Mercurial > repos > iuc > rrparser

annotate rrparser.xml @ 4:b97690ee00e7 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit 09b98dbaa3afe569a76577ab668dde6b4ee54b24
author iuc
date Mon, 14 Apr 2025 18:29:54 +0000
parents e5b1f1d99918
children
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4
b97690ee00e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit 09b98dbaa3afe569a76577ab668dde6b4ee54b24
iuc
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1 <tool id="rrparser" name="RRules Parser" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2" license="MIT">
0
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2 <description>Retrieve the reaction rules from RetroRules</description>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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3 <macros>
4
b97690ee00e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit 09b98dbaa3afe569a76577ab668dde6b4ee54b24
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4 <token name="@VERSION_SUFFIX@">1</token>
3
e5b1f1d99918 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit 2a3d0848e53a4030a54eff826521ccca6da45985
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5 <token name="@TOOL_VERSION@">2.7.0</token>
0
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6 </macros>
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7 <requirements>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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8 <requirement type="package" version="@TOOL_VERSION@">rrparser</requirement>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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9 </requirements>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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10 <stdio>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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11 <regex match="WARNING:" level="warning" />
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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12 <regex match="ERROR:" level="fatal" />
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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13 </stdio>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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14 <command detect_errors="exit_code"><![CDATA[
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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15 python -m rrparser
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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16 #if str($rules.type) != "rules-file":
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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17 --rules_file retrorules
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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18 --rule-type '$rules.type'
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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19 #else:
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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20 --rules_file '$rules.file'
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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21 --input-format '$rules.input_format'
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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22 #end if
4
b97690ee00e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit 09b98dbaa3afe569a76577ab668dde6b4ee54b24
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23 --diameters '$adv.diameters'
0
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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24 --output-format csv
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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25 --rules-dir "\${TMPDIR:-.}"
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b97690ee00e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit 09b98dbaa3afe569a76577ab668dde6b4ee54b24
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26 #if str($adv.compress) == "true":
0
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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27 --outfile '$out_rules'.csv.gz
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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28 && mv '$out_rules'.csv.gz '$out_rules'
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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29 #else:
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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30 --outfile '$out_rules'
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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31 #end if
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b97690ee00e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit 09b98dbaa3afe569a76577ab668dde6b4ee54b24
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32 #if str($adv.input_conditional_ec.input_type) == "in"
b97690ee00e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit 09b98dbaa3afe569a76577ab668dde6b4ee54b24
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33 --ec '$adv.input_conditional_ec.input_ec_in'
b97690ee00e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit 09b98dbaa3afe569a76577ab668dde6b4ee54b24
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34 #end if
b97690ee00e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit 09b98dbaa3afe569a76577ab668dde6b4ee54b24
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35 #if str($adv.input_conditional_ec.input_type) == "out"
b97690ee00e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit 09b98dbaa3afe569a76577ab668dde6b4ee54b24
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36 --ecx '$adv.input_conditional_ec.input_ec_out'
b97690ee00e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit 09b98dbaa3afe569a76577ab668dde6b4ee54b24
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37 #end if
b97690ee00e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit 09b98dbaa3afe569a76577ab668dde6b4ee54b24
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38 #if $adv.input_scores_file
b97690ee00e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit 09b98dbaa3afe569a76577ab668dde6b4ee54b24
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39 --scores '$adv.input_scores_file'
b97690ee00e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit 09b98dbaa3afe569a76577ab668dde6b4ee54b24
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40 #end if
0
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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41 ]]></command>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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42 <inputs>
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43 <conditional name="rules">
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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44 <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">
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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45 <option value="retro" selected="True">RetroRules (retro)</option>
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46 <option value="forward">RetroRules (forward)</option>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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47 <option value="all">RetroRules (all)</option>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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48 <option value="rules-file">Other reaction rules...</option>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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49 </param>
2
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50 <when value="retro"/>
14f811f46fe3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit 83279dc554c34566720f3857ac914a2e4fd85a8d
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51 <when value="forward"/>
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52 <when value="all"/>
0
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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53 <when value="rules-file">
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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54 <param name="file" type="data" format="csv" optional="False" label="Rules File" help="Filename of reaction rules"/>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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55 <param name="input_format" type="select" optional="False" label="File format" help="Input file format (default: csv)">
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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56 <option value="csv" selected="True">csv</option>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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57 <option value="tsv">tsv</option>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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58 </param>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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59 </when>
0a6e076541f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit fd0e355b0bef38185e830b0426757596f26c346d
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60 </conditional>
4
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61 <section name="adv" title="Advanced Options" expanded="false" >
b97690ee00e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit 09b98dbaa3afe569a76577ab668dde6b4ee54b24
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62 <param name="compress" type="boolean" checked="false" label="Compress output" />
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63 <param name="input_scores_file" type="data" format="csv" optional="True" label="Score File" help="Filename containing rules names and scores" />
b97690ee00e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit 09b98dbaa3afe569a76577ab668dde6b4ee54b24
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64 <conditional name="input_conditional_ec">
b97690ee00e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit 09b98dbaa3afe569a76577ab668dde6b4ee54b24
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65 <param name="input_type" type="select" label="Filter based on EC number">
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66 <option value="no" selected="True">No</option>
b97690ee00e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit 09b98dbaa3afe569a76577ab668dde6b4ee54b24
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67 <option value="in">EC numbers to keep</option>
b97690ee00e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit 09b98dbaa3afe569a76577ab668dde6b4ee54b24
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68 <option value="out">EC numbers to remove</option>
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69 </param>
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70 <when value="no" />
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71 <when value="in">
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72 <param name="input_ec_in" type="data" format="txt" label="File containing EC numbers to remove" help="EC numbers on one line separated by a comma">
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73 <sanitizer invalid_char="">
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74 <valid initial="string.ascii_letters,string.digits">
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75 <add value="," />
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76 <add value="." />
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77 </valid>
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78 </sanitizer>
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79 </param>
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80 </when>
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81 <when value="out">
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82 <param name="input_ec_out" type="data" format="txt" label="File containing EC numbers to remove" help="EC numbers on one line separated by a comma">
b97690ee00e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rrparser commit 09b98dbaa3afe569a76577ab668dde6b4ee54b24
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83 <sanitizer invalid_char="">
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84 <valid initial="string.ascii_letters,string.digits">
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85 <add value="," />
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86 <add value="." />
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87 </valid>
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88 </sanitizer>
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89 </param>
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90 </when>
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91 </conditional>
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92 <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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93 <option selected="true" value="2">2</option>
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94 <option selected="true" value="4">4</option>
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95 <option selected="true" value="6">6</option>
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96 <option selected="true" value="8">8</option>
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97 <option selected="true" value="10">10</option>
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98 <option selected="true" value="12">12</option>
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99 <option selected="true" value="14">14</option>
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100 <option selected="true" value="16">16</option>
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101 </param>
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102 </section>
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103
0
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104 </inputs>
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105 <outputs>
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106 <data name="out_rules" format="csv" label="${tool.name}(${rules.type}, d=$diameters)" >
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107 <change_format>
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108 <when input="compress" format="tar" value="true"/>
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109 </change_format>
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110 </data>
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111 </outputs>
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112 <tests>
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113 <test>
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114 <!-- test 1: check if identical outputs are produced with default parameters-->
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115 <output name="out_rules" md5="54806bd44f7a8414e78439e3bb99e6d8"/>
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116 </test>
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117 <test>
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118 <!-- test 2: check if identical outputs are produced with diameters=2,4,6-->
4
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119 <section name="adv">
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120 <param name="diameters" value="2,4,6"/>
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121 </section>
0
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122 <output name="out_rules" md5="12a55e1a3c7822a35ed799afa59b2aa2"/>
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123 </test>
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124 <test>
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125 <!-- test 3: check if identical outputs are produced with csv input rules file-->
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126 <conditional name="rules">
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127 <param name="type" value="rules-file"/>
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128 <param name="file" value="rules_in.csv" />
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129 </conditional>
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130 <output name="out_rules" file="rules_out.csv" ftype="csv" compare="diff"/>
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131 </test>
4
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132 <test>
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133 <!-- test 4 -->
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134 <conditional name="rules">
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135 <param name="type" value="rules-file"/>
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136 <param name="file" value="rules_in.csv" />
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137 </conditional>
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138 <section name="adv">
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139 <conditional name="input_conditional_ec">
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140 <param name="input_type" value="in"/>
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141 <param name="input_ec_in" value="ec.txt"/>
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142 </conditional>
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143 </section>
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144 <output name="out_rules" file="test.4.output.csv" ftype="csv" compare="diff"/>
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145 </test>
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146 <test>
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147 <!-- python -m rrparser -rules_file rules_in.csv -input-format csv -ecx ec.txt -diameters 2,4,6,8,10,12,14,16 -output-format csv -outfile test.5.output.csv -->
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148 <conditional name="rules">
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149 <param name="type" value="rules-file"/>
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150 <param name="file" value="rules_in.csv" />
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151 </conditional>
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152 <section name="adv">
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153 <conditional name="input_conditional_ec">
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154 <param name="input_type" value="out"/>
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155 <param name="input_ec_out" value="ec.txt"/>
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156 </conditional>
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157 </section>
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158 <output name="out_rules" file="test.5.output.csv" ftype="csv" compare="diff"/>
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159 </test>
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160 <test>
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161 <!-- python -m rrparser -rules_file rules_in.csv -input-format csv -diameters 2,4,6,8,10,12,14,16 -output-format csv -outfile rules_scores.csv -scores scores.csv -->
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162 <conditional name="rules">
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163 <param name="type" value="rules-file"/>
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164 <param name="file" value="rules_in.csv" />
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165 </conditional>
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166 <section name="adv" >
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167 <param name="input_scores_file" value="scores.csv" />
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168 </section>
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169 <output name="out_rules" file="rules_scores.csv" ftype="csv" compare="diff"/>
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170 </test>
0
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171 </tests>
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172 <help><![CDATA[
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173 RRulesParser
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174 ============
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175
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176 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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177
4
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178 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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180 Input
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181 -----
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183 * **Rule Type**: (string) Return the rules that are in reverse, forward, both direction or from an input user file
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184 * **rules-file**: (string) Filename of reaction rules provided in csv or tsv format.
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185 * **input_format**: (string) input file format (csv: default, tsv)
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186 * **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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187 * **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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188 * **Scores file**: file containing rules names and scores
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190 Ouput
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191 -----
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193 * **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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194 ]]></help>
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195 <creator>
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196 <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
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197 </creator>
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198 <citations>
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199 <citation type="doi">10.1093/nar/gky940</citation>
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200 </citations>
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201 </tool>