Mercurial > repos > tduigou > rp2biosensor

changeset 5:fdaf5a0af992 draft

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planemo upload for repository https://github.com/brsynth/rp2biosensor commit 1e01b679611d980f87089184e7d8a538b96d68c7
author tduigou
date Tue, 30 May 2023 21:08:46 +0000
parents b9aa7267df42
children 71f3a2616dd0
files config/job_conf.xml config/tool_conf.xml rp2biosensor.xml
diffstat 3 files changed, 6 insertions(+), 20 deletions(-) [+]
line wrap: on
line diff
--- a/config/job_conf.xml	Mon May 01 01:20:09 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-    <tool id="rp2biosensor" destination="local" />
--- a/config/tool_conf.xml	Mon May 01 01:20:09 2023 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-  <section id="sbc-util" name="SynBioCAD Utilities">
-    <tool file="synbiocad-galaxy-wrappers/rp2biosensor/rp2biosensor.xml" />
-  </section>
--- a/rp2biosensor.xml	Mon May 01 01:20:09 2023 +0000
+++ b/rp2biosensor.xml	Tue May 30 21:08:46 2023 +0000
@@ -1,8 +1,8 @@
-<tool id="rp2biosensor" name="rp2biosensor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
+<tool id="rp2biosensor" name="rp2biosensor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09" license="MIT">
     <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>
+        <token name="@TOOL_VERSION@">3.2.1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">rp2biosensor</requirement>
@@ -15,6 +15,7 @@
         #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."/>
@@ -43,7 +44,7 @@
     </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.
 
@@ -65,22 +66,11 @@
 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" />
+        <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
     </creator>
     <citations>
         <citation type="doi">10.1021/acssynbio.2c00138</citation>
     </citations>
-</tool>
\ No newline at end of file
+</tool>