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planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty
author tduigou
date Wed, 21 Sep 2022 09:25:09 +0000
parents c2da3a9e39e5
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1 <tool id="rpcompletion" name="Complete Reactions" version="@TOOL_VERSION@" profile="19.09"> 1 <tool id="rpcompletion" name="Complete Reactions" version="@TOOL_VERSION@" profile="21.09">
2 <description>From the output of RP2Paths and RetroPath2.0, generate SBML unique and complete (with cofactors) pathways with mono-component reactions</description> 2 <description>From the output of RP2Paths and RetroPath2.0, generate SBML unique and complete (with cofactors) pathways with mono-component reactions</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">5.12.3</token> 4 <token name="@TOOL_VERSION@">5.13.1</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
8 </requirements> 8 </requirements>
9 <stdio> 9 <stdio>
25 <param name="rp2paths_pathways" type="data" format="csv" label="RP2paths pathways" /> 25 <param name="rp2paths_pathways" type="data" format="csv" label="RP2paths pathways" />
26 <param name="rp2paths_compounds" type="data" format="tsv" label="RP2paths compounds" /> 26 <param name="rp2paths_compounds" type="data" format="tsv" label="RP2paths compounds" />
27 <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 metabolic network" /> 27 <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 metabolic network" />
28 <param name="sink" type="data" format="csv" label="Sink from SBML" /> 28 <param name="sink" type="data" format="csv" label="Sink from SBML" />
29 <section name="adv" title="Advanced Options" expanded="false"> 29 <section name="adv" title="Advanced Options" expanded="false">
30 <param name="max_subpaths_filter" type="integer" value="10" label="Max subpaths generated per pathway" /> 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." />
31 <param name="upper_flux_bound" type="integer" value="999999" label="Upper flux bound" /> 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." />
32 <param name="lower_flux_bound" type="integer" value="0" label="Lower flux bound" /> 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." />
33 </section> 33 </section>
34 </inputs> 34 </inputs>
35 <outputs> 35 <outputs>
36 <collection name="pathways" type="list" label="${tool.name}"> 36 <collection name="pathways" type="list" label="${tool.name}">
37 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.xml" format="xml" directory="completed_pathways" visible="false" /> 37 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.xml" format="xml" directory="completed_pathways" visible="false" />
59 </tests> 59 </tests>
60 <help><![CDATA[ 60 <help><![CDATA[
61 rpCompletion 61 rpCompletion
62 ============ 62 ============
63 63
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. 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.
65 65
66 Input 66 Input
67 ----- 67 -----
68 68
69 Required: 69 Required:
70 70
71 * **rp2_pathways**: (string) Path to the RetroPath2.0 pathways file 71 * **RetroPath2.0 metabolic network**: RetroPath2.0 pathways file
72 * **rp2_sink**: (string) Path to the rpextractsink file containing infos on molecules in the sink 72 * **Sink from SBML**: rpextractsink file containing infos on molecules in the sink
73 * **rp2paths_compounds**: (string) Path to the rp2paths compounds file 73 * **RP2paths compounds**: rp2paths compounds file
74 * **rp2paths_pathways**: (string) Path to the rp2paths pathways file 74 * **RP2paths pathways**: rp2paths pathways file
75 * **outdir**: (string) Path to the output directory containing sbml completed pathways
76 75
77 Advanced options: 76 Advanced options:
78 77
79 * **-upper_flux_bound**: (integer, default=9999) Upper flux bound value 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.
80 * **-lower_flux_bound**: (integer, default=0) Lower flux bound value 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.
81 * **-max_subpaths_filter**: (integer, default=10, 0=nofilter) Number of subpaths per path 80 * **Max subpaths generated per pathway**: (integer, default=10, 0=nofilter) Maximal number of subpaths to be created per master pathway.
81
82 Output
83 ------
84
85 * **pathways**: SBML completed pathways
82 86
83 Project Links 87 Project Links
84 --------------------- 88 ---------------------
85 * `GitHub <https://github.com/brsynth/rptools>`_ 89 * `GitHub <https://github.com/brsynth/rptools>`_
86 90
87 Version 91 Version
88 ---------- 92 ----------
89 93
90 5.12.1 94 5.13.1
91 95
92 Authors 96 Authors
93 ------- 97 -------
94 98
95 * **Melchior du Lac** 99 * **Melchior du Lac**