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annotate chembl.xml @ 3:8b6ba267714b draft

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"planemo upload for repository https://github.com/chembl/chembl_webresource_client commit 515aded04abf81089ebecf6fc6841447bd519b2f"
author bgruening
date Wed, 01 Apr 2020 07:04:25 -0400
parents 6f8458d1cf46
children 59eea7d0d720
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1 <tool id="chembl" name="Search ChEMBL database" version="@VERSION@">
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2 <macros>
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3 <token name="@VERSION@">0.10.1</token>
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4 </macros>
0
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5 <description>for compounds which are similar to a SMILES string</description>
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6 <requirements>
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7 <requirement type="package" version="@VERSION@">chembl_webresource_client</requirement>
0
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 python -W ignore '$__tool_directory__/chembl.py'
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11 $input.format '$input.smiles'
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12 -o $outfile
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13 $search.type
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14 #if $search.type == '-t':
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15 $search.tanimoto
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16 #end if
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17 $drugs
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18 $biotherapeutic
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19 $natprod
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20 $ro5
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21 ]]></command>
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22 <inputs>
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23 <conditional name="input">
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24 <param name='format' type='select' format='text' label="SMILES input type" help="Enter SMILES as either text or file.">
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25 <option value='-i'>Text</option>
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26 <option value='-f'>File</option>
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27 </param>
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28 <when value='-i'>
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29 <param name="smiles" type="text" label="SMILES input" help="Enter SMILES for a compound.">
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30 <validator type='length' min='5'/>
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31 </param>
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32 </when>
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33 <when value='-f'>
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34 <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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35 </when>
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36 </conditional>
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37
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38 <conditional name="search">
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39 <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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40 <option value='-t'>Similarity</option>
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41 <option value='-s'>Substructure</option>
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42 </param>
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43 <when value="-t">
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44 <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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45 </when>
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46 <when value="-s"/>
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47 </conditional>
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48
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49 <param name="drugs" type="boolean" value="false" label="Filter to return only approved drugs" truevalue="-d" falsevalue=""/>
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50 <param name="biotherapeutic" type="boolean" value="false" label="Filter to return only biotherapeutic molecules" truevalue="-b" falsevalue=""/>
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51 <param name="natprod" type="boolean" value="false" label="Filter to return only natural products" truevalue="-n" falsevalue=""/>
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52 <param name="ro5" type="boolean" value="false" label="Filter for Lipinski's Rule of Five" truevalue="-r" falsevalue=""/>
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53 </inputs>
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54 <outputs>
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55 <data name="outfile" format="smi" />
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56 </outputs>
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57 <tests>
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58 <test>
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59 <param name="format" value="-f"/>
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60 <param name="smiles" value="in1.smi"/>
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61 <param name='type' value='-t' />
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62 <param name='tanimoto' value='70' />
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63 <output name="outfile" ftype="smi" file='out1.smi' compare="sim_size"/>
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64 </test>
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65 <test>
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66 <param name="format" value="-f"/>
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67 <param name="smiles" value="in1.smi"/>
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68 <param name='type' value='-t' />
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69 <param name='tanimoto' value='70' />
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70 <param name='drugs' value='true'/>
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71 <output name="outfile" ftype="smi" file='out2.smi' compare="sim_size"/>
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72 </test>
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73 <test>
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74 <param name="format" value="-f"/>
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75 <param name="smiles" value="in1.smi"/>
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76 <param name='type' value='-s' />
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77 <output name="outfile" ftype="smi" file='out3.smi' compare="sim_size"/>
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78 </test>
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79 <test>
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80 <param name="format" value="-i"/>
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81 <param name="smiles" value="C1CCCCC1"/>
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82 <param name='type' value='-t' />
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83 <param name='tanimoto' value='70' />
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84 <output name="outfile" ftype="smi" file='out4.smi' compare="sim_size"/>
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85 </test>
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86 </tests>
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87 <help><![CDATA[
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88
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89 Search the ChEMBL database for compounds which resemble a SMILES string. Two
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90 search options are possible: similarity (searches for compounds which are
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91 similar to the input within a specified Tanimoto cutoff) and substructure
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92 (searches for compounds which contain the input substructure).
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93
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94 Results can be filtered for compounds which are 1) approved drugs 2) biotherapeutic
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95 3) natural products and 4) fulfil all of the Lipinski rule of five criteria.
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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 A single molecule in SMILES format. This can be submitted either as text or as a
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104 file containing the SMILES string on the first line. Note that if the file contains
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105 multiple lines, only the SMILES string on the first line will be used for the search.
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106
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107 -----
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108
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109 .. class:: infomark
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110
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111 **Output**
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112
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113 A SMILES file with search results, each on a new line.
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114
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115 ]]></help>
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116
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117 <citations>
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118 <citation type="doi">10.1093/nar/gkv352</citation>
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119 <citation type="doi">arXiv:1607.00378v1</citation>
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120 </citations>
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121 </tool>