
52 <param name="infile" type='data' format="sdf,smi,mol,mol2,cml,inchi" label="molecule file"/> 51 <param name="infile" type='data' format="sdf,smi,mol,mol2,cml,inchi" label="Molecule file"/>
53 <conditional name="fp_opts"> 52 <conditional name="fp_opts">
54 <param name="fp_opts_selector" type="select" label="Type of fingerprint"> 53 <param name="fp_opts_selector" type="select" label="Type of fingerprint">
55 <option value='--FP2' selected="True">Open Babel FP2 fingerprints</option> 54 <option value='--FP2' selected="True">Open Babel FP2 fingerprints</option>
56 <option value='--FP3'>Open Babel FP3 fingerprints</option> 55 <option value='--FP3'>Open Babel FP3 fingerprints</option>
57 <option value='--FP4'>Open Babel FP4 fingerprints</option> 56 <option value='--FP4'>Open Babel FP4 fingerprints</option>
66 <when value="--FP2" /> 65 <when value="--FP2" />
67 <when value="--FP3" /> 66 <when value="--FP3" />
68 <when value="--FP4" /> 67 <when value="--FP4" />
69 <when value="--MACCS" /> 68 <when value="--MACCS" />
70 <when value="--RDK"> 69 <when value="--RDK">
71 <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help=""> 70 <param name="fpSize" type="integer" value="2048" label="Number of bits in the fingerprint" help="">
72 <validator type="in_range" min="1" /> 71 <validator type="in_range" min="1" />
73 </param> 72 </param>
74 <param name="minPath" type="integer" value="1" label="minimum number of bonds to include in the subgraph" help=""> 73 <param name="minPath" type="integer" value="1" label="Minimum number of bonds to include in the subgraph" help="">
75 <validator type="in_range" min="1" /> 74 <validator type="in_range" min="1" />
76 </param> 75 </param>
77 <param name="maxPath" type="integer" value="7" label="maximum number of bonds to include in the subgraph" help=""> 76 <param name="maxPath" type="integer" value="7" label="Maximum number of bonds to include in the subgraph" help="">
78 <validator type="in_range" min="1" /> 77 <validator type="in_range" min="1" />
79 </param> 78 </param>
80 <param name="nBitsPerHash" type="integer" value="4" label="number of bits to set per path" help=""> 79 <param name="nBitsPerHash" type="integer" value="4" label="Number of bits to set per path" help="">
81 <validator type="in_range" min="1" /> 80 <validator type="in_range" min="1" />
82 </param> 81 </param>
83 <param name="useHs" type="boolean" truevalue="--useHs 1" falsevalue="--useHs 0" checked="true" 82 <param name="useHs" type="boolean" truevalue="--useHs 1" falsevalue="--useHs 0" checked="true"
84 label="include information about the number of hydrogens on each atom" /> 83 label="Include information about the number of hydrogens on each atom" />
85 </when> 84 </when>
86 <when value="--torsions"> 85 <when value="--torsions">
87 <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help=""> 86 <param name="fpSize" type="integer" value="2048" label="Number of bits in the fingerprint" help="">
88 <validator type="in_range" min="1" /> 87 <validator type="in_range" min="1" />
89 </param> 88 </param>
90 <param name="targetSize" type="integer" value="4" label="number of target bits in the fingerprint" help=""> 89 <param name="targetSize" type="integer" value="4" label="Number of target bits in the fingerprint" help="">
91 <validator type="in_range" min="1" /> 90 <validator type="in_range" min="1" />
92 </param> 91 </param>
93 </when> 92 </when>
94 <when value="--morgan"> 93 <when value="--morgan">
95 <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help=""> 94 <param name="fpSize" type="integer" value="2048" label="Number of bits in the fingerprint" help="">
96 <validator type="in_range" min="1" /> 95 <validator type="in_range" min="1" />
97 </param> 96 </param>
98 <param name="radius" type="integer" value="2" label="radius for the Morgan algorithm" help=""> 97 <param name="radius" type="integer" value="2" label="Radius for the Morgan algorithm" help="">
99 <validator type="in_range" min="1" /> 98 <validator type="in_range" min="1" />
100 </param> 99 </param>
101 <param name="useFeatures" type="boolean" truevalue="--useFeatures 1" falsevalue="--useFeatures 0" checked="false" 100 <param name="useFeatures" type="boolean" truevalue="--useFeatures 1" falsevalue="--useFeatures 0" checked="false"
102 label="include information about the number of hydrogens on each atom" /> 101 label="Include information about the number of hydrogens on each atom" />
103 <param name="useChirality" type="boolean" truevalue="--useChirality 1" falsevalue="--useChirality 0" checked="false" 102 <param name="useChirality" type="boolean" truevalue="--useChirality 1" falsevalue="--useChirality 0" checked="false"
104 label="include information about the number of hydrogens on each atom" /> 103 label="Include information about the number of hydrogens on each atom" />
105 <param name="useBondTypes" type="boolean" truevalue="--useBondTypes 1" falsevalue="--useBondTypes 0" checked="true" 104 <param name="useBondTypes" type="boolean" truevalue="--useBondTypes 1" falsevalue="--useBondTypes 0" checked="true"
106 label="include information about the number of hydrogens on each atom" /> 105 label="Include information about the number of hydrogens on each atom" />
107 </when> 106 </when>
108 <when value="--pairs"> 107 <when value="--pairs">
109 <param name="fpSize" type="integer" value="2048" label="number of bits in the fingerprint" help=""> 108 <param name="fpSize" type="integer" value="2048" label="Number of bits in the fingerprint" help="">
110 <validator type="in_range" min="1" /> 109 <validator type="in_range" min="1" />
111 </param> 110 </param>
112 <param name="minLength" type="integer" value="1" label="minimum bond count for a pair" help=""> 111 <param name="minLength" type="integer" value="1" label="Minimum bond count for a pair" help="">
113 <validator type="in_range" min="1" /> 112 <validator type="in_range" min="1" />
114 </param> 113 </param>
115 <param name="maxLength" type="integer" value="30" label="maximum bond count for a pair" help=""> 114 <param name="maxLength" type="integer" value="30" label="Maximum bond count for a pair" help="">
116 <validator type="in_range" min="1" /> 115 <validator type="in_range" min="1" />
117 </param> 116 </param>
118 </when> 117 </when>
119 <when value="--maccs166" /> 118 <when value="--maccs166" />
120 <when value="--substruct" /> 119 <when value="--substruct" />
126 </outputs> 125 </outputs>
127 <tests> 126 <tests>
128 <!-- FP2 --> 127 <!-- FP2 -->
129 <test> 128 <test>
130 <param name="infile" value="CID_2244.sdf" ftype="sdf" /> 129 <param name="infile" value="CID_2244.sdf" ftype="sdf" />
131 <param name="fp_opts.fp_opts_selector" value="--FP2" /> 130 <conditional name="fp_opts">
131 <param name="fp_opts_selector" value="--FP2" />
132 </conditional>
132 <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" lines_diff="4"/> 133 <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" lines_diff="4"/>
133 </test> 134 </test>
134 <test> 135 <test>
135 <param name="infile" value="CID_2244.smi" ftype="smi" /> 136 <param name="infile" value="CID_2244.smi" ftype="smi" />
136 <param name="fp_opts.fp_opts_selector" value="--FP2" /> 137 <conditional name="fp_opts">
138 <param name="fp_opts_selector" value="--FP2" />
139 </conditional>
137 <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" lines_diff="4"/> 140 <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" lines_diff="4"/>
138 </test> 141 </test>
139 <!-- FP3 --> 142 <!-- FP3 -->
140 <test> 143 <test>
141 <param name="infile" value="CID_2244.sdf" ftype="sdf" /> 144 <param name="infile" value="CID_2244.sdf" ftype="sdf" />
142 <param name="fp_opts.fp_opts_selector" value="--FP3" /> 145 <conditional name="fp_opts">
146 <param name="fp_opts_selector" value="--FP3" />
147 </conditional>
143 <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" lines_diff="4"/> 148 <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" lines_diff="4"/>
144 </test> 149 </test>
145 <test> 150 <test>
146 <param name="infile" value="CID_2244.smi" ftype="smi" /> 151 <param name="infile" value="CID_2244.smi" ftype="smi" />
147 <param name="fp_opts.fp_opts_selector" value="--FP3" /> 152 <conditional name="fp_opts">
153 <param name="fp_opts_selector" value="--FP3" />
154 </conditional>
148 <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" lines_diff="4"/> 155 <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" lines_diff="4"/>
149 </test> 156 </test>
150 <!-- FP4 --> 157 <!-- FP4 -->
151 <test> 158 <test>
152 <param name="infile" value="CID_2244.sdf" ftype="sdf" /> 159 <param name="infile" value="CID_2244.sdf" ftype="sdf" />
153 <param name="fp_opts.fp_opts_selector" value="--FP4" /> 160 <conditional name="fp_opts">
161 <param name="fp_opts_selector" value="--FP4" />
162 </conditional>
154 <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" lines_diff="4"/> 163 <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" lines_diff="4"/>
155 </test> 164 </test>
156 <test> 165 <test>
157 <param name="infile" value="CID_2244.smi" ftype="smi" /> 166 <param name="infile" value="CID_2244.smi" ftype="smi" />
158 <param name="fp_opts.fp_opts_selector" value="--FP4" /> 167 <conditional name="fp_opts">
168 <param name="fp_opts_selector" value="--FP4" />
169 </conditional>
159 <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" lines_diff="4"/> 170 <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" lines_diff="4"/>
160 </test> 171 </test>
161 <!-- MACCS --> 172 <!-- MACCS -->
162 <test> 173 <test>
163 <param name="infile" value="CID_2244.sdf" ftype="sdf" /> 174 <param name="infile" value="CID_2244.sdf" ftype="sdf" />
164 <param name="fp_opts.fp_opts_selector" value="--MACCS" /> 175 <conditional name="fp_opts">
176 <param name="fp_opts_selector" value="--MACCS" />
177 </conditional>
165 <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" lines_diff="4"/> 178 <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" lines_diff="4"/>
166 </test> 179 </test>
167 <test> 180 <test>
168 <param name="infile" value="CID_2244.smi" ftype="smi" /> 181 <param name="infile" value="CID_2244.smi" ftype="smi" />
169 <param name="fp_opts.fp_opts_selector" value="--MACCS" /> 182 <conditional name="fp_opts">
183 <param name="fp_opts_selector" value="--MACCS" />
184 </conditional>
170 <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" lines_diff="4"/> 185 <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" lines_diff="4"/>
186 </test>
187 <!-- RDKit2fps -->
188 <test>
189 <param name="infile" value="CID_2244.smi" ftype="smi" />
190 <conditional name="fp_opts">
191 <param name="fp_opts_selector" value="--torsions" />
192 </conditional>
193 <param name="fp_opts.fpSize" value="2048" />
194 <param name="fp_opts.targetSize" value="4" />
195 <output name="outfile" file="CID_2244_torsions.fps" ftype="fps" lines_diff="4"/>
171 </test> 196 </test>
172 </tests> 197 </tests>
173 <help> 198 <help>
174 <![CDATA[ 199 <![CDATA[
175 200
176 .. class:: infomark 201 .. class:: infomark
177 202
178 **What this tool does** 203 **What this tool does**
179 204
180 This tool uses chemfp_ to calculate 10 different fingerprints of common file formats. Chemfp uses `Open Babel`_, OpenEye_ and RDKit_. 205 This tool uses chemfp to calculate molecular fingerprints, supporting a number of common file formats. Chemfp uses OpenBabel, OpenEye and RDKit.
181 206
182 For more information check the websites listed below:: 207 For more information check the websites listed below::
183 208
184 - http://www.rdkit.org/docs/GettingStartedInPython.html#fingerprinting-and-molecular-similarity 209 - http://www.rdkit.org/docs/GettingStartedInPython.html#fingerprinting-and-molecular-similarity
185 - http://openbabel.org/wiki/Tutorial:Fingerprints 210 - http://openbabel.org/wiki/Tutorial:Fingerprints
192 217
193 FPS fingerprint file format 218 FPS fingerprint file format
194 219
195 * Example:: 220 * Example::
196 221
197 - SDF File 222 - SD-File
198 223
199 28434379 224 28434379
200 -OEChem-02031205132D 225 -OEChem-02031205132D
201 226
202 37 39 0 0 0 0 0 0 0999 V2000 227 37 39 0 0 0 0 0 0 0999 V2000