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comparison ob_grep.xml @ 6:99517f9b780d draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:33:55 -0400
parents b0311f002a5f
children 78640d0127ce
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5:50dc8ca09a50 6:99517f9b780d
1 <tool id="openbabel_obgrep" name="Compound Search" version="@VERSION@.0"> 1 <tool id="openbabel_obgrep" name="Compound search" version="@VERSION@.0">
2 <description>an advanced molecular grep program using SMARTS</description> 2 <description>- an advanced molecular search program using SMARTS</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>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 obgrep 10
11 $invert_matches 11 #if $input_type.inp == 'single':
12 #if $n_times: 12 obgrep
13 -t $n_times 13 $invert_matches
14 #end if 14 #if $n_times:
15 $only_name 15 -t $n_times
16 $full_match 16 #end if
17 $number_of_matches 17 $only_name
18 -i '${infile.ext}' 18 $full_match
19 '${smarts_pattern}' 19 $number_of_matches
20 '${infile}' 20 -i '${infile.ext}'
21 > '${outfile}' 21 '${input_type.smarts_pattern}'
22 '${infile}'
23 > '${outfile}'
24 #else if $input_type.inp == 'multi':
25 python '$__tool_directory__/multi_obgrep.py'
26 -i $infile
27 --iformat ${infile.ext}
28 -q '${input_type.query}'
29 -o '${outfile}'
30 $invert_matches
31 --n-times $n_times
32 $only_name
33 $full_match
34 $number_of_matches
35 --processors "\${GALAXY_SLOTS:-12}"
36 #end if
37
22 ]]> 38 ]]>
23 </command> 39 </command>
24 <inputs> 40 <inputs>
25 <expand macro="infile_all_types"/> 41 <expand macro="infile_all_types"/>
26 <param name="smarts_pattern" type="text" format="text" label="SMARTS Pattern" help="Specify a SMARTS Pattern for your search."/> 42 <conditional name="input_type">
27 <param name="invert_matches" type="boolean" label="Invert the matching, print non-matching molecules" truevalue="-v" falsevalue="" checked="false" /> 43 <param name="inp" type="select" label="Input">
28 <param name="n_times" type="integer" value="" min="1" optional="True" 44 <option value="single">Enter a single SMARTS pattern</option>
29 label="Print a molecule only if the pattern occurs # times inside the molecule" /> 45 <option value="multi">Upload one or more SMARTS patterns in a text file</option>
46 </param>
47 <when value="single">
48 <param name="smarts_pattern" type="text" format="text" label="SMARTS Pattern" help="Specify a SMARTS Pattern for your search."/>
49 </when>
50 <when value="multi">
51 <param name="query" type='data' format="tabular,text" label="Query file" help="One SMARTS pattern in each line."/>
52 </when>
53 </conditional>
54 <param name="invert_matches" type="boolean" label="Perform an inverted search, i.e. print non-matching molecules" truevalue="-v" falsevalue="" checked="false" />
55 <param name="n_times" type="integer" value="0" min="0" optional="True"
56 label="Print a molecule only if the pattern occurs this often inside the molecule" />
30 <param name="only_name" type="boolean" label="Only print the name of the molecules" truevalue="-n" falsevalue="" checked="false" /> 57 <param name="only_name" type="boolean" label="Only print the name of the molecules" truevalue="-n" falsevalue="" checked="false" />
31 <param name="full_match" type="boolean" label="Full match, print matching-molecules only when the number of heavy atoms is also equal to the number of atoms in the SMARTS pattern" truevalue="-f" falsevalue="" checked="false" /> 58 <param name="full_match" type="boolean" label="Full match" help="Print matching molecules only when the number of heavy atoms equals the number of atoms in the SMARTS pattern" truevalue="-f" falsevalue="" checked="false" />
32 <param name="number_of_matches" type="boolean" label="Print the number of matches" truevalue="-c" falsevalue="" checked="false" /> 59 <param name="number_of_matches" type="boolean" label="Print the number of matches" truevalue="-c" falsevalue="" checked="false" />
33 </inputs> 60 </inputs>
34 <options sanitize="False"/> 61 <options sanitize="False"/>
35 <outputs> 62 <outputs>
36 <expand macro="output_like_input"/> 63 <expand macro="output_like_input"/>
37 </outputs> 64 </outputs>
38 <tests> 65 <tests>
39 <test> 66 <test>
40 <param name="infile" ftype="smi" value="8_mol.smi"/> 67 <param name="infile" ftype="smi" value="8_mol.smi"/>
68 <param name="inp" value="single"/>
41 <param name="smarts_pattern" value="CO"/> 69 <param name="smarts_pattern" value="CO"/>
42 <param name="invert_matches" value="False" /> 70 <param name="invert_matches" value="False" />
43 <param name="only_name" value="False" /> 71 <param name="only_name" value="False" />
44 <param name="full_match" value="False" /> 72 <param name="full_match" value="False" />
45 <param name="number_of_matches" value="False" /> 73 <param name="number_of_matches" value="False" />
46 <output name="outfile" ftype="smi" file="obgrep_on_8_mol.smi"/> 74 <output name="outfile" ftype="smi" file="obgrep_on_8_mol.smi"/>
75 </test>
76 <test>
77 <param name="infile" ftype="smi" value="2_mol.smi"/>
78 <param name="inp" value="multi"/>
79 <param name="query" value="pattern.smarts" />
80 <output name="outfile" ftype="smi" file="ob_multi_obgrep.smi" />
47 </test> 81 </test>
48 </tests> 82 </tests>
49 <help> 83 <help>
50 <![CDATA[ 84 <![CDATA[
51 85
52 .. class:: infomark 86 .. class:: infomark
53 87
54 **What this tool does** 88 **What this tool does**
55 89
56 Uses the Open Babel Obgrep_ to search for molecules inside multi-molecule files (e.g. SMI, SDF, etc.) or across multiple files. 90 Uses the Open Babel Obgrep_ to search for molecules inside multi-molecule files (e.g. SMI, SDF, etc.) or across multiple files. Not all SMARTS features from the original implementation in the Daylight Toolkit are supported by OpenBabel; please have a look here_.
57 It is known that not all SMARTS features from the Daylight Toolkit are supported, please have a look here_.
58 91
92 The search query can be submitted either as a single SMARTS pattern or as a file containing multiple SMARTS patterns.
59 93
60 .. _Obgrep: http://openbabel.org/wiki/Obgrep 94 .. _Obgrep: http://openbabel.org/wiki/Obgrep
61 .. _here: http://openbabel.org/wiki/SMARTS 95 .. _here: http://openbabel.org/wiki/SMARTS
62 96
63 ----- 97 -----