Mercurial > repos > tduigou > rpcompletion

annotate rpcompletion.xml @ 4:e8d56cb2be03 draft

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author tduigou
date Wed, 21 Sep 2022 09:41:34 +0000
parents fcc8f3e2d4da
children 37bed74bbd44
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1 <tool id="rpcompletion" name="Complete Reactions" version="@TOOL_VERSION@" profile="21.09">
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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@">5.13.1</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 '$adv.max_subpaths_filter'
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23 ]]></command>
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24 <inputs>
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25 <param name="rp2paths_pathways" type="data" format="csv" label="RP2paths pathways" />
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26 <param name="rp2paths_compounds" type="data" format="tsv" label="RP2paths compounds" />
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27 <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 metabolic network" />
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28 <param name="sink" type="data" format="csv" label="Sink from SBML" />
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29 <section name="adv" title="Advanced Options" expanded="false">
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30 <param argument="max_subpaths_filter" type="integer" value="10" min="1" max="1000" label="Max subpaths generated per pathway" help="Maximal number of subpaths to be created per master pathway." />
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31 <param argument="upper_flux_bound" type="integer" value="10000" min="-10000" max="10000" label="Upper flux bound" help="Upper flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created." />
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32 <param argument="lower_flux_bound" type="integer" value="0" min="-10000" max="10000" label="Lower flux bound" help="Lower flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created." />
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33 </section>
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34 </inputs>
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35 <outputs>
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36 <collection name="pathways" type="list" label="${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 <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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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 * **RetroPath2.0 metabolic network**: RetroPath2.0 pathways file
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72 * **Sink from SBML**: rpextractsink file containing infos on molecules in the sink
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73 * **RP2paths compounds**: rp2paths compounds file
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74 * **RP2paths pathways**: rp2paths pathways file
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75
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76 Advanced options:
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77
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78 * **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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79 * **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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80 * **Max subpaths generated per pathway**: (integer, default=10, 0=nofilter) Maximal number of subpaths to be created per master pathway.
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81
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82 Output
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83 ------
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84
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85 * **pathways**: SBML completed pathways
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86
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87 Project Links
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88 ---------------------
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89 * `GitHub <https://github.com/brsynth/rptools>`_
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90
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91 Version
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92 ----------
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93
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94 5.13.1
0
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95
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96 Authors
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97 -------
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98
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99 * **Melchior du Lac**
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100 * **Joan Hérisson**
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101
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102 Acknowledgments
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103 ---------------
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104
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105 * Thomas Duigou
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106
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107 Licence
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108 -------
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109
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110 `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
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111
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112 ]]></help>
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113 </tool>