Mercurial > repos > tduigou > retropath2
changeset 14:1edb49dfa335 draft default tip
planemo upload for repository https://github.com/brsynth/retropath2_wrapper commit 4f228a8dcee36f8c5282ff3e30f67a87254a2837-dirty
author | tduigou |
---|---|
date | Thu, 09 Oct 2025 09:50:03 +0000 |
parents | f26e7e4a42b7 |
children | |
files | retropath2_wrapper.xml |
diffstat | 1 files changed, 9 insertions(+), 20 deletions(-) [+] |
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--- a/retropath2_wrapper.xml Wed Oct 08 11:10:57 2025 +0000 +++ b/retropath2_wrapper.xml Thu Oct 09 09:50:03 2025 +0000 @@ -2,7 +2,7 @@ profile="21.09" license="MIT"> <description>Build a reaction network from a set of source compounds to a set of sink compounds</description> <macros> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@TOOL_VERSION@">3.5.0</token> </macros> <requirements> @@ -10,27 +10,20 @@ </requirements> <stdio> <!-- Fatal --> - <exit_code range="1" level="fatal" description="Cannot find source-in-sink file" /> <regex match="It seems that the target product is already in the chassis" source="both" - level="fatal" description="It seems that the target product is already in the chassis" /> - <exit_code range="2" level="fatal" - description="Running the RetroPath2.0 Knime program produced an OSError" /> + level="fatal" + description="It seems that the target product is already in the chassis (Exit code: 1)" /> <regex match="The following error occured" source="both" level="fatal" - description="The following error occured" /> - <exit_code range="3" level="fatal" description="The InChI string is malformed" /> + description="The following error occured (Exit code: 2)" /> <regex match="is not a valid InChI notation" source="both" level="fatal" - description="is not a valid InChI notation" /> - <exit_code range="4" level="fatal" description="Sink file is malformed" /> + description="is not a valid InChI notation (Exit code: 3)" /> <regex match="The sink file is malformed" source="both" level="fatal" - description="The sink file is malformed" /> - <exit_code range="5" level="fatal" description="Knime installation error" /> + description="The sink file is malformed (Exit code: 4)" /> <!-- Warning --> - <exit_code range="10" level="warning" description="Source has been found in the sink" /> <regex match="Source has been found in the sink" source="both" level="warning" - description="Source has been found in the sink" /> - <exit_code range="11" level="warning" description="RetroPath2.0 has found no solution" /> + description="Source has been found in the sink (Exit code: 10)" /> <regex match="No solution has been found" source="both" level="warning" - description="No solution has been found" /> + description="No solution has been found (Exit code: 11)" /> </stdio> <command detect_errors="exit_code"><![CDATA[ #if $sink.emptysink: @@ -55,11 +48,7 @@ --quiet #end if --msc_timeout '$adv.timeout' && - if compgen -G 'out/*_scope.csv' > /dev/null; then - cp out/*_scope.csv '$Reaction_Network'; - else - cp out/results.csv '$Reaction_Network'; - fi + cp out/*_scope.csv "$Reaction_Network" 2>/dev/null || cp out/results.csv "$Reaction_Network" ]]></command> <inputs> <param name="rulesfile" type="data" format="csv,tar" label="Rules File"