Mercurial > repos > tduigou > rrparser

annotate rrparser.xml @ 3:392f18980ff4 draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Wed, 02 Feb 2022 14:26:53 +0000
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children 3f39c7d3c14e
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1 <tool id="rrparser" name="RRules Parser" version="@TOOL_VERSION@" profile="19.09">
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2 <description>Retrieve the reaction rules from RetroRules</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">2.4.6</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">rrparser</requirement>
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8 </requirements>
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9 <stdio>
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10 <regex match="WARNING:" level="warning" />
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11 <regex match="ERROR:" level="fatal" />
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12 </stdio>
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13 <command detect_errors="exit_code"><![CDATA[
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14 python -m rrparser
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15 #if str($rules.type) != "other":
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16 retrorules
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17 --rule-type '$rules.type'
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18 #else:
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19 '$rules.file'
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20 --input-format '$rules.format'
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21 #end if
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22 --diameters '$diameters'
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23 --output-format csv
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24 #if str($compress) == "true":
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25 --outfile '$out_rules'.csv.gz
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26 && mv '$out_rules'.csv.gz '$out_rules'
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27 #else:
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28 --outfile '$out_rules'
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29 #end if
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30 ]]></command>
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31 <inputs>
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32 <conditional name="rules">
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33 <param name="type" type="select" label="Rule Type" help="">
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34 <option value="retro" selected="True">RetroRules (retro)</option>
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35 <option value="forward">RetroRules (forward)</option>
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36 <option value="all">RetroRules (all)</option>
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37 <option value="other">Other reaction rules...</option>
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38 </param>
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39 <when value="other">
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40 <param name="file" type="data" format="csv" optional="False" label="Rules File"/>
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41 <param name="format" type="select" optional="False" label="File format">
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42 <option value="csv" selected="True">csv</option>
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43 <option value="tsv">tsv</option>
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44 </param>
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45 </when>
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46 </conditional>
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47 <param name="diameters" type="select" display="checkboxes" multiple="True" label="Select the diameters of the reactions rules">
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48 <option selected="true" value="2">2</option>
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49 <option selected="true" value="4">4</option>
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50 <option selected="true" value="6">6</option>
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51 <option selected="true" value="8">8</option>
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52 <option selected="true" value="10">10</option>
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53 <option selected="true" value="12">12</option>
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54 <option selected="true" value="14">14</option>
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55 <option selected="true" value="16">16</option>
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56 </param>
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57 <param name="compress" type="boolean" display="checkboxes" label="Compress output" />
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58 </inputs>
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59 <outputs>
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60 <data name="out_rules" format="csv" label="${tool.name}(${rules.type}, d=$diameters)" >
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61 <change_format>
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62 <when input="compress" format="tar" value="true"/>
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63 </change_format>
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64 </data>
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65 </outputs>
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66 <tests>
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67 <test>
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68 <!-- test 1: check if identical outputs are produced with default parameters-->
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69 <output name="out_rules" md5="54806bd44f7a8414e78439e3bb99e6d8"/>
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70 </test>
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71 <test>
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72 <!-- test 2: check if identical outputs are produced with diameters=2,4,6-->
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73 <param name="diameters" value="2,4,6"/>
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74 <output name="out_rules" md5="12a55e1a3c7822a35ed799afa59b2aa2"/>
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75 </test>
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76 <test>
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77 <!-- test 3: check if identical outputs are produced with csv input rules file-->
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78 <conditional name="rules">
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79 <param name="type" value="other"/>
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80 <param name="file" value="rules_in.csv" />
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81 </conditional>
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82 <output name="out_rules" file="rules_out.csv" ftype="csv" compare="diff"/>
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83 </test>
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84 </tests>
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85 <help><![CDATA[
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86 RRulesParser
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87 ============
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88
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89 Retrieve the reaction rules from `RetroRules <https://retrorules.org/>`_
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90
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91 Input
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92 -----
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93
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94 * **rules-file**: (string) Filename of reaction rules
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95 * **input-format**: (string) input file format (default: csv)
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96 * **rule-type**: (string) {all,retro,forward} rule usage to filter from rules file
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97 * **diameters**: (integer list) diameter of the sphere including the atoms around the reacting center (default is including all values: 2,4,6,8,10,12,14,16). The higher is the diameter, the more specific are the rules
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98 * **output-format**: (string) {csv,tsv} output file format (default: csv)
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99
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100 Ouput
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101 -----
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102
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103 * **outfile**: (string): file where results are written. If file ends with '.gz', it will be gzipped.
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104
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105
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106 Version
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107 -------
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108
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109 v2.4.6
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110
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111 Authors
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112 -------
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113
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114 * **Thomas Duigou**
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115 * Melchior du Lac
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116 * Joan Hérisson
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117
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118 License
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119 -------
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120
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121 This project is licensed under the MIT License - see the `LICENSE <https://github.com/brsynth/RRParser/blob/master/LICENSE>`_ file for details
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122
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123 Acknowledgments
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124 ---------------
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125
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126 * Joan Hérisson
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127
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128 ]]></help>
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129 <citations>
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130 <citation type="doi">10.1093/nar/gky940 </citation>
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131 </citations>
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132 </tool>