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planemo upload commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
author tduigou
date Fri, 18 Nov 2022 16:07:59 +0000
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4:e8d56cb2be03 5:37bed74bbd44
1 <tool id="rpcompletion" name="Complete Reactions" version="@TOOL_VERSION@" profile="21.09"> 1 <tool id="rpcompletion" name="Complete Reactions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" 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>Completes mono-component reactions output by RetroPath2.0 with the appropriate cofactors</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">5.13.1</token> 4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@TOOL_VERSION@">6.0.1</token>
5 </macros> 6 </macros>
6 <requirements> 7 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
8 </requirements> 9 </requirements>
9 <stdio> 10 <stdio>
18 '$rp2paths_pathways' 19 '$rp2paths_pathways'
19 completed_pathways 20 completed_pathways
20 --upper_flux_bound '$adv.upper_flux_bound' 21 --upper_flux_bound '$adv.upper_flux_bound'
21 --lower_flux_bound '$adv.lower_flux_bound' 22 --lower_flux_bound '$adv.lower_flux_bound'
22 --max_subpaths_filter '$adv.max_subpaths_filter' 23 --max_subpaths_filter '$adv.max_subpaths_filter'
24 --cache-dir "\${TMPDIR:-.}"
23 ]]></command> 25 ]]></command>
24 <inputs> 26 <inputs>
25 <param name="rp2paths_pathways" type="data" format="csv" label="RP2paths pathways" /> 27 <param name="rp2paths_pathways" type="data" format="csv" label="RP2paths pathways" />
26 <param name="rp2paths_compounds" type="data" format="tsv" label="RP2paths compounds" /> 28 <param name="rp2paths_compounds" type="data" format="tabular" label="RP2paths compounds" />
27 <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 metabolic network" /> 29 <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" /> 30 <param name="sink" type="data" format="csv" label="Sink from SBML" />
29 <section name="adv" title="Advanced Options" expanded="false"> 31 <section name="adv" title="Advanced Options" expanded="false">
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." /> 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." />
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." /> 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." />
86 88
87 Project Links 89 Project Links
88 --------------------- 90 ---------------------
89 * `GitHub <https://github.com/brsynth/rptools>`_ 91 * `GitHub <https://github.com/brsynth/rptools>`_
90 92
91 Version
92 ----------
93
94 5.13.1
95
96 Authors
97 -------
98
99 * **Melchior du Lac**
100 * **Joan Hérisson**
101
102 Acknowledgments 93 Acknowledgments
103 --------------- 94 ---------------
104 95
105 * Thomas Duigou 96 * Thomas Duigou
106 97
108 ------- 99 -------
109 100
110 `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_ 101 `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
111 102
112 ]]></help> 103 ]]></help>
104 <creator>
105 <person givenName="Joan" familyName="Hérisson" email="joan.herisson@univ-evry.fr" identifier="https://orcid.org/0000-0001-9741-0847" />
106 <person givenName="Melchior" familyName="du Lac" identifier="https://orcid.org/0000-0002-9984-4689" />
107 </creator>
113 </tool> 108 </tool>