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annotate chembl.xml @ 8:a43a00845834 draft

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"planemo upload for repository https://github.com/chembl/chembl_webresource_client commit e062e8287369e08bacf084e445acbeceb38c8ede"
author bgruening
date Wed, 27 Jan 2021 18:41:45 +0000
parents a57de37f12c2
children a446ea7e2bc1
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1 <tool id="chembl" name="Search ChEMBL database" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description>for compounds which are similar to a SMILES string</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">0.10.1</token>
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5 <token name="@GALAXY_VERSION@">3</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">chembl_webresource_client</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 python -W ignore '$__tool_directory__/chembl.py'
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12 $input.format '$input.smiles'
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13 -o $outfile
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14 $search.type
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15 #if $search.type == '-t':
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16 $search.tanimoto
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17 #end if
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18 $drugs
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19 $biotherapeutic
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20 $natprod
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21 $ro5
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22 ]]></command>
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23 <inputs>
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24 <conditional name="input">
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25 <param name='format' type='select' format='text' label="SMILES input type" help="Enter SMILES as either text or file.">
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26 <option value='-i'>Text</option>
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27 <option value='-f'>File</option>
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28 </param>
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29 <when value='-i'>
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30 <param name="smiles" type="text" label="SMILES input" help="Enter SMILES for a compound.">
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31 <validator type='length' min='5'/>
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32 </param>
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33 </when>
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34 <when value='-f'>
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35 <param name="smiles" type="data" format="smi" label="Input file" help="File containing a single compound in SMILES format. Note only the first line of the file will be read, if the file contains multiple compounds."/>
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36 </when>
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37 </conditional>
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38
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39 <conditional name="search">
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40 <param name='type' type='select' format='text' label="Search type" help="Search for compounds are similar to the SMILES input, or which contain the SMILES input as a substructure">
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41 <option value='-t'>Similarity</option>
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42 <option value='-s'>Substructure</option>
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43 </param>
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44 <when value="-t">
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45 <param type="integer" name="tanimoto" label="Tanimoto cutoff score" help="Score for similarity search. Minimum value is 70." value="70" min="70" max="100"/>
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46 </when>
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47 <when value="-s"/>
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48 </conditional>
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49
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50 <param name="drugs" type="boolean" value="false" label="Filter to return only approved drugs" truevalue="-d" falsevalue=""/>
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51 <param name="biotherapeutic" type="boolean" value="false" label="Filter to return only biotherapeutic molecules" truevalue="-b" falsevalue=""/>
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52 <param name="natprod" type="boolean" value="false" label="Filter to return only natural products" truevalue="-n" falsevalue=""/>
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53 <param name="ro5" type="boolean" value="false" label="Filter for Lipinski's Rule of Five" truevalue="-r" falsevalue=""/>
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54 </inputs>
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55 <outputs>
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56 <data name="outfile" format="smi" />
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57 </outputs>
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58 <tests>
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59 <test>
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60 <param name="format" value="-f"/>
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61 <param name="smiles" value="in1.smi"/>
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62 <param name='type' value='-t' />
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63 <param name='tanimoto' value='70' />
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64 <output name="outfile" ftype="smi" file='out1.smi' compare="sim_size"/>
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65 </test>
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66 <test>
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67 <param name="format" value="-f"/>
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68 <param name="smiles" value="in1.smi"/>
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69 <param name='type' value='-t' />
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70 <param name='tanimoto' value='70' />
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71 <param name='drugs' value='true'/>
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72 <output name="outfile" ftype="smi" file='out2.smi' compare="sim_size"/>
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73 </test>
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74 <test>
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75 <param name="format" value="-f"/>
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76 <param name="smiles" value="in1.smi"/>
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77 <param name='type' value='-s' />
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78 <output name="outfile" ftype="smi" file='out3.smi' compare="sim_size"/>
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79 </test>
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80 <test>
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81 <param name="format" value="-i"/>
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82 <param name="smiles" value="C1CCCCC1"/>
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83 <param name='type' value='-t' />
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84 <param name='tanimoto' value='70' />
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85 <output name="outfile" ftype="smi" file='out4.smi' compare="sim_size"/>
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86 </test>
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87 </tests>
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88 <help><![CDATA[
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89
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90 Search the ChEMBL database for compounds which resemble a SMILES string. Two
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91 search options are possible: similarity (searches for compounds which are
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92 similar to the input within a specified Tanimoto cutoff) and substructure
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93 (searches for compounds which contain the input substructure).
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94
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95 Results can be filtered for compounds which are 1) approved drugs 2) biotherapeutic
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96 3) natural products and 4) fulfil all of the Lipinski rule of five criteria.
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97
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98 -----
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99
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100 .. class:: infomark
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101
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102 **Input**
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103
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104 A single molecule in SMILES format. This can be submitted either as text or as a
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105 file containing the SMILES string on the first line. Note that if the file contains
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106 multiple lines, only the SMILES string on the first line will be used for the search.
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107
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108 -----
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109
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110 .. class:: infomark
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111
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112 **Output**
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113
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114 A SMILES file with search results, each on a new line.
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115
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116 ]]></help>
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117
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118 <citations>
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119 <citation type="doi">10.1093/nar/gkv352</citation>
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120 <citation type="doi">arXiv:1607.00378v1</citation>
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121 </citations>
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122 </tool>