Mercurial > repos > tduigou > rp2biosensor

changeset 4:b9aa7267df42 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/brsynth/rp2biosensor commit 2e8aa2e7c0581c7eed2074d15f7e4317ecde2ad6
author tduigou
date Mon, 01 May 2023 01:20:09 +0000
parents 4b2318e9b097
children fdaf5a0af992
files config/job_conf.xml config/tool_conf.xml rp2biosensor.xml
diffstat 3 files changed, 29 insertions(+), 22 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/config/job_conf.xml	Mon May 01 01:20:09 2023 +0000
@@ -0,0 +1,1 @@
+    <tool id="rp2biosensor" destination="local" />
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/config/tool_conf.xml	Mon May 01 01:20:09 2023 +0000
@@ -0,0 +1,3 @@
+  <section id="sbc-util" name="SynBioCAD Utilities">
+    <tool file="synbiocad-galaxy-wrappers/rp2biosensor/rp2biosensor.xml" />
+  </section>
--- a/rp2biosensor.xml	Fri Mar 25 13:01:27 2022 +0000
+++ b/rp2biosensor.xml	Mon May 01 01:20:09 2023 +0000
@@ -1,6 +1,7 @@
-<tool id="rp2biosensor" name="rp2biosensor" version="@TOOL_VERSION@" profile="19.09">
+<tool id="rp2biosensor" name="rp2biosensor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
     <description>Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output</description>
     <macros>
+        <token name="@VERSION_SUFFIX@">0</token>
         <token name="@TOOL_VERSION@">3.1.0</token>
     </macros>
     <requirements>
@@ -16,7 +17,7 @@
         #end if
     ]]></command>
     <inputs>
-        <param name="rp2_results" type="data" format="csv" label="RetroPath2 output"/>
+        <param name="rp2_results" type="data" format="csv" label="RetroPath2 output" help="Retrosynthesis network generated by RetroPath2.0 in CSV format."/>
         <param name="sink_file" type="data" format="csv" label="Sink file used for RetroPath2.0"/>
         <section name="adv" title="Advanced Options" expanded="false">
             <param name="json_graph" type="boolean" label="Output Graph in JSON?" checked="false" />
@@ -30,54 +31,56 @@
     </outputs>
     <tests>
         <test>
-        <!-- test 1: check if identical outputs are produced -->
-        <param name="rp2_results" value="rp2-results-lactate.csv" />
-        <param name="sink_file" value="sink-h2o2.csv" />
-        <output name="html_file" md5="88ba7cd2501c4d671b9eac396e7b4af9"/>
+            <!-- test 1: check if identical outputs are produced -->
+            <param name="rp2_results" value="rp2-results-lactate.csv" />
+            <param name="sink_file" value="sink-h2o2.csv" />
+            <output name="html_file" >
+                <assert_contents>
+                    <has_line_matching expression='^((?!"svg": "data:image).)*$' />
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[
 rp2biosensor
 ================
 
-Generate HTML outputs to explore Sensing Enabling Metabolic Pathway from RetroPath2 results.
+**rp2biosensor** is an open-source Python software that extracts from the retrosynthetic network generated by `RetroPath2.0 <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_ the subnetwork of interest, linking the biosensor to the compound to be detected, and produce an interactive web page showing the transducing reactions.
+
+Briefly, rp2biosensor parses the retrosynthesis network outputted by RetroPath2.0, completes the predicted reactions by putting back co-substrates and co-products omitted during the retrosynthesis using the `rxn_rebuild <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_ Python package, enumerates the shortest path linking the compound of interest, i.e. the biosensor, to the compound to be detected, e.g. lactate, and finally outputs the resulting subnetwork as an interactive web page to let the user browse the results.
 
 Input
 -----
 
 Required:
 
-* **rp2_results**\ : (string) RetroPath2.0 results.
-* **sink_file**\ : (string) Sink file used for RetroPath2.0.
+* **RetroPath2 output**\ : Retrosynthesis network generated by RetroPath2.0 in CSV format.
+* **Sink file**\ : (string) Sink file used for RetroPath2.0.
 
 Output
 ------
 
-* **opath**\ : (string) Output path. Default: biosensor.html.
+* **HTML file**\ : interactive web page showing the transducing reactions.
 
-* **otype**\ : (string) Output type. This could be either (i) "dir" which means ouput files will outputted into this directory, or (ii) "file" which means that all files will be embedded into a single HTML page. Default: file.
+Optional:
 
-* **ojson**\ : (string) Output the graph as json file if the path is not None. Default: None
+* **JSON file**\ : Output the graph as JSON file.
 
 Project Links
 ------------------
 
 * `GitHub <https://github.com/brsynth/rp2biosensor>`_
 
-Version
-----------
-
-3.1.0
-
-Authors
--------
-
-* **Thomas Duigou**
-
 License
 -------
 
 * `MIT <https://github.com/brsynth/rp2biosensor/blob/master/LICENSE.md>`_
 
     ]]></help>
+    <creator>
+        <person givenName="Thomas" familyName="Duigou" email="thomas.duigou@inrae.fr" identifier="https://orcid.org/0000-0002-2649-2950" />
+    </creator>
+    <citations>
+        <citation type="doi">10.1021/acssynbio.2c00138</citation>
+    </citations>
 </tool>
\ No newline at end of file