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author tduigou
date Fri, 18 Nov 2022 16:07:59 +0000
parents e8d56cb2be03
children
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1 <tool id="rpcompletion" name="Complete Reactions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
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2 <description>Completes mono-component reactions output by RetroPath2.0 with the appropriate cofactors</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@">6.0.1</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
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9 </requirements>
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10 <stdio>
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11 <exit_code range="1" level="fatal" description="Could not Xref compartment_id" />
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12 <exit_code range="2" level="fatal" description="ValueError returned" />
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13 </stdio>
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14 <command detect_errors="exit_code"><![CDATA[
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15 python -m rptools.rpcompletion
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16 '$rp2_pathways'
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17 '$sink'
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18 '$rp2paths_compounds'
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19 '$rp2paths_pathways'
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20 completed_pathways
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21 --upper_flux_bound '$adv.upper_flux_bound'
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22 --lower_flux_bound '$adv.lower_flux_bound'
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23 --max_subpaths_filter '$adv.max_subpaths_filter'
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24 --cache-dir "\${TMPDIR:-.}"
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25 ]]></command>
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26 <inputs>
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27 <param name="rp2paths_pathways" type="data" format="csv" label="RP2paths pathways" />
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28 <param name="rp2paths_compounds" type="data" format="tabular" label="RP2paths compounds" />
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29 <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 metabolic network" />
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30 <param name="sink" type="data" format="csv" label="Sink from SBML" />
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31 <section name="adv" title="Advanced Options" expanded="false">
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32 <param argument="max_subpaths_filter" type="integer" value="10" min="1" max="1000" label="Max subpaths generated per pathway" help="Maximal number of subpaths to be created per master pathway." />
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33 <param argument="upper_flux_bound" type="integer" value="10000" min="-10000" max="10000" label="Upper flux bound" help="Upper flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created." />
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34 <param argument="lower_flux_bound" type="integer" value="0" min="-10000" max="10000" label="Lower flux bound" help="Lower flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created." />
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35 </section>
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36 </inputs>
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37 <outputs>
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38 <collection name="pathways" type="list" label="${tool.name}">
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39 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.xml" format="xml" directory="completed_pathways" visible="false" />
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40 </collection>
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41 </outputs>
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42 <tests>
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43 <test>
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44 <!-- test 1: check if identical outputs are produced with default parameters -->
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45 <param name="rp2paths_pathways" value="4-rp2paths_pathways.csv" />
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46 <param name="rp2paths_compounds" value="3-rp2paths_compounds.tsv" />
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47 <param name="rp2_pathways" value="1-rp2_metnet.csv" />
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48 <param name="sink" value="2-sink.csv" />
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49 <output_collection name="pathways" type="list">
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50 <element name="rp_001_0001" ftype="xml" file="rp_001_0001.xml" sort="true"/>
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51 <element name="rp_001_0006" ftype="xml" file="rp_001_0006.xml" sort="true"/>
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52 <element name="rp_001_0011" ftype="xml" file="rp_001_0011.xml" sort="true"/>
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53 <element name="rp_002_0001" ftype="xml" file="rp_002_0001.xml" sort="true"/>
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54 <element name="rp_002_0011" ftype="xml" file="rp_002_0011.xml" sort="true"/>
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55 <element name="rp_002_0021" ftype="xml" file="rp_002_0021.xml" sort="true"/>
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56 <element name="rp_003_0001" ftype="xml" file="rp_003_0001.xml" sort="true"/>
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57 <element name="rp_003_0131" ftype="xml" file="rp_003_0131.xml" sort="true"/>
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58 <element name="rp_003_0261" ftype="xml" file="rp_003_0261.xml" sort="true"/>
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59 </output_collection>
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60 </test>
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61 </tests>
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62 <help><![CDATA[
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63 rpCompletion
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64 ============
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65
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66 Completes mono-component reactions output by `RetroPath2.0 <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_ 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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67
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68 Input
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69 -----
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70
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71 Required:
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72
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73 * **RetroPath2.0 metabolic network**: RetroPath2.0 pathways file
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74 * **Sink from SBML**: rpextractsink file containing infos on molecules in the sink
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75 * **RP2paths compounds**: rp2paths compounds file
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76 * **RP2paths pathways**: rp2paths pathways file
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77
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78 Advanced options:
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79
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80 * **Upper flux bound**: (integer, default=9999) Upper flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created.
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81 * **Lower flux bound**: (integer, default=0) Lower flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created.
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82 * **Max subpaths generated per pathway**: (integer, default=10, 0=nofilter) Maximal number of subpaths to be created per master pathway.
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83
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84 Output
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85 ------
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86
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87 * **pathways**: SBML completed pathways
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88
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89 Project Links
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90 ---------------------
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91 * `GitHub <https://github.com/brsynth/rptools>`_
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92
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93 Acknowledgments
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94 ---------------
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95
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96 * Thomas Duigou
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97
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98 Licence
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99 -------
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100
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101 `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
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102
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103 ]]></help>
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104 <creator>
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105 <person givenName="Joan" familyName="Hérisson" email="joan.herisson@univ-evry.fr" identifier="https://orcid.org/0000-0001-9741-0847" />
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106 <person givenName="Melchior" familyName="du Lac" identifier="https://orcid.org/0000-0002-9984-4689" />
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107 </creator>
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108 </tool>