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comparison ob_filter.xml @ 10:da03b00048b1 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
author bgruening
date Sat, 21 Mar 2020 10:26:39 -0400
parents 0e382252d23d
children 340f8d63c1f4
comparison
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9:a9ea2eac7300 10:da03b00048b1
1 <tool id="openbabel_filter" name="Filter" version="@VERSION@.0"> 1 <tool id="openbabel_filter" name="Filter" version="@VERSION@.1">
2 <description> a set of molecules from a file</description> 2 <description> a set of molecules from a file</description>
3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism--> 3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
8 <command detect_errors="aggressive"> 8 <command detect_errors="aggressive">
9 <![CDATA[ 9 <![CDATA[
10 python '$__tool_directory__/ob_filter.py' 10 python '$__tool_directory__/ob_filter.py'
11 -i '${infile}' 11 -i '${infile}'
12 -o '${outfile}' 12 -o '${outfile}'
13 -iformat "${infile.ext}" 13 -iformat '${infile.ext}'
14 -oformat "${infile.ext}" 14 -oformat '${infile.ext}'
15 --filters '{ 15 #if $filter_methods.filter_methods_opts == "__filter_by_name__":
16 #if $filter_methods.filter_methods_opts == "ruleof5": 16 --list_of_names '$name_file'
17 "hbd" : [0, 5], 17 --filters '__filter_by_name__'
18 "hba" : [0, 10], 18 #else
19 "molwt" : [0, 500], 19 --filters '{
20 "logp" : [-5, 5], 20 #if $filter_methods.filter_methods_opts == "ruleof5":
21 #elif $filter_methods.filter_methods_opts == "LeadLike": 21 "hbd" : [0, 5],
22 "rotbonds" : [0, 7], 22 "hba" : [0, 10],
23 "molwt" : [0, 350], 23 "molwt" : [0, 500],
24 "logp" : [-5, 3.5], 24 "logp" : [-5, 5],
25 #elif $filter_methods.filter_methods_opts == "DrugLike": 25 #elif $filter_methods.filter_methods_opts == "LeadLike":
26 "hba" : [0, 10], 26 "rotbonds" : [0, 7],
27 "rotbonds" : [0, 8], 27 "molwt" : [0, 350],
28 "molwt" : [150, 500], 28 "logp" : [-5, 3.5],
29 "logp" : [-5, 5], 29 #elif $filter_methods.filter_methods_opts == "DrugLike":
30 "psa" : [0, 150], 30 "hba" : [0, 10],
31 #elif $filter_methods.filter_methods_opts == "FragmentLike": 31 "rotbonds" : [0, 8],
32 "rotbonds" : [0, 5], 32 "molwt" : [150, 500],
33 "molwt" : [0, 250], 33 "logp" : [-5, 5],
34 "logp" : [-5, 2.5], 34 "psa" : [0, 150],
35 #else: 35 #elif $filter_methods.filter_methods_opts == "FragmentLike":
36 #for $filter in $filter_methods.filter_set: 36 "rotbonds" : [0, 5],
37 #set $filter_selected = $filter.filter_sel.filter_sel_opts 37 "molwt" : [0, 250],
38 #set $filter_min = $filter_selected + "_min" 38 "logp" : [-5, 2.5],
39 #set $filter_max = $filter_selected + "_max" 39 #else:
40 "$filter_selected" : [$filter.filter_sel[$filter_min], $filter.filter_sel[$filter_max] ], 40 #for $filter in $filter_methods.filter_set:
41 #end for 41 #set $filter_selected = $filter.filter_sel.filter_sel_opts
42 #set $filter_min = $filter_selected + "_min"
43 #set $filter_max = $filter_selected + "_max"
44 "$filter_selected" : [$filter.filter_sel[$filter_min], $filter.filter_sel[$filter_max] ],
45 #end for
46 #end if
47 }'
42 #end if 48 #end if
43 }'
44 ]]> 49 ]]>
45 </command> 50 </command>
46 <inputs> 51 <inputs>
47 <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi" 52 <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi"
48 label="Select input file (can be previously annotated with the 'Compute physico-chemical properties' tool)"/> 53 label="Select input file (can be previously annotated with the 'Compute physico-chemical properties' tool)"/>
51 <option value="user">User-defined properties</option> 56 <option value="user">User-defined properties</option>
52 <option value="ruleof5">Lipinski's Rule-of-Five</option> 57 <option value="ruleof5">Lipinski's Rule-of-Five</option>
53 <option value="LeadLike">Lead-like properties</option> 58 <option value="LeadLike">Lead-like properties</option>
54 <option value="DrugLike">Drug-like properties</option> 59 <option value="DrugLike">Drug-like properties</option>
55 <option value="FragmentLike">Fragment-like properties</option> 60 <option value="FragmentLike">Fragment-like properties</option>
61 <option value="__filter_by_name__">Filter by molecule name</option>
56 </param> 62 </param>
63 <when value="__filter_by_name__">
64 <param name="name_file" type="data" format="txt,tabular"
65 label="File with molecule names that match the names in the SDF file" help="Every name one line."/>
66 </when>
57 <when value="ruleof5" /> 67 <when value="ruleof5" />
58 <when value="LeadLike" /> 68 <when value="LeadLike" />
59 <when value="DrugLike" /> 69 <when value="DrugLike" />
60 <when value="FragmentLike" /> 70 <when value="FragmentLike" />
61 <when value="user"> 71 <when value="user">
119 <outputs> 129 <outputs>
120 <expand macro="output_like_input"/> 130 <expand macro="output_like_input"/>
121 </outputs> 131 </outputs>
122 <tests> 132 <tests>
123 <test> 133 <test>
134 <param name="infile" value="ligands_with_title.sdf" ftype="sdf" />
135 <param name="filter_methods_opts" value="__filter_by_name__" />
136 <param name="name_file" value="name_file.txt" />
137 <output name="outfile" file="filterd_by_name.sdf" ftype="sdf" lines_diff="4" />
138 </test>
139 <test>
124 <param name="infile" ftype="smi" value="CID_2244.smi"/> 140 <param name="infile" ftype="smi" value="CID_2244.smi"/>
125 <param name="filter_methods_opts" value="ruleof5" /> 141 <param name="filter_methods_opts" value="ruleof5" />
126 <output name="outfile" ftype="smi" file="ob_filter_on_CID2244.smi" /> 142 <output name="outfile" ftype="smi" file="ob_filter_on_CID2244.smi" />
127 </test> 143 </test>
128 <!-- 144 <!--