Mercurial > repos > bgruening > openbabel_obgrep

annotate ob_grep.xml @ 8:14712e15f196 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit a889b6ed75666406a95e29d672b58a8fee6e8784"
author bgruening
date Thu, 22 Aug 2019 10:23:46 -0400
parents 99517f9b780d
children 78640d0127ce
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1 <tool id="openbabel_obgrep" name="Compound search" version="@VERSION@.0">
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2 <description>- an advanced molecular search program using SMARTS</description>
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3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command>
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9 <![CDATA[
6
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11 #if $input_type.inp == 'single':
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12 obgrep
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13 $invert_matches
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14 #if $n_times:
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15 -t $n_times
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16 #end if
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17 $only_name
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18 $full_match
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19 $number_of_matches
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20 -i '${infile.ext}'
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21 '${input_type.smarts_pattern}'
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22 '${infile}'
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23 > '${outfile}'
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24 #else if $input_type.inp == 'multi':
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25 python '$__tool_directory__/multi_obgrep.py'
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26 -i $infile
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27 --iformat ${infile.ext}
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28 -q '${input_type.query}'
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29 -o '${outfile}'
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30 $invert_matches
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31 --n-times $n_times
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32 $only_name
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33 $full_match
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34 $number_of_matches
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35 --processors "\${GALAXY_SLOTS:-12}"
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36 #end if
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37
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38 ]]>
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39 </command>
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40 <inputs>
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41 <expand macro="infile_all_types"/>
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42 <conditional name="input_type">
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43 <param name="inp" type="select" label="Input">
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44 <option value="single">Enter a single SMARTS pattern</option>
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45 <option value="multi">Upload one or more SMARTS patterns in a text file</option>
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46 </param>
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47 <when value="single">
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48 <param name="smarts_pattern" type="text" format="text" label="SMARTS Pattern" help="Specify a SMARTS Pattern for your search."/>
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49 </when>
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50 <when value="multi">
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51 <param name="query" type='data' format="tabular,text" label="Query file" help="One SMARTS pattern in each line."/>
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52 </when>
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53 </conditional>
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54 <param name="invert_matches" type="boolean" label="Perform an inverted search, i.e. print non-matching molecules" truevalue="-v" falsevalue="" checked="false" />
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55 <param name="n_times" type="integer" value="0" min="0" optional="True"
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56 label="Print a molecule only if the pattern occurs this often inside the molecule" />
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57 <param name="only_name" type="boolean" label="Only print the name of the molecules" truevalue="-n" falsevalue="" checked="false" />
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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" />
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59 <param name="number_of_matches" type="boolean" label="Print the number of matches" truevalue="-c" falsevalue="" checked="false" />
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60 </inputs>
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61 <options sanitize="False"/>
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62 <outputs>
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63 <expand macro="output_like_input"/>
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64 </outputs>
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65 <tests>
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66 <test>
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67 <param name="infile" ftype="smi" value="8_mol.smi"/>
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68 <param name="inp" value="single"/>
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69 <param name="smarts_pattern" value="CO"/>
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70 <param name="invert_matches" value="False" />
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71 <param name="only_name" value="False" />
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72 <param name="full_match" value="False" />
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73 <param name="number_of_matches" value="False" />
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74 <output name="outfile" ftype="smi" file="obgrep_on_8_mol.smi"/>
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75 </test>
6
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76 <test>
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77 <param name="infile" ftype="smi" value="2_mol.smi"/>
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78 <param name="inp" value="multi"/>
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79 <param name="query" value="pattern.smarts" />
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80 <output name="outfile" ftype="smi" file="ob_multi_obgrep.smi" />
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81 </test>
0
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82 </tests>
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83 <help>
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84 <![CDATA[
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85
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86 .. class:: infomark
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87
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88 **What this tool does**
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89
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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_.
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91
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92 The search query can be submitted either as a single SMARTS pattern or as a file containing multiple SMARTS patterns.
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93
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94 .. _Obgrep: http://openbabel.org/wiki/Obgrep
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95 .. _here: http://openbabel.org/wiki/SMARTS
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96
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97 -----
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98
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99 .. class:: infomark
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100
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101 **Input**
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102
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103 | - `SD-Format`_
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104 | - `SMILES Format`_
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105
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106 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
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107 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
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108
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109 -----
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110
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111 .. class:: infomark
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112
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113 **Output**
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114
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115 Same as input format.
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116
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117 ]]>
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118 </help>
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119 <expand macro="citations"/>
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120 </tool>