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planemo upload commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
author tduigou
date Fri, 18 Nov 2022 16:11:40 +0000
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1 <tool id="rpextractsink" name="Sink from SBML" version="@TOOL_VERSION@" profile="19.09"> 1 <tool id="rpextractsink" name="Sink from SBML" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
2 <description>Generate the RetroPath2.0 sink file from an SBML input</description> 2 <description>Generate the RetroPath2.0 sink file from an SBML input</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">5.12.1</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>
12 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
13 python -m rptools.rpextractsink 14 python -m rptools.rpextractsink
14 '$input' 15 '$input'
15 '$sink' 16 '$sink'
16 --compartment_id '$compartment_id' 17 --compartment_id '$compartment_id'
17 #if str($adv.remove_dead_end) == "true": 18 $adv.remove_dead_end
18 --remove_dead_end 19 --cache-dir "\${TMPDIR:-.}"
19 #end if
20 ]]></command> 20 ]]></command>
21 <inputs> 21 <inputs>
22 <param name="input" type="data" format="xml" optional="false" label="Strain" /> 22 <param name="input" type="data" format="sbml" optional="false" label="Strain" help="The structure of metabolites present in the chosen chassis strain in SBML format" />
23 <param name="compartment_id" type="text" value="c" label="SBML compartment ID" > 23 <param name="compartment_id" type="text" value="c" label="SBML compartment ID" help="Specify the compartment from which to extract the sink molecules. The default are for BiGG models (cytosol)" >
24 <validator type="empty_field" message="SBML compartment ID is required"/> 24 <validator type="empty_field" message="SBML compartment ID is required"/>
25 </param> 25 </param>
26 <section name="adv" title="Advanced Options" expanded="false"> 26 <section name="adv" title="Advanced Options" expanded="false">
27 <param name="remove_dead_end" type="boolean" checked="true" label="Remove dead-end metabolites using FVA evaluation?" /> 27 <param argument="--remove_dead_end" type="boolean" truevalue="--remove_dead_end" falsevalue="" checked="true" label="Remove dead-end metabolites using FVA evaluation?" help="Perform FVA (Flux Variability Analysis) evaluation to remove dead end metabolites" />
28 </section> 28 </section>
29 </inputs> 29 </inputs>
30 <outputs> 30 <outputs>
31 <data name="sink" format="csv" metadata_source="input" label="Sink - ${input.name}" /> 31 <data name="sink" format="csv" metadata_source="input" label="Sink - ${input.name}" />
32 </outputs> 32 </outputs>
40 <help><![CDATA[ 40 <help><![CDATA[
41 41
42 Sink from SBML 42 Sink from SBML
43 ================= 43 =================
44 44
45 Sink refers to the collection of chemical species used by the restrosynthesis algorithm of RetroPath2.0 to finish metabolic route exploration. This tool uses an SBML file of the desired chassis organism, parses all the molecules within a specified compartment (example: cytoplasm, Golgi apparatus, nucleus, etc) and uses its MIRIAM annotation to find their InChI structures. You can use "Remove dead-end metabolites using FVA evaluation? to conduct Flux Variability Analysis to remove metabolites that lack the requisite flux that would account for their production or consumption within the metabolic network. 45 Sink refers to the collection of chemical species used by the restrosynthesis algorithm of `RetroPath2.0 <https://doi.org/10.1016/j.ymben.2017.12.002>`_ to finish metabolic route exploration. This tool uses an SBML (Systems Biology Markup Language) file of the desired chassis organism, parses all the molecules within a specified compartment (example: cytosol, Golgi apparatus, nucleus, etc) and uses its MIRIAM (Minimal Information Requested In the Annotation of Models) annotation to find their InChI (International Chemical Identifier) structures. In *Advanced Options*, You can use *Remove dead-end metabolites using FVA evaluation?* to conduct Flux Variability Analysis to remove metabolites that lack the requisite flux that would account for their production or consumption within the metabolic network.
46 46
47 In the advanced options, one can specify the compartment from which the tool will extract the chemical species. The default is 'c', the BiGG code for the cytoplasm. If the user wishes to upload an SBML file from another source, then this value must be changed. 47 The user can also specify the compartment from which the tool will extract the chemical species. The default is 'c', the BiGG code for the cytosol. If the user wishes to upload an SBML file from another source, then this value must be changed.
48 48
49 The results are written to a RetroPath2.0 friendly CSV file format that can be used as sink input. 49 The results are written to a RetroPath2.0 friendly CSV file format that can be used as sink input.
50
51 50
52 Input 51 Input
53 ----- 52 -----
54 53
55 Required: 54 Required:
56 55
57 * **input_sbml**\ : (string) Path to the input SBML file 56 * **Strain**\ : The structure of metabolites present in the chosen chassis strain in SBML format.
58 * **compartment_id**\ : (string, default: c) Specify the compartment from which to extract the sink molecules. The default are for BiGG models 57 * **SBML compartment ID**\ : (string, default: c) Specify the compartment from which to extract the sink molecules. The default are for BiGG models (cytosol).
59 58
60 Advanced options: 59 Advanced options:
61 60
62 * **remove_dead_end**\ : (boolean, default: True) Perform FVA evaluation to remove dead end metabolites 61 * **Remove dead-end metabolites using FVA evaluation?**\ : (boolean, default: True) Perform FVA (Flux Variability Analysis) evaluation to remove dead end metabolites.
63 62
64 Output 63 Output
65 ------ 64 ------
66 65
67 * **output_sink**\ : (string) Path to the output csv file 66 * **Sink**\ : CSV file containing a collection of chemical species used by the restrosynthesis algorithm of `RetroPath2.0 <https://doi.org/10.1016/j.ymben.2017.12.002>`_.
68 67
69 Project Links 68 Project Links
70 --------------------- 69 ---------------------
71 70
72 * `GitHub <https://github.com/brsynth/rptools>`_ 71 * `GitHub <https://github.com/brsynth/rptools>`_
73
74 Version
75 ----------
76
77 5.12.1
78
79 Authors
80 -------
81
82 * **Melchior du Lac**
83 * Joan Hérisson
84 72
85 License 73 License
86 ------- 74 -------
87 75
88 `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_ 76 `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
91 --------------- 79 ---------------
92 80
93 * Thomas Duigou 81 * Thomas Duigou
94 82
95 ]]></help> 83 ]]></help>
84 <creator>
85 <person givenName="Joan" familyName="Hérisson" email="joan.herisson@univ-evry.fr" identifier="https://orcid.org/0000-0001-9741-0847" />
86 <person givenName="Melchior" familyName="du Lac" identifier="https://orcid.org/0000-0002-9984-4689" />
87 </creator>
96 <citations> 88 <citations>
97 <citation type="doi">10.1038/nbt1156</citation> 89 <citation type="doi">10.1038/nbt1156</citation>
98 <citation type="doi">10.1016/j.ymben.2017.12.002</citation> 90 <citation type="doi">10.1016/j.ymben.2017.12.002</citation>
99 <citation type="doi">10.1186/1752-0509-7-74</citation> 91 <citation type="doi">10.1186/1752-0509-7-74</citation>
100 <citation type="doi">10.1093/bioinformatics/btn051</citation> 92 <citation type="doi">10.1093/bioinformatics/btn051</citation>