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annotate rp2paths.xml @ 6:6b2ae398f4b0 draft

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planemo upload for repository https://github.com/brsynth/rp2paths commit 0718e1c463ce94ee76679ec10db8bc839a9a3199-dirty
author tduigou
date Fri, 03 Oct 2025 11:16:40 +0000
parents bdde1d9dfaee
children f3843f6b7332
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1 <tool id="rp2paths" name="RP2paths" version="@TOOL_VERSION@" profile="21.09" license="MIT">
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2 <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">2.1.0</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">rp2paths</requirement>
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8 </requirements>
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9 <stdio>
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10 <regex match="TIMEOUT:" level="fatal" />
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11 <regex match="ERROR:" level="fatal" />
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12 <regex match="WARNING:" level="warning" />
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13 </stdio>
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14 <command detect_errors="exit_code"><![CDATA[
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15 mkdir out &&
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16 python -m rp2paths all
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17 '$rp2_pathways'
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18 --outdir out
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19 --timeout '$adv.timeout'
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20 #if str($adv.forward) == 'true'
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21 --forward
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22 #end if
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23 #if $adv.cofile
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24 --cofile '$adv.cofile'
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25 #end if
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26 #if str($adv.mindepth) == 'true'
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27 --minDepth
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28 #end if
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29 #if $adv.sink
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30 --customsinkfile '$adv.sink'
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31 #end if
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32 --maxsteps '$adv.maxsteps'
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33 --maxpaths '$adv.maxpaths'
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34 #if str($adv.unfold) == 'true'
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35 --unfold_compounds
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36 #end if
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37 #set cmp_ids = []
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38 #for $x in $adv.rep_include_path
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39 #silent cmp_ids.append(str($x.cmp_id))
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40 #end for
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41 #if len(cmp_ids) > 0
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42 #set cmp_id = ' '.join($cmp_ids)
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43 --onlyPathsStartingBy $cmp_id
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44 #end if
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45 #set cmp_ids = []
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46 #for $x in $adv.rep_exclude_path
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47 #silent cmp_ids.append(str($x.cmp_id))
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48 #end for
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49 #if len(cmp_ids) > 0
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50 #set cmp_id = ' '.join($cmp_ids)
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51 --notPathsStartingBy $cmp_id
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52 #end if
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53 #if $adv.cmpfile
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54 --cmpdnamefile '$adv.cmpfile'
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55 #end if
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56 --target '$adv.target' &&
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57 mv out/compounds.txt out/compounds.tsv &&
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58 cp out/compounds.tsv '$compounds' &&
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59 if test -f 'out/out_paths.csv'; then
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60 cp out/out_paths.csv '$master_pathways';
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61 fi
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62 ]]></command>
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63 <inputs>
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64 <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 Pathways"
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65 help="Retrosynthesis network CSV file outputted by the RetroPath2 tool which desribes the network linking the targeted compound to the chassis." />
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66 <section name="adv" title="Advanced Options" expanded="false">
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67 <param name="timeout" type="integer" value="1800" label="Time Out"
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68 help="Time out before killing a process (in seconds), default: 30 minutes." />
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69 <param
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70 name="forward" type="boolean" checked="false" label="Forward"
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71 help="Consider reactions in the forward direction" />
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72 <param name="cofile"
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73 type="data" format="csv" optional="True" label="List of cofactors" />
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74 <param
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75 name="mindepth" type="boolean" checked="false" label="Minimal depth scope"
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76 help="Use minimal depth scope, i.e. stop the scope computation as as soon an a first minimal path linking target to sink is found" />
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77 <param
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78 name="sink" type="data" format="tabular" optional="True" label="List of sinks"
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79 help="Listing compounds to consider as sink compounds. Sink compounds should be provided by their IDs, as used in the reaction.erxn file" />
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80 <param
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81 name="maxsteps" type="integer" min="0" value="0" max="20" label="Max steps"
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82 help="Cutoff on the maximum number of steps in a pathways. 0 (default) for unlimited number of steps" />
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83 <param
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84 name="maxpaths" type="integer" min="0" value="0" max="20" label="Max pathways"
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85 help="Cutoff on the maximum number of pathways. 0 (default) for unlimited number of pathways" />
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86 <param
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87 name="unfold" type="boolean" checked="false" label="Unfold pathways"
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88 help="Unfold pathways based on equivalencie of compounds (can lead to combinatorial explosion)." />
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89 <repeat name="rep_include_path" title="Include path starting by">
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90 <param name="cmp_id" type="text" label="Path label"
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91 help="List of compounds IDs to consider. If specified, only paths making use of at least one of these compounds as initial substrate (first step of a pathway) are kept.">
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92 <validator type="empty_field" message="Not empty" />
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93 </param>
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94 </repeat>
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95 <repeat name="rep_exclude_path" title="Include path starting by">
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96 <param name="cmp_id" type="text" label="Path label"
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97 help="List of compounds IDs. If specifed, paths making use of one of these compounds as unique initial substrate will be filtered out">
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98 <validator type="empty_field" message="Not empty" />
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99 </param>
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100 </repeat>
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101 <param name="cmpfile" type="data" format="tabular"
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102 optional="True" label="List of compounds" help="File with name of compounds" />
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103 <param
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104 name="target" type="text" value="TARGET_0000000001"
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105 label="Target compound internal ID"
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106 help="This internal ID specifies which compound should be considered as the targeted compound. The default behavior is to consider as the target the first compound used as a source compound in a first iteration of a metabolic exploration. Let this value as it is except if you know what you are doing" />
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107 </section>
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108 </inputs>
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109 <outputs>
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110 <data name="master_pathways" format="csv"
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111 label="${tool.name} on ${rp2_pathways.name} : Enumerated Pathways" />
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112 <data name="compounds" format="tabular"
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113 label="${tool.name} on ${rp2_pathways.name} : Compounds" />
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114 </outputs>
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115 <tests>
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116 <test>
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117 <!-- test 1: check if identical outputs are produced with default parameters -->
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118 <param name="rp2_pathways" value="retropath2_pathways.csv" />
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119 <output name="master_pathways" file="rp2paths_pathways.csv" ftype="csv" compare="diff" />
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120 <output name="compounds" file="rp2paths_compounds.tsv" ftype="tabular" compare="diff" />
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121 </test>
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122 </tests>
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123 <help><![CDATA[
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124 RP2paths
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125 ========
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126
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127
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128 **RP2paths** extracts the set of heterologous pathways that lies in a metabolic space file outputted by the `RetroPath2.0 workflow <https://www.myexperiment.org/workflows/4987.html>`_ into individual pathways and enumerate them. This analysis is required to ensure that only pathways fulfilling all the precursor needs are retained for further analysis. This tool takes as input a retrosynthesis network in the CSV file produced by `RetroPath2.0 <https://toolshed.g2.bx.psu.edu/view/tduigou/retropath2/9c8ac9980bd6>`_ , and outputs the enumerated pathways (using EC numbers) as well as the structure of involved chemicals (as SMILES: Simplified Molecular-Input Line-Entry System) in TSV format.
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129
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130
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131 .. image:: ${static_path}/images/enumerated_pathways.png
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132 :width: 40 %
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133 :align: center
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134
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135 |
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136
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137 Output
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138 ------
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139
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140 * **Enumerated Pathways**\ : Describes all the indiviudal enumerated pathways that produce the compound of interest.
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141 * **Compounds**\ : Describes the structure of all the chemical species involved in all pathways as SMILES (Simplified Molecular-Input Line-Entry System).
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142 ]]></help>
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143 <creator>
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144 <organization name="BioRetroSynth" url="https://github.com/brsynth" />
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145 </creator>
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146 <citations>
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147 <citation type="doi">10.1016/j.ymben.2017.12.002</citation>
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148 </citations>
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149 </tool>