Rptools, bugs

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>

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
 -----

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.
 

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>

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.
 

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>

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.
 

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).

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
 -----