Mercurial > repos > bgruening > openbabel_filter
comparison ob_filter.xml @ 10:da03b00048b1 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
author | bgruening |
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date | Sat, 21 Mar 2020 10:26:39 -0400 |
parents | 0e382252d23d |
children | 340f8d63c1f4 |
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9:a9ea2eac7300 | 10:da03b00048b1 |
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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 <!-- |