Mercurial > repos > tduigou > retropath2

annotate retropath2_wrapper.xml @ 13:f26e7e4a42b7 draft

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planemo upload for repository https://github.com/brsynth/retropath2_wrapper commit 4f228a8dcee36f8c5282ff3e30f67a87254a2837-dirty
author tduigou
date Wed, 08 Oct 2025 11:10:57 +0000
parents 805988211e6c
children 1edb49dfa335
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1 <tool id="retropath2" name="RetroPath2.0" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
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2 profile="21.09" license="MIT">
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3 <description>Build a reaction network from a set of source compounds to a set of sink compounds</description>
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4 <macros>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 <token name="@TOOL_VERSION@">3.5.0</token>
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7 </macros>
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8 <requirements>
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9 <requirement type="package" version="@TOOL_VERSION@">retropath2_wrapper</requirement>
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10 </requirements>
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11 <stdio>
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12 <!-- Fatal -->
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13 <exit_code range="1" level="fatal" description="Cannot find source-in-sink file" />
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14 <regex match="It seems that the target product is already in the chassis" source="both"
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15 level="fatal" description="It seems that the target product is already in the chassis" />
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16 <exit_code range="2" level="fatal"
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17 description="Running the RetroPath2.0 Knime program produced an OSError" />
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18 <regex match="The following error occured" source="both" level="fatal"
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19 description="The following error occured" />
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20 <exit_code range="3" level="fatal" description="The InChI string is malformed" />
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21 <regex match="is not a valid InChI notation" source="both" level="fatal"
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22 description="is not a valid InChI notation" />
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23 <exit_code range="4" level="fatal" description="Sink file is malformed" />
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24 <regex match="The sink file is malformed" source="both" level="fatal"
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25 description="The sink file is malformed" />
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26 <exit_code range="5" level="fatal" description="Knime installation error" />
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27 <!-- Warning -->
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28 <exit_code range="10" level="warning" description="Source has been found in the sink" />
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29 <regex match="Source has been found in the sink" source="both" level="warning"
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30 description="Source has been found in the sink" />
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31 <exit_code range="11" level="warning" description="RetroPath2.0 has found no solution" />
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32 <regex match="No solution has been found" source="both" level="warning"
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33 description="No solution has been found" />
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34 </stdio>
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35 <command detect_errors="exit_code"><![CDATA[
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36 #if $sink.emptysink:
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37 echo '"Name","InChI"' > empty_sink.csv &&
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38 #set $sinkfile = "empty_sink.csv"
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39 #end if
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40 python -m retropath2_wrapper
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41 '$sinkfile'
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42 '$rulesfile'
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43 out
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44 --source_inchi '$source_inchi'
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45 --source_name '$source_name'
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46 --rp2_version '$adv.version'
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47 --max_steps '$max_steps'
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48 --topx '$adv.topx'
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49 --dmin '$adv.dmin'
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50 --dmax '$adv.dmax'
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51 --mwmax_source '$adv.mwmax_source'
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52 --kinstall "\${TMPDIR:-.}"
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53 --std_hydrogen '$adv.std_hydrogen'
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54 #if not $sink.error_codes:
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55 --quiet
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56 #end if
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57 --msc_timeout '$adv.timeout' &&
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58 if compgen -G 'out/*_scope.csv' > /dev/null; then
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59 cp out/*_scope.csv '$Reaction_Network';
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60 else
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61 cp out/results.csv '$Reaction_Network';
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62 fi
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63 ]]></command>
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64 <inputs>
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65 <param name="rulesfile" type="data" format="csv,tar" label="Rules File"
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66 help="File containing reaction rules which reflect the enzymatic potential of the chassis organism." />
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67 <conditional name="sink">
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68 <param name="emptysink" type="boolean" checked="false" label="Empty sink" />
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69 <when value="false">
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70 <param name="sinkfile" type="data" format="csv" label="Sink File"
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71 help="Sink file which comprises all compounds that are considered as granted in your system." />
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72 <param name="error_codes" type="boolean" checked="true" label="Return error codes" />
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73 </when>
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74 <when value="true">
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75 <param name="error_codes" type="boolean" checked="false" label="Return error codes" />
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76 </when>
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77 </conditional>
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78 <param name="source_inchi" type="text" label="Source InChI" optional="false"
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79 help="InChI of compound to produce.">
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80 <validator type="empty_field" message="You must provide the InChI string" />
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81 </param>
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82 <param name="max_steps" type="integer" value="3" min="1" max="10"
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83 label="Maximal Pathway length"
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84 help="The maximal number of metabolic steps (i.e. reactions) for exploring around the target." />
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85 <param name="source_name" type="text" value="target" optional="true" label="Source name"
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86 help="Name of compound to produce.">
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87 <validator type="empty_field" message="Source name is required." />
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88 </param>
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89 <section name="adv" title="Advanced Options" expanded="false">
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90 <param name="version" type="select" label="Workflow version"
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91 help="Retropath2.0 Workflow versions, formatted as 'r{year}{month}{day}' (the latest version 'r20220104' is used by default).">
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92 <option value="v9">v9</option>
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93 <option value="r20210127">r20210127</option>
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94 <option value="r20220104">r20220104</option>
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95 <option value="r20220224">r20220224</option>
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96 <option value="r20250728" selected="true">r20250728</option>
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97 </param>
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98 <param name="topx" type="integer" value="100" min="1" max="1000" label="TopX"
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99 help="The maximal number of intermediate compounds to use as new starting points for a next iteration of the retrosynthesis algorithm." />
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100 <param name="dmin" type="integer" value="0" min="0" max="1000"
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101 label="Minimum rule diameter"
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102 help="Minimum rule diameter of the sphere including the atoms around the reacting center. The higher is the diameter, the more specific are the rules." />
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103 <param name="dmax" type="integer" value="1000" min="0" max="1000"
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104 label="Maximum rule diameter"
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105 help="Maximum rule diameter of the sphere including the atoms around the reacting center. The higher is the diameter, the more specific are the rules." />
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106 <param name="mwmax_source" type="integer" value="1000" min="0" max="2000"
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107 label="Molecular weight of source (Da)"
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108 help="The molecular weight cutoff (in Da), above which initial source (ie target) and intermediate compounds will be filtered out." />
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109 <param name="timeout" type="integer" value="60" min="30" max="600" label="Timeout (min)"
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110 help="Maximal time of RetroPath2.0 execution (60 minutes by default)." />
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111 <param name="std_hydrogen" type="select" label="Hygrogens in chemical rules"
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112 help="How hydrogens are represented in chemical rules, auto mode will try to guess from the chemical rules">
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113 <option value="auto" selected="true">auto</option>
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114 <option value="implicit">Aromatized (no Hs added)</option>
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115 <option value="explicit">H added + Aromatized</option>
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116 </param>
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117 </section>
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118 </inputs>
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119 <outputs>
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120 <data name="Reaction_Network" format="csv" label="${tool.name}">
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121 <actions>
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122 <action name="column_names" type="metadata"
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123 default="Initial source,Transformation ID,Reaction SMILES,Substrate SMILES,Substrate InChI,Product SMILES,Product InChI,In Sink,Sink name,Diameter,Rule ID,EC number,Score,Starting Source SMILES,Iteration" />
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124 </actions>
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125 </data>
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126 </outputs>
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127 <tests>
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128 <test>
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129 <!-- test 1: check if identical outputs are produced with default parameters -->
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130 <param name="rulesfile" value="rules.csv" />
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131 <conditional name="sink">
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132 <param name="emptysink" value="false" />
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133 <param name="sinkfile" value="sink.csv" />
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134 </conditional>
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135 <param name="source_inchi"
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136 value="InChI=1S/C40H56/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3/b12-11+,25-15+,26-16+,31-17+,32-18+,35-21+,36-22+,37-27+,38-28+,39-29+,40-30+" />
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137 <output name="Reaction_Network" file="results_retropath2.csv" ftype="csv" compare="diff" />
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138 </test>
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139 <test>
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140 <!-- test 2: check empty sink file -->
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141 <param name="rulesfile" value="rules.csv" />
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142 <conditional name="sink">
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143 <param name="emptysink" value="true" />
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144 </conditional>
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145 <param name="source_inchi"
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146 value="InChI=1S/C40H56/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3/b12-11+,25-15+,26-16+,31-17+,32-18+,35-21+,36-22+,37-27+,38-28+,39-29+,40-30+" />
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147 <output name="Reaction_Network" file="results_emptysink.csv" ftype="csv" compare="diff" />
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148 </test>
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149 </tests>
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150 <help><![CDATA[
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151 Retropath2.0 wrapper
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152 ====================
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153
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154 Perform retrosynthesis search of possible metabolic routes between a source molecule and a collection of sink molecules. This tool is an implementation of the `KNIME retropath2.0 workflow <https://www.myexperiment.org/workflows/4987.html>`_. It takes for input the minimal (dmin) and maximal (dmax) diameter for the reaction rules and the maximal path length (maxSteps). The tool expects the following files: rules.csv, sink.csv and source.csv and produce a retrosynthesis network as a CSV file providing reactions in the reaction SMILES format and chemicals in both SMILES and InChI formats along with other information like the score for each reaction. Only a single source molecule is processed at this time.
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155
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156 Output
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157 ------
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158
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159 * **Reaction Network**\ : CSV file containing retrosynthesis network which provides reactions in the reaction SMILES format and chemicals in both SMILES and InChI formats along with other information like the score for each reaction.
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160 ]]></help>
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161 <creator>
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162 <organization name="BioRetroSynth" url="https://github.com/brsynth" />
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163 </creator>
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164 <citations>
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165 <citation type="doi">10.1016/j.ymben.2017.12.002 </citation>
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166 </citations>
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167 </tool>