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annotate rpcompletion.xml @ 1:b8242cf18cc0 draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Wed, 09 Feb 2022 16:05:48 +0000
parents 98d925a75257
children d5c53a916005
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1 <tool id="rpcompletion" name="Complete Reactions" version="@TOOL_VERSION@" profile="19.09">
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2 <description>From the output of RP2Paths and RetroPath2.0, generate SBML unique and complete (with cofactors) pathways with mono-component reactions</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">5.12.1</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
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8 </requirements>
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9 <stdio>
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10 <exit_code range="1" level="fatal" description="Could not Xref compartment_id" />
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11 <exit_code range="2" level="fatal" description="ValueError returned" />
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12 </stdio>
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13 <command detect_errors="exit_code"><![CDATA[
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14 python -m rptools.rpcompletion
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15 '$rp2_pathways'
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16 '$sink'
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17 '$rp2paths_compounds'
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18 '$rp2paths_pathways'
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19 completed_pathways
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20 --upper_flux_bound '$adv.upper_flux_bound'
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21 --lower_flux_bound '$adv.lower_flux_bound'
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22 --max_subpaths_filter '$adv.max_subpaths_filter'
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23 ]]></command>
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24 <inputs>
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25 <param name="rp2paths_pathways" type="data" format="csv" label="RP2paths pathways" />
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26 <param name="rp2paths_compounds" type="data" format="tsv" label="RP2paths compounds" />
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27 <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 metabolic network" />
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28 <param name="sink" type="data" format="csv" label="Sink from SBML" />
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29 <section name="adv" title="Advanced Options" expanded="false">
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30 <param name="max_subpaths_filter" type="integer" value="10" label="Max subpaths generated per pathway" />
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31 <param name="upper_flux_bound" type="integer" value="999999" label="Upper flux bound" />
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32 <param name="lower_flux_bound" type="integer" value="0" label="Lower flux bound" />
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33 </section>
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34 </inputs>
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35 <outputs>
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36 <collection name="pathways" type="list" label="${tool.name}">
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37 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.xml" format="xml" directory="completed_pathways" visible="false" />
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38 </collection>
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39 </outputs>
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40 <tests>
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41 <test>
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42 <!-- test 1: check if identical outputs are produced with default parameters -->
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43 <param name="rp2paths_pathways" value="4-rp2paths_pathways.csv" />
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44 <param name="rp2paths_compounds" value="3-rp2paths_compounds.tsv" />
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45 <param name="rp2_pathways" value="1-rp2_metnet.csv" />
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46 <param name="sink" value="2-sink.csv" />
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47 <output_collection name="pathways" type="list">
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48 <element name="rp_001_0001" ftype="xml" file="rp_001_0001.xml" sort="true"/>
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49 <element name="rp_001_0006" ftype="xml" file="rp_001_0006.xml" sort="true"/>
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50 <element name="rp_001_0011" ftype="xml" file="rp_001_0011.xml" sort="true"/>
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51 <element name="rp_002_0001" ftype="xml" file="rp_002_0001.xml" sort="true"/>
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52 <element name="rp_002_0011" ftype="xml" file="rp_002_0011.xml" sort="true"/>
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53 <element name="rp_002_0021" ftype="xml" file="rp_002_0021.xml" sort="true"/>
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54 <element name="rp_003_0001" ftype="xml" file="rp_003_0001.xml" sort="true"/>
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55 <element name="rp_003_0131" ftype="xml" file="rp_003_0131.xml" sort="true"/>
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56 <element name="rp_003_0261" ftype="xml" file="rp_003_0261.xml" sort="true"/>
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57 </output_collection>
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58 </test>
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59 </tests>
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60 <help><![CDATA[
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61 rpCompletion
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62 ============
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63
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64 Completes mono-component reactions output by RetroPath2.0 with the appropriate cofactors. Creates sub-paths when multiple reaction rules are associated with a single reaction. Input is a single pathways file produced by RP2Paths. It stands on rpCache which store pre-computed data.
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65
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66 Input
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67 -----
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68
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69 Required:
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70
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71 * **rp2_pathways**: (string) Path to the RetroPath2.0 pathways file
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72 * **rp2_sink**: (string) Path to the rpextractsink file containing infos on molecules in the sink
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73 * **rp2paths_compounds**: (string) Path to the rp2paths compounds file
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74 * **rp2paths_pathways**: (string) Path to the rp2paths pathways file
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75 * **outdir**: (string) Path to the output directory containing sbml completed pathways
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76
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77 Advanced options:
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78
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79 * **-upper_flux_bound**: (integer, default=9999) Upper flux bound value
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80 * **-lower_flux_bound**: (integer, default=0) Lower flux bound value
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81 * **-max_subpaths_filter**: (integer, default=10, 0=nofilter) Number of subpaths per path
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82
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83 Project Links
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84 ---------------------
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85 * `GitHub <https://github.com/brsynth/rptools>`_
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86
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87 Version
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88 ----------
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89
1
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90 5.12.1
0
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91
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92 Authors
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93 -------
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94
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95 * **Melchior du Lac**
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96 * **Joan Hérisson**
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97
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98 Acknowledgments
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99 ---------------
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100
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101 * Thomas Duigou
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102
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103 Licence
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104 -------
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105
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106 `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
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107
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108 ]]></help>
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109 </tool>