Mercurial > repos > tduigou > retropath2
comparison retropath2_wrapper.xml @ 11:5f4a981d6bc3 draft
planemo upload for repository https://github.com/brsynth/retropath2_wrapper commit b7e98c7f0ee70edd536215e3dfe0cd66957e6dae
author | tduigou |
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date | Mon, 22 Jul 2024 12:08:24 +0000 |
parents | fe60c5bd7a9d |
children | da083c323f5c |
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10:fe60c5bd7a9d | 11:5f4a981d6bc3 |
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1 <tool id="retropath2" name="RetroPath2.0" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09" license="MIT"> | 1 <tool id="retropath2" name="RetroPath2.0" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09" license="MIT"> |
2 <description>Build a reaction network from a set of source compounds to a set of sink compounds</description> | 2 <description>Build a reaction network from a set of source compounds to a set of sink compounds</description> |
3 <macros> | 3 <macros> |
4 <token name="@VERSION_SUFFIX@">0</token> | 4 <token name="@VERSION_SUFFIX@">0</token> |
5 <token name="@TOOL_VERSION@">3.1.1</token> | 5 <token name="@TOOL_VERSION@">3.2.0</token> |
6 </macros> | 6 </macros> |
7 <requirements> | 7 <requirements> |
8 <requirement type="package" version="@TOOL_VERSION@">retropath2_wrapper</requirement> | 8 <requirement type="package" version="@TOOL_VERSION@">retropath2_wrapper</requirement> |
9 </requirements> | 9 </requirements> |
10 <stdio> | 10 <stdio> |
27 --topx '$adv.topx' | 27 --topx '$adv.topx' |
28 --dmin '$adv.dmin' | 28 --dmin '$adv.dmin' |
29 --dmax '$adv.dmax' | 29 --dmax '$adv.dmax' |
30 --mwmax_source '$adv.mwmax_source' | 30 --mwmax_source '$adv.mwmax_source' |
31 --kinstall "\${TMPDIR:-.}" | 31 --kinstall "\${TMPDIR:-.}" |
32 #if str($adv.network) == "true": | |
33 --no-network | |
34 #end if | |
32 --msc_timeout '$adv.timeout' && | 35 --msc_timeout '$adv.timeout' && |
33 if compgen -G 'out/*_scope.csv' > /dev/null; then | 36 if compgen -G 'out/*_scope.csv' > /dev/null; then |
34 cp out/*_scope.csv '$Reaction_Network'; | 37 cp out/*_scope.csv '$Reaction_Network'; |
35 else | 38 else |
36 cp out/results.csv '$Reaction_Network'; | 39 cp out/results.csv '$Reaction_Network'; |
55 <param name="topx" type="integer" value="100" min="1" max="1000" label="TopX" help="The maximal number of intermediate compounds to use as new starting points for a next iteration of the retrosynthesis algorithm." /> | 58 <param name="topx" type="integer" value="100" min="1" max="1000" label="TopX" help="The maximal number of intermediate compounds to use as new starting points for a next iteration of the retrosynthesis algorithm." /> |
56 <param name="dmin" type="integer" value="0" min="0" max="1000" label="Minimum rule diameter" help="Minimum rule diameter of the sphere including the atoms around the reacting center. The higher is the diameter, the more specific are the rules." /> | 59 <param name="dmin" type="integer" value="0" min="0" max="1000" label="Minimum rule diameter" help="Minimum rule diameter of the sphere including the atoms around the reacting center. The higher is the diameter, the more specific are the rules." /> |
57 <param name="dmax" type="integer" value="1000" min="0" max="1000" label="Maximum rule diameter" help="Maximum rule diameter of the sphere including the atoms around the reacting center. The higher is the diameter, the more specific are the rules."/> | 60 <param name="dmax" type="integer" value="1000" min="0" max="1000" label="Maximum rule diameter" help="Maximum rule diameter of the sphere including the atoms around the reacting center. The higher is the diameter, the more specific are the rules."/> |
58 <param name="mwmax_source" type="integer" value="1000" min="0" max="2000" label="Molecular weight of source (Da)" help="The molecular weight cutoff (in Da), above which initial source (ie target) and intermediate compounds will be filtered out." /> | 61 <param name="mwmax_source" type="integer" value="1000" min="0" max="2000" label="Molecular weight of source (Da)" help="The molecular weight cutoff (in Da), above which initial source (ie target) and intermediate compounds will be filtered out." /> |
59 <param name="timeout" type="integer" value="60" min="30" max="600" label="Timeout (min)" help="Maximal time of RetroPath2.0 execution (60 minutes by default)." /> | 62 <param name="timeout" type="integer" value="60" min="30" max="600" label="Timeout (min)" help="Maximal time of RetroPath2.0 execution (60 minutes by default)." /> |
63 <param name="network" type="boolean" checked="false" label="Do not use network" /> | |
60 </section> | 64 </section> |
61 </inputs> | 65 </inputs> |
62 <outputs> | 66 <outputs> |
63 <data name="Reaction_Network" format="csv" label="${tool.name}" > | 67 <data name="Reaction_Network" format="csv" label="${tool.name}" > |
64 <actions> | 68 <actions> |