| Previous changeset 1:21a900eee812 (2022-02-09) Next changeset 3:4525f388f3ac (2022-11-18) |
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Commit message:
planemo upload commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty |
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modified:
rpthermo.xml |
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rpreport.xml |
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| diff -r 21a900eee812 -r 310645d4c5e6 rpreport.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpreport.xml Fri Nov 18 16:18:02 2022 +0000 |
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| @@ -0,0 +1,91 @@ +<tool id="rpreport" name="Pathways HTML Report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> + <description>Explore the main characteristics of pathways predicted with RetroPath suite</description> + <macros> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@TOOL_VERSION@">6.0.1</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">rptools</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + #if str($input_type_conditional.input_type) == "sbml": + #set input_folder="tmp_folder" + mkdir -p '$input_folder' && + #for $input in $input_type_conditional.input_sbml.keys(): + ln -sfn $input_type_conditional.input_sbml[$input] '$input_folder/$input' && + #end for + python -m rptools.rpreport -d '$input_folder' + #elif str($input_type_conditional.input_type) == "tar": + python -m rptools.rpreport '${input_type_conditional.input_tar}' + #end if + '$html_file.files_path' + && cp '$html_file.files_path'/index.html '$html_file' + ]]></command> + <inputs> + <conditional name="input_type_conditional"> + <param name="input_type" type="select" label="Source SBML format"> + <option value="tar" selected="True">TAR</option> + <option value="sbml">Collection</option> + </param> + <when value="tar"> + <param name="input_tar" type="data" format="tar" label="Source SBML" help="rpSBML file(s) containing pathways predicted with RetroPath suite in TAR format"/> + </when> + <when value="sbml"> + <param name="input_sbml" type="data_collection" format="sbml" collection_type="list" label="Source SBML" help="Collection of rpSBML files containing pathways predicted with RetroPath suite"/> + </when> + </conditional> + </inputs> + <outputs> + <data name="html_file" format="html" label="Pathways HTML Report"/> + </outputs> + <tests> + <test> + <!-- test 1: check if identical html output is produced (tar input) --> + <conditional name="input_type_conditional"> + <param name="input_type" value="tar"/> + <param name="input_tar" value="input_rpSBML.tar" /> + </conditional> + <output name="html_file" file="rpreport_output.html" compare="diff"/> + </test> + </tests> + <help><![CDATA[ +rpReport +========= + +Generates HTML pages to explore the main characteristics (thermodynamics, +fluxes, number of metabolic steps, reaction rule score) of pathways predicted +with `RetroPath suite <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_. + + +Input +----- + +Required: + +* **Source SBML**: rpSBML file(s) containing pathways predicted with RetroPath suite. + +Output +------ + +* **Pathways HTML Report**: Pathways HTML Report + +Project Links +--------------------- + +* `GitHub <https://github.com/brsynth/rptools>`_ + +Acknowledgments +--------------- + +* Thomas Duigou +* Joan Hérisson + +Licence +------- + +`MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_ + ]]></help> + <creator> + <person givenName="Olivier" familyName="Telle" email="olivier.telle@inrae.fr" /> + </creator> +</tool> \ No newline at end of file |
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| diff -r 21a900eee812 -r 310645d4c5e6 rpthermo.xml --- a/rpthermo.xml Wed Feb 09 13:07:30 2022 +0000 +++ b/rpthermo.xml Fri Nov 18 16:18:02 2022 +0000 |
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| @@ -1,7 +1,7 @@ -<tool id="rpthermo" name="Thermo" version="@TOOL_VERSION@" profile="19.09"> +<tool id="rpthermo" name="Thermo" version="@TOOL_VERSION@" profile="21.09"> <description>Calculate the formation energy of chemical species and the Gibbs free energy of their reactions and pathways in an SBML</description> <macros> - <token name="@TOOL_VERSION@">5.12.1</token> + <token name="@TOOL_VERSION@">6.0.1</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">rptools</requirement> @@ -20,11 +20,11 @@ --pMg '$adv.pMg' ]]></command> <inputs> - <param name="input" type="data" format="xml" label="Input File" /> + <param name="input" type="data" format="sbml" label="SBML Input File" help="Pathways in SBML format" /> <section name="adv" title="Advanced Options" expanded="false"> <param name="ph" type="float" value="7.5" min="0" max="14" label="Compartment pH of the pathway" /> <param name="ionic_strength" type="float" value="0.25" min="0" max="500" label="Compartment ionic strength of the pathway" /> - <param name="pMg" type="float" value="3.0" label="Compartment pMg of the pathway" /> + <param name="pMg" type="float" value="3.0" label="Compartment pMg (Magnesium vapor pressure) of the pathway" /> </section> </inputs> <outputs> @@ -52,6 +52,8 @@ =============== Calculate the formation energy of chemical species either using an internal database or estimate it by decomposing them using the `component contribution <https://gitlab.com/elad.noor/component-contribution>`_ method. Thereafter this tool predicts the Gibbs free energy of reactions and of the whole heterologous pathway by combining the formation energy of each individual compound. +The goal of the thermodynamic analysis is to estimate the feasibility of the predicted pathways toward target production, in physiological conditions (PH, ionic strength). + .. image:: https://raw.githubusercontent.com/Galaxy-SynBioCAD/rpThermo/standalone/galaxy/img/rpThermo.png :width: 80 % :align: center @@ -64,30 +66,27 @@ Required: -* **input**\ : (string) Path to the input file -* **output**\ : (string) Path to the output file +Inputs +------ + +* **SBML Input File**\ : Pathways in SBML format Advanced Options: -* **--ph**\ :(float) Compartment PH of the pathway -* **--ionic_strength**\ :(float) Compartment ionic strength of the pathway -* **--pMg**\ :(float) Compartment pMg of the pathway +* **PH**\ :(float) Compartment PH of the pathway +* **Ionic strength**\ :(float) Compartment ionic strength of the pathway +* **pMg**\ :(float) Compartment pMg (Magnesium vapor pressure) of the pathway + +Output +------ + +* **Pathway with thermo**\ : annotated pathways (with thermodynamics information for each reaction) in SBML(Systems Biology Markup Language) format. Project Links --------------------- * `GitHub <https://github.com/brsynth/rptools/tree/master/rptools/rpthermo>`_ -Version ----------- - -v5.12.1 - -Authors -------- - -* **Melchior du Lac** - Acknowledgments --------------- @@ -98,4 +97,7 @@ <citations> <citation type="doi">10.1371/journal.pcbi.1003098</citation> </citations> + <creator> + <person givenName="Melchior" familyName="du Lac" identifier="https://orcid.org/0000-0002-9984-4689" /> + </creator> </tool> \ No newline at end of file |