Mercurial > repos > tduigou > rpthermo

changeset 2:310645d4c5e6 draft

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planemo upload commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty
author tduigou
date Fri, 18 Nov 2022 16:18:02 +0000
parents 21a900eee812
children 4525f388f3ac
files rpreport.xml rpthermo.xml
diffstat 2 files changed, 112 insertions(+), 19 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rpreport.xml	Fri Nov 18 16:18:02 2022 +0000
@@ -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
--- a/rpthermo.xml	Wed Feb 09 13:07:30 2022 +0000
+++ b/rpthermo.xml	Fri Nov 18 16:18:02 2022 +0000
@@ -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