# HG changeset patch
# User tduigou
# Date 1668787900 0
# Node ID 191665a689defc6124b054a0243049bac888919a
# Parent  47bb93e7832b516190afbd1d2ebafd2ecde761ea
planemo upload commit 3bc34bfc82850daa2229724c396dcd9454039273-dirty

diff -r 47bb93e7832b -r 191665a689de rpextractsink.xml
--- a/rpextractsink.xml	Wed Feb 09 14:37:06 2022 +0000
+++ b/rpextractsink.xml	Fri Nov 18 16:11:40 2022 +0000
@@ -1,7 +1,8 @@
-<tool id="rpextractsink" name="Sink from SBML" version="@TOOL_VERSION@" profile="19.09">
+<tool id="rpextractsink" name="Sink from SBML" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
     <description>Generate the RetroPath2.0 sink file from an SBML input</description>
     <macros>
-        <token name="@TOOL_VERSION@">5.12.1</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@TOOL_VERSION@">6.0.1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
@@ -14,17 +15,16 @@
             '$input'
             '$sink'
             --compartment_id '$compartment_id'
-        #if str($adv.remove_dead_end) == "true":
-            --remove_dead_end
-        #end if
+            $adv.remove_dead_end
+            --cache-dir "\${TMPDIR:-.}"
     ]]></command>
     <inputs>
-        <param name="input" type="data" format="xml" optional="false" label="Strain" />
-        <param name="compartment_id" type="text" value="c" label="SBML compartment ID" >
+        <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" />
+        <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)" >
             <validator type="empty_field" message="SBML compartment ID is required"/>
         </param>
         <section name="adv" title="Advanced Options" expanded="false">
-            <param name="remove_dead_end" type="boolean" checked="true" label="Remove dead-end metabolites using FVA evaluation?" />
+            <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" />
         </section>
     </inputs>
     <outputs>
@@ -42,46 +42,34 @@
 Sink from SBML
 =================
 
-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.
+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.
 
-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.
+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.
 
 The results are written to a RetroPath2.0 friendly CSV file format that can be used as sink input.
 
-
 Input
 -----
 
 Required:
 
-* **input_sbml**\ : (string) Path to the input SBML file
-* **compartment_id**\ : (string, default: c) Specify the compartment from which to extract the sink molecules. The default are for BiGG models
+* **Strain**\ : The structure of metabolites present in the chosen chassis strain in SBML format.
+* **SBML compartment ID**\ : (string, default: c) Specify the compartment from which to extract the sink molecules. The default are for BiGG models (cytosol).
 
 Advanced options:
 
-* **remove_dead_end**\ : (boolean, default: True) Perform FVA evaluation to remove dead end metabolites
+* **Remove dead-end metabolites using FVA evaluation?**\ : (boolean, default: True) Perform FVA (Flux Variability Analysis) evaluation to remove dead end metabolites.
 
 Output
 ------
 
-* **output_sink**\ : (string) Path to the output csv file
+* **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>`_.
 
 Project Links
 ---------------------
 
 * `GitHub <https://github.com/brsynth/rptools>`_
 
-Version
-----------
-
-5.12.1
-
-Authors
--------
-
-* **Melchior du Lac**
-* Joan Hérisson
-
 License
 -------
 
@@ -93,6 +81,10 @@
 * Thomas Duigou
 
     ]]></help>
+    <creator>
+        <person givenName="Joan" familyName="Hérisson" email="joan.herisson@univ-evry.fr" identifier="https://orcid.org/0000-0001-9741-0847" />
+        <person givenName="Melchior" familyName="du Lac" identifier="https://orcid.org/0000-0002-9984-4689" />
+    </creator>
     <citations>
         <citation type="doi">10.1038/nbt1156</citation>
         <citation type="doi">10.1016/j.ymben.2017.12.002</citation>