diff rpthermo.xml @ 0:e9d05fc83186 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rpthermo.xml	Tue Mar 28 12:08:14 2023 +0000
@@ -0,0 +1,90 @@
+<tool id="rptools_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>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <stdio>
+        <regex match="WARNING:" level="warning" />
+        <regex match="ERROR:" level="fatal" />
+        <regex match="ERROR:root:ChemAxon" level="warning" />
+    </stdio>
+    <command detect_errors="exit_code"><![CDATA[
+        python -m rptools.rpthermo
+        '$input'
+        '$pathway_with_thermo' 
+        --pH '$adv.ph'
+        --ionic_strength '$adv.ionic_strength'
+        --pMg '$adv.pMg'
+    ]]></command>
+    <environment_variables>
+        <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable>
+    </environment_variables>
+    <inputs>
+        <param name="input" type="data" format="sbml" label="SBML Input File" help="Pathways in SBML format" />
+        <section name="adv" title="Advanced Options" expanded="false">
+            <param name="ph" type="float" value="7.5" min="0" max="14" label="Compartment pH of the pathway" />
+            <param name="ionic_strength" type="float" value="0.25" min="0" max="500" label="Compartment ionic strength of the pathway" />
+            <param name="pMg" type="float" value="3.0" label="Compartment pMg (Magnesium vapor pressure) of the pathway" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="pathway_with_thermo" format="sbml" label="${tool.name} - ${input.name}" />
+    </outputs>
+    <tests>
+        <test>
+        <!-- test 1: check if identical outputs are produced with default parameters  -->
+            <param name="input" value="rp_013_0001.xml" />
+            <output name="pathway_with_thermo">
+                <assert_contents>
+                    <is_valid_xml />
+                    <!--check thermo_dG0_prime value-->
+                    <has_text text="-2308.11630" />
+                    <!--check thermo_dG value-->
+                    <has_text text="-2151.84763" />
+                    <has_n_lines n="483" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+Thermodynamics
+==============
+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
+
+
+|
+
+
+Above is an illustration of the Gibbs free energy calculation using the component contribution package. The color-coded arrows from red (best) to blue (worst) show the best and worst-performing reactions.
+
+Required:
+
+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 (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.
+    ]]></help>
+    <expand macro="creator"/>
+    <citations>
+        <citation type="doi">10.1371/journal.pcbi.1003098</citation>
+        <citation type="doi">10.1038/s41467-022-32661-x</citation>
+    </citations>
+</tool>