Mercurial > repos > tduigou > rptools_rpcompletion

comparison rpcompletion.xml @ 4:e59d28e31f88 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 96a30e92eab3144b924fdba7b63be10b218160a7
author tduigou
date Wed, 24 Jul 2024 08:42:16 +0000
parents eeb447ee56e4
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3:7f684f4519f1 4:e59d28e31f88
20 --max_subpaths_filter '$adv.max_subpaths_filter' 20 --max_subpaths_filter '$adv.max_subpaths_filter'
21 --cache-dir "\${TMPDIR:-.}" 21 --cache-dir "\${TMPDIR:-.}"
22 ]]></command> 22 ]]></command>
23 <inputs> 23 <inputs>
24 <param name="rp2paths_pathways" type="data" format="csv" label="RP2paths pathways" /> 24 <param name="rp2paths_pathways" type="data" format="csv" label="RP2paths pathways" />
25 <param name="rp2paths_compounds" type="data" format="csv" label="RP2paths compounds" /> 25 <param name="rp2paths_compounds" type="data" format="tabular" label="RP2paths compounds" />
26 <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 metabolic network" /> 26 <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 metabolic network" />
27 <param name="sink" type="data" format="csv" label="Sink from SBML" /> 27 <param name="sink" type="data" format="csv" label="Sink from SBML" />
28 <section name="adv" title="Advanced Options" expanded="false"> 28 <section name="adv" title="Advanced Options" expanded="false">
29 <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." /> 29 <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." />
30 <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." /> 30 <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." />
41 <!-- test 1: check if outputs are represented in an expected number --> 41 <!-- test 1: check if outputs are represented in an expected number -->
42 <param name="rp2paths_pathways" value="4-rp2paths_pathways.csv" /> 42 <param name="rp2paths_pathways" value="4-rp2paths_pathways.csv" />
43 <param name="rp2paths_compounds" value="3-rp2paths_compounds.tsv" /> 43 <param name="rp2paths_compounds" value="3-rp2paths_compounds.tsv" />
44 <param name="rp2_pathways" value="1-rp2_metnet.csv" /> 44 <param name="rp2_pathways" value="1-rp2_metnet.csv" />
45 <param name="sink" value="2-sink.csv" /> 45 <param name="sink" value="2-sink.csv" />
46 <output_collection name="pathways" type="list" count="9"/> 46 <output_collection name="pathways" type="list" count="10"/>
47 </test> 47 </test>
48 </tests> 48 </tests>
49 <help><![CDATA[ 49 <help><![CDATA[
50 rpCompletion 50 rpCompletion
51 ============ 51 ============
52 52
53 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. 53 Completes mono-component reactions output by `RetroPath2.0 <https://www.doi.org/10.1016/j.ymben.2017.12.002>`_ 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.
54 54
55 Input 55 Input
56 ----- 56 -----
57 57
58 Required: 58 Required: