Mercurial > repos > tduigou > rptools_rpcompletion

diff rpcompletion.xml @ 4:e59d28e31f88 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 96a30e92eab3144b924fdba7b63be10b218160a7
author tduigou
date Wed, 24 Jul 2024 08:42:16 +0000
parents eeb447ee56e4
children
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--- a/rpcompletion.xml	Fri Dec 01 14:29:29 2023 +0000
+++ b/rpcompletion.xml	Wed Jul 24 08:42:16 2024 +0000
@@ -22,7 +22,7 @@
     ]]></command>
     <inputs>
         <param name="rp2paths_pathways" type="data" format="csv" label="RP2paths pathways" />
-        <param name="rp2paths_compounds" type="data" format="csv" label="RP2paths compounds" />
+        <param name="rp2paths_compounds" type="data" format="tabular" label="RP2paths compounds" />
         <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 metabolic network" />
         <param name="sink" type="data" format="csv" label="Sink from SBML" />
         <section name="adv" title="Advanced Options" expanded="false">
@@ -43,14 +43,14 @@
             <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"/>
+            <output_collection name="pathways" type="list" count="10"/>
         </test>
     </tests>
     <help><![CDATA[
 rpCompletion
 ============
 
-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 <https://www.doi.org/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
 -----