Mercurial > repos > tduigou > retropath2
changeset 15:2f79335c4137 draft default tip
planemo upload for repository https://github.com/brsynth/retropath2_wrapper commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
| author | tduigou |
|---|---|
| date | Fri, 18 Apr 2025 07:13:14 +0000 |
| parents | eb072181af57 |
| children | |
| files | retropath2_wrapper.xml test-data/results_emptysink.csv |
| diffstat | 2 files changed, 40 insertions(+), 7 deletions(-) [+] |
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--- a/retropath2_wrapper.xml Fri Mar 07 10:19:05 2025 +0000 +++ b/retropath2_wrapper.xml Fri Apr 18 07:13:14 2025 +0000 @@ -1,7 +1,7 @@ <tool id="retropath2" name="RetroPath2.0" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" 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@">3.3.1</token> </macros> <requirements> @@ -24,6 +24,10 @@ <regex match="No solution has been found" source="both" level="warning" description="No solution has been found" /> </stdio> <command detect_errors="exit_code"><![CDATA[ + #if $sink.emptysink: + echo '"Name","InChI"' > empty_sink.csv && + #set $sinkfile = "empty_sink.csv" + #end if python -m retropath2_wrapper '$sinkfile' '$rulesfile' @@ -37,10 +41,10 @@ --dmax '$adv.dmax' --mwmax_source '$adv.mwmax_source' --kinstall "\${TMPDIR:-.}" - #if str($adv.network) == "true": + #if not $adv.network: --no-network #end if - #if str($adv.quiet) == "true": + #if not $sink.error_codes: --quiet #end if --msc_timeout '$adv.timeout' && @@ -52,7 +56,16 @@ ]]></command> <inputs> <param name="rulesfile" type="data" format="csv,tar" label="Rules File" help="File containing reaction rules which reflect the enzymatic potential of the chassis organism."/> - <param name="sinkfile" type="data" format="csv" label="Sink File" help=" Sink file which comprises all compounds that are considered as granted in your system."/> + <conditional name="sink"> + <param name="emptysink" type="boolean" checked="false" label="Empty sink" /> + <when value="false"> + <param name="sinkfile" type="data" format="csv" label="Sink File" help="Sink file which comprises all compounds that are considered as granted in your system."/> + <param name="error_codes" type="boolean" checked="true" label="Return error codes" /> + </when> + <when value="true"> + <param name="error_codes" type="boolean" checked="false" label="Return error codes" /> + </when> + </conditional> <param name="source_inchi" type="text" label="Source InChI" optional="false" help="InChI of compound to produce."> <validator type="empty_field" message="You must provide the InChI string"/> </param> @@ -72,8 +85,7 @@ <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."/> <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." /> <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)." /> - <param name="network" type="boolean" checked="false" label="Do not use network" /> - <param name="quiet" type="boolean" checked="false" label="Do not return error codes" /> + <param name="network" type="boolean" checked="true" label="Use network" /> </section> </inputs> <outputs> @@ -87,10 +99,22 @@ <test> <!-- test 1: check if identical outputs are produced with default parameters --> <param name="rulesfile" value="rules.csv" /> - <param name="sinkfile" value="sink.csv" /> + <conditional name="sink"> + <param name="emptysink" value="false" /> + <param name="sinkfile" value="sink.csv" /> + </conditional> <param name="source_inchi" value="InChI=1S/C40H56/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3/b12-11+,25-15+,26-16+,31-17+,32-18+,35-21+,36-22+,37-27+,38-28+,39-29+,40-30+" /> <output name="Reaction_Network" file="results_retropath2.csv" ftype="csv" compare="diff"/> </test> + <test> + <!-- test 2: check empty sink file --> + <param name="rulesfile" value="rules.csv" /> + <conditional name="sink"> + <param name="emptysink" value="true" /> + </conditional> + <param name="source_inchi" value="InChI=1S/C40H56/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3/b12-11+,25-15+,26-16+,31-17+,32-18+,35-21+,36-22+,37-27+,38-28+,39-29+,40-30+" /> + <output name="Reaction_Network" file="results_emptysink.csv" ftype="csv" compare="diff"/> + </test> </tests> <help><![CDATA[ Retropath2.0 wrapper
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results_emptysink.csv Fri Apr 18 07:13:14 2025 +0000 @@ -0,0 +1,9 @@ +"Initial source","Transformation ID","Reaction SMILES","Substrate SMILES","Substrate InChI","Product SMILES","Product InChI","In Sink","Sink name","Diameter","Rule ID","EC number","Score","Iteration" 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RR-02-e62744f3d66572ac-16-F, RR-02-5ec28ff7626d8843-16-F, RR-02-f85f00f767901186-16-F, RR-02-eccb66924968a69c-16-F, RR-02-191a4711915b04c8-16-F, RR-02-b2fd54ae659d0db8-16-F]","[2.5.1.-, 2.5.1.31, 2.5.1, 2.5.1.29, 2.5.1.88, 2.5.1.81, NOEC, 2.5.1.84, 2.5.1.85]","0.4771212547196624","2" +"[target]","TRS_0_2_2","[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]>>[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H].[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]","[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]","InChI=1S/C20H36O7P2/c1-17(2)9-6-10-18(3)11-7-12-19(4)13-8-14-20(5)15-16-26-29(24,25)27-28(21,22)23/h9,11,13,15H,6-8,10,12,14,16H2,1-5H3,(H,24,25)(H2,21,22,23)","[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]","InChI=1S/C15H28O7P2/c1-13(2)7-5-8-14(3)9-6-10-15(4)11-12-21-24(19,20)22-23(16,17)18/h7,9,11H,5-6,8,10,12H2,1-4H3,(H,19,20)(H2,16,17,18)","0","[None]","16","[RR-02-224bf1f3c9ea5f3c-16-F, RR-02-e62744f3d66572ac-16-F, RR-02-5ec28ff7626d8843-16-F, RR-02-f85f00f767901186-16-F, RR-02-eccb66924968a69c-16-F, RR-02-191a4711915b04c8-16-F, RR-02-b2fd54ae659d0db8-16-F]","[2.5.1.-, 2.5.1.31, 2.5.1, 2.5.1.29, 2.5.1.88, 2.5.1.81, NOEC, 2.5.1.84, 2.5.1.85]","0.4771212547196624","2"