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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2biosensor commit a1c35a3286b25ef4b03d0973d1f1ab49bee8d0e6
author iuc
date Thu, 05 Jan 2023 14:17:45 +0000
parents
children
files rp2biosensor.xml test-data/rp2-results-lactate.csv test-data/sink-h2o2.csv
diffstat 3 files changed, 149 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rp2biosensor.xml	Thu Jan 05 14:17:45 2023 +0000
@@ -0,0 +1,87 @@
+<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@">3.2.1</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">rp2biosensor</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python -m rp2biosensor
+        '$rp2_results'
+        '$sink_file'
+        --opath '$html_file'
+        #if str($adv.json_graph) == "true"
+            --ojson '$json_file'
+        #end if
+	--cache-dir "\${TMPDIR:-.}"
+    ]]></command>
+    <inputs>
+        <param name="rp2_results" type="data" format="csv" label="RetroPath2 output" help="Retrosynthesis network generated by RetroPath2.0 in CSV format."/>
+        <param name="sink_file" type="data" format="csv" label="Sink file used for RetroPath2.0"/>
+        <section name="adv" title="Advanced Options" expanded="false">
+            <param name="json_graph" type="boolean" label="Output Graph in JSON?" checked="false" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="html_file" format="html" label="${tool.name} - ${rp2_results.name}"/>
+        <data name="json_file" format="json" label="${tool.name} -${rp2_results.name}">
+            <filter> adv['json_graph'] </filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <!-- test 1: check if identical outputs are produced -->
+            <param name="rp2_results" value="rp2-results-lactate.csv" />
+            <param name="sink_file" value="sink-h2o2.csv" />
+            <output name="html_file" >
+                <assert_contents>
+                    <has_line_matching expression='^((?!"svg": "data:image).)*$' />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+rp2biosensor
+================
+
+**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:
+
+* **RetroPath2 output**\ : Retrosynthesis network generated by RetroPath2.0 in CSV format.
+* **Sink file**\ : (string) Sink file used for RetroPath2.0.
+
+Output
+------
+
+* **HTML file**\ : interactive web page showing the transducing reactions.
+
+Optional:
+
+* **JSON file**\ : Output the graph as JSON file.
+
+Project Links
+------------------
+
+* `GitHub <https://github.com/brsynth/rp2biosensor>`_
+
+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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rp2-results-lactate.csv	Thu Jan 05 14:17:45 2023 +0000
@@ -0,0 +1,60 @@
+"Initial source","Transformation ID","Reaction SMILES","Substrate SMILES","Substrate InChI","Product SMILES","Product InChI","In Sink","Sink name","Diameter","Rule ID","EC number","Score","Iteration"
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sink-h2o2.csv	Thu Jan 05 14:17:45 2023 +0000
@@ -0,0 +1,2 @@
+"Name","inchi"
+"H2O2","InChI=1S/H2O2/c1-2/h1-2H"
\ No newline at end of file