diff --git a/tools/rptools/macros.xml b/tools/rptools/macros.xml
index 9ac9d279..36127303 100644
--- a/tools/rptools/macros.xml
+++ b/tools/rptools/macros.xml
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">6.4.1</token>
+    <token name="@TOOL_VERSION@">6.5.0</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
diff --git a/tools/rptools/rpcompletion.xml b/tools/rptools/rpcompletion.xml
index b0ddc496..52697a99 100644
--- a/tools/rptools/rpcompletion.xml
+++ b/tools/rptools/rpcompletion.xml
@@ -4,21 +4,20 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
-    <stdio>
-        <exit_code range="1" level="fatal" description="Could not Xref compartment_id" />
-        <exit_code range="2" level="fatal" description="ValueError returned" />
-    </stdio>
     <command detect_errors="exit_code"><![CDATA[
+        echo "launch !!!!!!!!!!!!!!!!!" &&
+        pip list &&
         python -m rptools.rpcompletion
-        '$rp2_pathways'
-        '$sink'
-        '$rp2paths_compounds'
-        '$rp2paths_pathways'
-        completed_pathways
-        --upper_flux_bound '$adv.upper_flux_bound'
-        --lower_flux_bound '$adv.lower_flux_bound'
-        --max_subpaths_filter '$adv.max_subpaths_filter'
-        --cache-dir "\${TMPDIR:-.}"
+            '$rp2_pathways'
+            '$sink'
+            '$rp2paths_compounds'
+            '$rp2paths_pathways'
+            completed_pathways
+            --upper_flux_bound '$adv.upper_flux_bound'
+            --lower_flux_bound '$adv.lower_flux_bound'
+            --max_subpaths_filter '$adv.max_subpaths_filter'
+            --cache-dir "\${TMPDIR:-.}" &&
+        echo "Finish!!!!!!!!"
     ]]></command>
     <inputs>
         <param name="rp2paths_pathways" type="data" format="csv" label="RP2paths pathways" />
@@ -39,18 +38,18 @@
     <tests>
         <test>
         <!-- test 1: check if outputs are represented in an expected number  -->
-            <param name="rp2paths_pathways" value="4-rp2paths_pathways.csv" />
-            <param name="rp2paths_compounds" value="3-rp2paths_compounds.tsv" />
             <param name="rp2_pathways" value="1-rp2_metnet.csv" />
             <param name="sink" value="2-sink.csv" />
-            <output_collection name="pathways" type="list" count="9"/>
+            <param name="rp2paths_compounds" value="3-rp2paths_compounds.tsv" />
+            <param name="rp2paths_pathways" value="4-rp2paths_pathways.csv" />
+            <output_collection name="pathways" type="list" count="10"/>
         </test>
     </tests>
     <help><![CDATA[
-rpCompletion
-============
+rpCompletion - Complete pathway
+===============================
 
-Completes mono-component reactions output by `RetroPath2.0 <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_ with the appropriate cofactors. Creates sub-paths when multiple reaction rules are associated with a single reaction. Input is a single pathways file produced by RP2Paths. It stands on rpCache which store pre-computed data.
+Completes mono-component reactions output by RetroPath2.0 (10.1016/j.ymben.2017.12.002) with the appropriate cofactors. Creates sub-paths when multiple reaction rules are associated with a single reaction. Input is a single pathways file produced by RP2Paths. It stands on rpCache which store pre-computed data.
 
 Input
 -----
diff --git a/tools/rptools/rpextractsink.xml b/tools/rptools/rpextractsink.xml
index 2f09798f..7e4d424a 100644
--- a/tools/rptools/rpextractsink.xml
+++ b/tools/rptools/rpextractsink.xml
@@ -37,8 +37,8 @@
         </test>
     </tests>
     <help><![CDATA[
-Sink from SBML
-=================
+rpExtractSink - Sink from SBML
+==============================
 
 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.
 
diff --git a/tools/rptools/rpfba.xml b/tools/rptools/rpfba.xml
index 93a86921..278217dd 100644
--- a/tools/rptools/rpfba.xml
+++ b/tools/rptools/rpfba.xml
@@ -15,8 +15,8 @@
             #end if
                 --objective_rxn_id '$objective_rxn_id'
                 --sim '$input_sim_type.sim_type'
-            #if str($adv.ignore_orphan_species) == "true":
-                --ignore_orphan_species
+            #if str($adv.with_orphan_species) == "true":
+                --with_orphan_species
             #end if
                 --log "error"
             #if str($input_sim_type.sim_type)=="fba"
@@ -55,7 +55,7 @@
         </conditional>
         <section name="adv" title="Advanced Options" expanded="false">
             <param name="merge" type="boolean" label="Output the merged model?" checked="false" display="checkboxes" />
-            <param name="ignore_orphan_species" type="boolean" label="Ignore metabolites that are only consumed or produced?" checked="true" />
+            <param name="with_orphan_species" type="boolean" label="Add metabolites that are only consumed or produced?" checked="false" />
         </section>
     </inputs>
     <outputs>
@@ -119,8 +119,8 @@
         </test>
     </tests>
     <help><![CDATA[
-FBA
-=====
+rpFba - FBA
+===========
 
 
 Flux balance analysis is a mathematical approach for analyzing the flow of metabolites through a metabolic network. It is performed for heterologous pathways generated by RetroPath2.0. The tool performs the following steps:
@@ -165,7 +165,7 @@ Optional:
 Advanced options:
 
 * **Output the merged model?**\ : (boolean, default=False) output the full merged model instead of heterologous pathway only
-* **Ignore Orphan Species?**\ : (boolean, default=True) ignore metabolites that are only consumed or produced
+* **With Orphan Species?**\ : (boolean, default=False) add metabolites that are only consumed or produced
     ]]></help>
     <expand macro="creator"/>
     <citations>
diff --git a/tools/rptools/rpranker.xml b/tools/rptools/rpranker.xml
index 8cd95d10..12b2d323 100644
--- a/tools/rptools/rpranker.xml
+++ b/tools/rptools/rpranker.xml
@@ -36,8 +36,8 @@
         </test>
     </tests>
     <help><![CDATA[
-Rank Pathways
-================
+rpRanker - Rank Pathways
+========================
 
 Sort a list of pathways according to their global score.
 
diff --git a/tools/rptools/rpreport.xml b/tools/rptools/rpreport.xml
index 39b16029..a7314c93 100644
--- a/tools/rptools/rpreport.xml
+++ b/tools/rptools/rpreport.xml
@@ -46,25 +46,20 @@
         </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>`_.
+rpReport - Report for RetroPath
+===============================
 
+Generates HTML pages to explore the main characteristics (thermodynamics, fluxes, number of metabolic steps, reaction rule score) of pathways predicted with RetroPath suite (10.1016/j.ymben.2017.12.002).
 
 Input
 -----
 
-Required:
-
 * **Source SBML**: rpSBML file(s) containing pathways predicted with RetroPath suite.
 
 Output
 ------
 
-* **Pathways HTML Report**: Pathways HTML Report
+* **Pathways HTML Report**: Pathways HTML Report.
     ]]></help>
     <expand macro="creator"/>
     <citations>
diff --git a/tools/rptools/rpscore.xml b/tools/rptools/rpscore.xml
index b07ab288..1442e03e 100644
--- a/tools/rptools/rpscore.xml
+++ b/tools/rptools/rpscore.xml
@@ -26,8 +26,8 @@
         </test>
     </tests>
     <help><![CDATA[
-Score Pathway
-==============
+rpScore - Score Pathway
+=======================
 
 Computes a global score for a heterologous pathway. The score is calculated from a learning process based on reaction rules score, flux balance analysis and thermodynamics metrics, and the number of reactions in the pathway.
 
diff --git a/tools/rptools/rpthermo.xml b/tools/rptools/rpthermo.xml
index 44f28d07..a6072e88 100644
--- a/tools/rptools/rpthermo.xml
+++ b/tools/rptools/rpthermo.xml
@@ -49,8 +49,9 @@
         </test>
     </tests>
     <help><![CDATA[
-Thermodynamics
-==============
+rpThermo - 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).
diff --git a/tools/rptools/rpviz.xml b/tools/rptools/rpviz.xml
index 690ec81d..e93b77bc 100644
--- a/tools/rptools/rpviz.xml
+++ b/tools/rptools/rpviz.xml
@@ -76,10 +76,10 @@
         </test>
     </tests>
     <help><![CDATA[
-RPVIZ
-=====
+rpViz - Pathway viewer
+======================
 
-Visualize pathways from the `RetroPath Suite <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_.
+Visualize pathways from the RetroPath Suite (10.1016/j.ymben.2017.12.002).
 
 Input
 -----
diff --git a/tools/rptools/test-data/medium.fmt.a.csv b/tools/rptools/test-data/medium.fmt.a.csv
deleted file mode 100644
index 253cf0a0..00000000
--- a/tools/rptools/test-data/medium.fmt.a.csv
+++ /dev/null
@@ -1,3 +0,0 @@
-compound_id,compound_annotation,compound_group,upper_bound,medium_name
-MNXM9,pi,ion,1000,m9
-MNXM196,fe3,ion,1000,m9
diff --git a/tools/rptools/test-data/minimal_medium.csv b/tools/rptools/test-data/minimal_medium.csv
deleted file mode 100644
index 0b44af73..00000000
--- a/tools/rptools/test-data/minimal_medium.csv
+++ /dev/null
@@ -1 +0,0 @@
-,minimize_flux,minimize_component