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comparison rpextractsink.xml @ 3:47bb93e7832b draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Wed, 09 Feb 2022 14:37:06 +0000
parents 8d16a0f08d0a
children 191665a689de
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2:8d16a0f08d0a 3:47bb93e7832b
1 <tool id="rpextractsink" name="Sink from SBML" version="5.11.1" profile="19.09"> 1 <tool id="rpextractsink" name="Sink from SBML" version="@TOOL_VERSION@" profile="19.09">
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>
4 <token name="@TOOL_VERSION@">5.12.1</token>
5 </macros>
3 <requirements> 6 <requirements>
4 <requirement type="package" version="5.11.1">rptools</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
5 </requirements> 8 </requirements>
6 <stdio> 9 <stdio>
7 <regex match="Could not retreive any species in the compartment" level="fatal" /> 10 <regex match="Could not retreive any species in the compartment" level="fatal" />
8 </stdio> 11 </stdio>
9 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
10 python -m rptools.rpextractsink 13 python -m rptools.rpextractsink
11 '$input' 14 '$input'
12 '$sink' 15 '$sink'
13 --compartment_id '$adv.compartment_id' 16 --compartment_id '$compartment_id'
14 #if str($adv.remove_dead_end) == "true": 17 #if str($adv.remove_dead_end) == "true":
15 --remove_dead_end 18 --remove_dead_end
16 #end if 19 #end if
17 ]]></command> 20 ]]></command>
18 <inputs> 21 <inputs>
19 <param name="input" type="data" format="xml" optional="false" label="Strain" /> 22 <param name="input" type="data" format="xml" optional="false" label="Strain" />
23 <param name="compartment_id" type="text" value="c" label="SBML compartment ID" >
24 <validator type="empty_field" message="SBML compartment ID is required"/>
25 </param>
20 <section name="adv" title="Advanced Options" expanded="false"> 26 <section name="adv" title="Advanced Options" expanded="false">
21 <param name="compartment_id" type="text" value="c" label="SBML compartment ID" />
22 <param name="remove_dead_end" type="boolean" checked="true" label="Remove dead-end metabolites using FVA evaluation?" /> 27 <param name="remove_dead_end" type="boolean" checked="true" label="Remove dead-end metabolites using FVA evaluation?" />
23 </section> 28 </section>
24 </inputs> 29 </inputs>
25 <outputs> 30 <outputs>
26 <data name="sink" format="csv" label="${tool.name} - ${input.name}" /> 31 <data name="sink" format="csv" metadata_source="input" label="Sink - ${input.name}" />
27 </outputs> 32 </outputs>
28 <tests> 33 <tests>
29 <test> 34 <test>
30 <!-- test 1: check if identical outputs are produced with iCN718 model input --> 35 <!-- test 1: check if identical outputs are produced with iCN718 model input -->
31 <param name="input" value="iCN718.xml.gz" /> 36 <param name="input" value="iCN718.xml.gz" />
37 Sink from SBML 42 Sink from SBML
38 ================= 43 =================
39 44
40 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 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.
41 46
42 In the advanced options, one can specify the compartment from which the tool will extract the chemical species. The default is MNXC3, the MetaNetX code for the cytoplasm. If the user wishes to upload an SBML file from another source, then this value must be changed. 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.
43 48
44 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.
45 50
46 51
47 Input 52 Input
48 ----- 53 -----
49 54
50 Required: 55 Required:
51 56
52 * **input_sbml**\ : (string) Path to the input SBML file 57 * **input_sbml**\ : (string) Path to the input SBML file
58 * **compartment_id**\ : (string, default: c) Specify the compartment from which to extract the sink molecules. The default are for BiGG models
53 59
54 Advanced options: 60 Advanced options:
55 61
56 * **remove_dead_end**\ : (boolean, default: True) Perform FVA evaluation to remove dead end metabolites 62 * **remove_dead_end**\ : (boolean, default: True) Perform FVA evaluation to remove dead end metabolites
57 * **compartment_id**\ : (string, default: MNXC3) Specify the compartment from which to extract the sink molecules. The default are for MetaNetX files
58 63
59 Output 64 Output
60 ------ 65 ------
61 66
62 * **output_sink**\ : (string) Path to the output csv file 67 * **output_sink**\ : (string) Path to the output csv file
67 * `GitHub <https://github.com/brsynth/rptools>`_ 72 * `GitHub <https://github.com/brsynth/rptools>`_
68 73
69 Version 74 Version
70 ---------- 75 ----------
71 76
72 5.11.1 77 5.12.1
73 78
74 Authors 79 Authors
75 ------- 80 -------
76 81
77 * **Melchior du Lac** 82 * **Melchior du Lac**