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annotate rpcompletion.xml @ 0:98d925a75257 draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Tue, 23 Nov 2021 13:45:45 +0000
parents
children b8242cf18cc0
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1 <tool id="rpCompletion" name="Complete Reactions" version="5.9.2">
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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 <requirements>
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4 <requirement type="package" version="5.9.2">rptools</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1" level="fatal" description="Could not Xref compartment_id" />
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8 <exit_code range="2" level="fatal" description="ValueError returned" />
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9 </stdio>
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10 <command detect_errors="exit_code"><![CDATA[
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11 python -m rptools.rpcompletion
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12 '$rp2_pathways'
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13 '$sink'
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14 '$rp2paths_compounds'
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15 '$rp2paths_pathways'
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16 completed_pathways
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17 --upper_flux_bound '$adv.upper_flux_bound'
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18 --lower_flux_bound '$adv.lower_flux_bound'
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19 --max_subpaths_filter '$adv.max_subpaths_filter'
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20 ]]></command>
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21 <inputs>
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22 <param name="rp2paths_pathways" type="data" format="csv" label="RP2paths pathways" />
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23 <param name="rp2paths_compounds" type="data" format="tsv" label="RP2paths compounds" />
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24 <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 metabolic network" />
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25 <param name="sink" type="data" format="csv" label="Sink from SBML" />
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26 <section name="adv" title="Advanced Options" expanded="false">
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27 <param name="max_subpaths_filter" type="integer" value="10" label="Max subpaths generated per pathway" />
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28 <param name="upper_flux_bound" type="integer" value="999999" label="Upper flux bound" />
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29 <param name="lower_flux_bound" type="integer" value="0" label="Lower flux bound" />
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30 </section>
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31 </inputs>
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32 <outputs>
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33 <collection name="pathways" type="list" label="${tool.name}">
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34 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.xml" format="xml" directory="completed_pathways" visible="false" />
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35 </collection>
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36 </outputs>
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37 <tests>
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38 <test>
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39 <!-- test 1: check if identical outputs are produced with default parameters -->
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40 <param name="rp2paths_pathways" value="4-rp2paths_pathways.csv" />
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41 <param name="rp2paths_compounds" value="3-rp2paths_compounds.tsv" />
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42 <param name="rp2_pathways" value="1-rp2_metnet.csv" />
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43 <param name="sink" value="2-sink.csv" />
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44 <output_collection name="pathways" type="list">
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45 <element name="rp_001_0001" ftype="xml" file="rp_001_0001.xml" sort="true"/>
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46 <element name="rp_001_0006" ftype="xml" file="rp_001_0006.xml" sort="true"/>
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47 <element name="rp_001_0011" ftype="xml" file="rp_001_0011.xml" sort="true"/>
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48 <element name="rp_002_0001" ftype="xml" file="rp_002_0001.xml" sort="true"/>
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49 <element name="rp_002_0011" ftype="xml" file="rp_002_0011.xml" sort="true"/>
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50 <element name="rp_002_0021" ftype="xml" file="rp_002_0021.xml" sort="true"/>
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51 <element name="rp_003_0001" ftype="xml" file="rp_003_0001.xml" sort="true"/>
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52 <element name="rp_003_0131" ftype="xml" file="rp_003_0131.xml" sort="true"/>
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53 <element name="rp_003_0261" ftype="xml" file="rp_003_0261.xml" sort="true"/>
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54 </output_collection>
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55 </test>
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56 </tests>
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57 <help><![CDATA[
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58 rpCompletion
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59 ============
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60
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61 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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62
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63 Input
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64 -----
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65
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66 Required:
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67
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68 * **rp2_pathways**: (string) Path to the RetroPath2.0 pathways file
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69 * **rp2_sink**: (string) Path to the rpextractsink file containing infos on molecules in the sink
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70 * **rp2paths_compounds**: (string) Path to the rp2paths compounds file
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71 * **rp2paths_pathways**: (string) Path to the rp2paths pathways file
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72 * **outdir**: (string) Path to the output directory containing sbml completed pathways
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73
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74 Advanced options:
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75
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76 * **-upper_flux_bound**: (integer, default=9999) Upper flux bound value
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77 * **-lower_flux_bound**: (integer, default=0) Lower flux bound value
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78 * **-max_subpaths_filter**: (integer, default=10, 0=nofilter) Number of subpaths per path
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79
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80 Project Links
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81 ---------------------
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82 * `GitHub <https://github.com/brsynth/rptools>`_
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83
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84 Version
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85 ----------
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86
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87 5.9.2
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88
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89 Authors
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90 -------
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91
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92 * **Melchior du Lac**
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93 * **Joan Hérisson**
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94
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95 Acknowledgments
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96 ---------------
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97
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98 * Thomas Duigou
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99
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100 Licence
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101 -------
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102
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103 `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
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104
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105 ]]></help>
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106 </tool>