Mercurial > repos > tduigou > rptools_rpextractsink
annotate rpextractsink.xml @ 0:b803ac9d24ab draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
author | tduigou |
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date | Wed, 16 Nov 2022 11:12:36 +0000 |
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children | caf2b5731a5e |
rev | line source |
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b803ac9d24ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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1 <tool id="rptools_rpextractsink" name="Sink from SBML" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> |
b803ac9d24ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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2 <description>Generate the RetroPath2.0 sink file from an SBML input</description> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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3 <macros> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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4 <token name="@VERSION_SUFFIX@">0</token> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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5 <token name="@TOOL_VERSION@">5.13.1</token> |
b803ac9d24ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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6 </macros> |
b803ac9d24ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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7 <requirements> |
b803ac9d24ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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8 <requirement type="package" version="@TOOL_VERSION@">rptools</requirement> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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9 </requirements> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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10 <stdio> |
b803ac9d24ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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11 <regex match="Could not retreive any species in the compartment" level="fatal" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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12 </stdio> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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13 <command detect_errors="exit_code"><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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14 python -m rptools.rpextractsink |
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15 '$input' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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16 '$sink' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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17 --compartment_id '$compartment_id' |
b803ac9d24ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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18 $adv.remove_dead_end |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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19 --cache-dir "\${TMPDIR:-.}" |
b803ac9d24ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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20 ]]></command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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21 <inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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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" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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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)" > |
b803ac9d24ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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24 <validator type="empty_field" message="SBML compartment ID is required"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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25 </param> |
b803ac9d24ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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26 <section name="adv" title="Advanced Options" expanded="false"> |
b803ac9d24ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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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" /> |
b803ac9d24ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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28 </section> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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29 </inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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30 <outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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31 <data name="sink" format="csv" metadata_source="input" label="Sink - ${input.name}" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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32 </outputs> |
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33 <tests> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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34 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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35 <!-- test 1: check if identical outputs are produced with iCN718 model input --> |
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36 <param name="input" value="iCN718.xml.gz" /> |
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37 <output name="sink" file="sink.csv" ftype="csv" compare="diff"/> |
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38 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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39 </tests> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
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40 <help><![CDATA[ |
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41 |
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42 Sink from SBML |
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43 ================= |
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44 |
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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. |
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46 |
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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. |
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48 |
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49 The results are written to a RetroPath2.0 friendly CSV file format that can be used as sink input. |
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50 |
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51 Input |
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52 ----- |
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53 |
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54 Required: |
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55 |
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56 * **Strain**\ : The structure of metabolites present in the chosen chassis strain in SBML format. |
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57 * **SBML compartment ID**\ : (string, default: c) Specify the compartment from which to extract the sink molecules. The default are for BiGG models (cytosol). |
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58 |
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59 Advanced options: |
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60 |
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61 * **Remove dead-end metabolites using FVA evaluation?**\ : (boolean, default: True) Perform FVA (Flux Variability Analysis) evaluation to remove dead end metabolites. |
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62 |
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63 Output |
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64 ------ |
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65 |
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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>`_. |
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67 |
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68 Project Links |
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69 --------------------- |
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70 |
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71 * `GitHub <https://github.com/brsynth/rptools>`_ |
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72 |
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73 License |
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74 ------- |
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75 |
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76 `MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_ |
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77 |
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78 Acknowledgments |
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79 --------------- |
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80 |
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81 * Thomas Duigou |
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82 |
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83 ]]></help> |
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84 <creator> |
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85 <person givenName="Joan" familyName="Hérisson" email="joan.herisson@univ-evry.fr" identifier="https://orcid.org/0000-0001-9741-0847" /> |
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86 <person givenName="Melchior" familyName="du Lac" identifier="https://orcid.org/0000-0002-9984-4689" /> |
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87 </creator> |
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88 <citations> |
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89 <citation type="doi">10.1038/nbt1156</citation> |
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90 <citation type="doi">10.1016/j.ymben.2017.12.002</citation> |
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91 <citation type="doi">10.1186/1752-0509-7-74</citation> |
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92 <citation type="doi">10.1093/bioinformatics/btn051</citation> |
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93 </citations> |
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94 </tool> |