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comparison retropath2_wrapper.xml @ 14:1edb49dfa335 draft default tip

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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
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13:f26e7e4a42b7 14:1edb49dfa335
1 <tool id="retropath2" name="RetroPath2.0" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" 1 <tool id="retropath2" name="RetroPath2.0" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
2 profile="21.09" license="MIT"> 2 profile="21.09" license="MIT">
3 <description>Build a reaction network from a set of source compounds to a set of sink compounds</description> 3 <description>Build a reaction network from a set of source compounds to a set of sink compounds</description>
4 <macros> 4 <macros>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 <token name="@TOOL_VERSION@">3.5.0</token> 6 <token name="@TOOL_VERSION@">3.5.0</token>
7 </macros> 7 </macros>
8 <requirements> 8 <requirements>
9 <requirement type="package" version="@TOOL_VERSION@">retropath2_wrapper</requirement> 9 <requirement type="package" version="@TOOL_VERSION@">retropath2_wrapper</requirement>
10 </requirements> 10 </requirements>
11 <stdio> 11 <stdio>
12 <!-- Fatal --> 12 <!-- Fatal -->
13 <exit_code range="1" level="fatal" description="Cannot find source-in-sink file" />
14 <regex match="It seems that the target product is already in the chassis" source="both" 13 <regex match="It seems that the target product is already in the chassis" source="both"
15 level="fatal" description="It seems that the target product is already in the chassis" /> 14 level="fatal"
16 <exit_code range="2" level="fatal" 15 description="It seems that the target product is already in the chassis (Exit code: 1)" />
17 description="Running the RetroPath2.0 Knime program produced an OSError" />
18 <regex match="The following error occured" source="both" level="fatal" 16 <regex match="The following error occured" source="both" level="fatal"
19 description="The following error occured" /> 17 description="The following error occured (Exit code: 2)" />
20 <exit_code range="3" level="fatal" description="The InChI string is malformed" />
21 <regex match="is not a valid InChI notation" source="both" level="fatal" 18 <regex match="is not a valid InChI notation" source="both" level="fatal"
22 description="is not a valid InChI notation" /> 19 description="is not a valid InChI notation (Exit code: 3)" />
23 <exit_code range="4" level="fatal" description="Sink file is malformed" />
24 <regex match="The sink file is malformed" source="both" level="fatal" 20 <regex match="The sink file is malformed" source="both" level="fatal"
25 description="The sink file is malformed" /> 21 description="The sink file is malformed (Exit code: 4)" />
26 <exit_code range="5" level="fatal" description="Knime installation error" />
27 <!-- Warning --> 22 <!-- Warning -->
28 <exit_code range="10" level="warning" description="Source has been found in the sink" />
29 <regex match="Source has been found in the sink" source="both" level="warning" 23 <regex match="Source has been found in the sink" source="both" level="warning"
30 description="Source has been found in the sink" /> 24 description="Source has been found in the sink (Exit code: 10)" />
31 <exit_code range="11" level="warning" description="RetroPath2.0 has found no solution" />
32 <regex match="No solution has been found" source="both" level="warning" 25 <regex match="No solution has been found" source="both" level="warning"
33 description="No solution has been found" /> 26 description="No solution has been found (Exit code: 11)" />
34 </stdio> 27 </stdio>
35 <command detect_errors="exit_code"><![CDATA[ 28 <command detect_errors="exit_code"><![CDATA[
36 #if $sink.emptysink: 29 #if $sink.emptysink:
37 echo '"Name","InChI"' > empty_sink.csv && 30 echo '"Name","InChI"' > empty_sink.csv &&
38 #set $sinkfile = "empty_sink.csv" 31 #set $sinkfile = "empty_sink.csv"
53 --std_hydrogen '$adv.std_hydrogen' 46 --std_hydrogen '$adv.std_hydrogen'
54 #if not $sink.error_codes: 47 #if not $sink.error_codes:
55 --quiet 48 --quiet
56 #end if 49 #end if
57 --msc_timeout '$adv.timeout' && 50 --msc_timeout '$adv.timeout' &&
58 if compgen -G 'out/*_scope.csv' > /dev/null; then 51 cp out/*_scope.csv "$Reaction_Network" 2>/dev/null || cp out/results.csv "$Reaction_Network"
59 cp out/*_scope.csv '$Reaction_Network';
60 else
61 cp out/results.csv '$Reaction_Network';
62 fi
63 ]]></command> 52 ]]></command>
64 <inputs> 53 <inputs>
65 <param name="rulesfile" type="data" format="csv,tar" label="Rules File" 54 <param name="rulesfile" type="data" format="csv,tar" label="Rules File"
66 help="File containing reaction rules which reflect the enzymatic potential of the chassis organism." /> 55 help="File containing reaction rules which reflect the enzymatic potential of the chassis organism." />
67 <conditional name="sink"> 56 <conditional name="sink">