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annotate rrparser.xml @ 7:de7b4c226b02 draft

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planemo upload for repository https://github.com/brsynth/rrparser commit a57357b9a0a5a7f5a4ac0e6fe3d00233afd11327
author tduigou
date Mon, 17 Mar 2025 14:56:07 +0000
parents ada9a9847d10
children d72f31975a06
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1 <tool id="rrparser" name="RRules Parser" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09" license="MIT">
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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="@VERSION_SUFFIX@">0</token>
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5 <token name="@TOOL_VERSION@">2.6.0</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">rrparser</requirement>
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9 </requirements>
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10 <stdio>
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11 <regex match="WARNING:" level="warning" />
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12 <regex match="ERROR:" level="fatal" />
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13 </stdio>
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14 <command detect_errors="exit_code"><![CDATA[
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15 python -m rrparser
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16 #if str($rules.type) != "rules-file":
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17 --rules_file retrorules
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18 --rule-type '$rules.type'
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19 #else:
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20 --rules_file '$rules.file'
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21 --input-format '$rules.input_format'
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22 #end if
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23 --diameters '$diameters'
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24 --output-format csv
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25 --rules-dir "\${TMPDIR:-.}"
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26 #if str($compress) == "true":
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27 --outfile '$out_rules'.csv.gz
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28 && mv '$out_rules'.csv.gz '$out_rules'
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29 #else:
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30 --outfile '$out_rules'
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31 #end if
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32 #if str($input_conditional_ec.input_type) == "in"
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33 --ec '$input_conditional_ec.input_ec_in'
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34 #end if
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35 #if str($input_conditional_ec.input_type) == "out"
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36 --ecx '$input_conditional_ec.input_ec_out'
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37 #end if
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38 ]]></command>
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39 <inputs>
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40 <conditional name="rules">
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41 <param name="type" type="select" label="Rule Type" help="Return the rules that are in reverse, forward, both direction or from an input user file">
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42 <option value="retro" selected="True">RetroRules (retro)</option>
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43 <option value="forward">RetroRules (forward)</option>
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44 <option value="all">RetroRules (all)</option>
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45 <option value="rules-file">Other reaction rules...</option>
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46 </param>
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47 <when value="retro"/>
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48 <when value="forward"/>
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49 <when value="all"/>
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50 <when value="rules-file">
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51 <param name="file" type="data" format="csv" optional="False" label="Rules File" help="Filename of reaction rules"/>
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52 <param name="input_format" type="select" optional="False" label="File format" help="Input file format (default: csv)">
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53 <option value="csv" selected="True">csv</option>
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54 <option value="tsv">tsv</option>
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55 </param>
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56 </when>
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57 </conditional>
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58 <param argument="--diameters" type="select" display="checkboxes" multiple="True" label="Select the diameters of the reactions rules" help=" 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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59 <option selected="true" value="2">2</option>
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60 <option selected="true" value="4">4</option>
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61 <option selected="true" value="6">6</option>
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62 <option selected="true" value="8">8</option>
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63 <option selected="true" value="10">10</option>
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64 <option selected="true" value="12">12</option>
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65 <option selected="true" value="14">14</option>
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66 <option selected="true" value="16">16</option>
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67 </param>
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68 <param name="compress" type="boolean" checked="false" label="Compress output" />
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69 <conditional name="input_conditional_ec">
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70 <param name="input_type" type="select" label="Filter based on EC number">
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71 <option value="no" selected="True">No</option>
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72 <option value="in">EC numbers to keep</option>
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73 <option value="out">EC numbers to remove</option>
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74 </param>
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75 <when value="no" />
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76 <when value="in">
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77 <param name="input_ec_in" type="data" format="csv" label="File containing EC numbers" help="EC numbers on one line separted by a comma" />
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78 </when>
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79 <when value="out">
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80 <param name="input_ec_out" type="data" format="csv" label="File containing EC numbers" help="EC numbers on one line separted by a comma" />
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81 </when>
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82 </conditional>
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83 </inputs>
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84 <outputs>
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85 <data name="out_rules" format="csv" label="${tool.name}(${rules.type}, d=$diameters)" >
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86 <change_format>
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87 <when input="compress" format="tar" value="true"/>
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88 </change_format>
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89 </data>
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90 </outputs>
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91 <tests>
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92 <test>
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93 <!-- test 1: check if identical outputs are produced with default parameters-->
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94 <output name="out_rules" md5="54806bd44f7a8414e78439e3bb99e6d8"/>
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95 </test>
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96 <test>
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97 <!-- test 2: check if identical outputs are produced with diameters=2,4,6-->
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98 <param name="diameters" value="2,4,6"/>
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99 <output name="out_rules" md5="12a55e1a3c7822a35ed799afa59b2aa2"/>
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100 </test>
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101 <test>
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102 <!-- test 3: check if identical outputs are produced with csv input rules file-->
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103 <conditional name="rules">
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104 <param name="type" value="rules-file"/>
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105 <param name="file" value="rules_in.csv" />
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106 </conditional>
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107 <output name="out_rules" file="rules_out.csv" ftype="csv" compare="diff"/>
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108 </test>
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109 <test>
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110 <!-- test 4 -->
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111 <conditional name="rules">
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112 <param name="type" value="rules-file"/>
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113 <param name="file" value="rules_in.csv" />
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114 </conditional>
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115 <conditional name="input_conditional_ec">
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116 <param name="input_type" value="in"/>
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117 <param name="input_ec_in" value="ec.csv"/>
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118 </conditional>
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119 <output name="out_rules" file="test.4.output.csv" ftype="csv" compare="diff"/>
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120 </test>
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121 <test>
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122 <!-- test 5 -->
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123 <conditional name="rules">
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124 <param name="type" value="rules-file"/>
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125 <param name="file" value="rules_in.csv" />
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126 </conditional>
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127 <conditional name="input_conditional_ec">
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128 <param name="input_type" value="out"/>
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129 <param name="input_ec_out" value="ec.csv"/>
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130 </conditional>
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131 <output name="out_rules" file="test.5.output.csv" ftype="csv" compare="diff"/>
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132 </test>
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133
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134 </tests>
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135 <help><![CDATA[
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136 RRulesParser
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137 ============
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138
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139 Retrieve the reaction rules from `RetroRules <https://retrorules.org/>`_ extracted from public databases and expressed in the community-standard SMARTS (SMILES arbitrary target specification) format, augmented by a rule representation at different levels of specificity (the atomic environment around the reaction center).
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140
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141 The generated output is a file containing reaction rules which are generic descriptions of chemical reactions that can be used in retrosynthesis workflows (e.g. `Retrosynthesis KNIME Workflow <https://www.myexperiment.org/workflows/4987.html>`_) in order to enumerate all possible biosynthetic routes connecting a target molecule to its precursors.
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142
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143 Input
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144 -----
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145
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146 * **Rule Type**: (string) Return the rules that are in reverse, forward, both direction or from an input user file
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147 * **rules-file**: (string) Filename of reaction rules provided in csv or tsv format.
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148 * **input_format**: (string) input file format (csv: default, tsv)
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149 * **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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150 * **EC numbers to filter**: retain or remove some EC numbers. A file is expected containing EC numbers separated by a comma on the first line.
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151
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152 Ouput
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153 -----
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154
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155 * **out_rules**: (string): file containing the parsed reactions rules (default=csv). It will be zipped if *Compress output* is set to yes.
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156 ]]></help>
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157 <creator>
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158 <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
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159 </creator>
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160 <citations>
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161 <citation type="doi">10.1093/nar/gky940</citation>
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162 </citations>
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163 </tool>