# HG changeset patch # User tduigou # Date 1644247235 0 # Node ID 8a04f97b785dc3f30447864ccae29b8866b837d3 # Parent d3f66245c4a6e2294dbb65109db35eb32eab37e8 "planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty" diff -r d3f66245c4a6 -r 8a04f97b785d retropath2.xml --- a/retropath2.xml Mon Dec 20 15:24:52 2021 +0000 +++ b/retropath2.xml Mon Feb 07 15:20:35 2022 +0000 @@ -1,7 +1,7 @@ - + Build a reaction network from a set of source compounds to a set of sink compounds - retropath2_wrapper + retropath2_wrapper @@ -15,10 +15,9 @@ '$sinkfile' '$rulesfile' out - --source_inchi '$source_inchi' - #if $source_name: - --source_name '$source_name' - #end if + --source_inchi '$source_inchi_type.source_inchi' + --source_name '$source_name' + --rp2_version '$adv.version' --max_steps '$adv.max_steps' --topx '$adv.topx' --dmin '$adv.dmin' @@ -33,14 +32,27 @@ fi ]]> - - - - - - + + + + + + + + + + + + + +
- + + + + + + @@ -73,16 +85,20 @@ Required: - * **-sinkfile**\ : (string) Path to the sink file * **-sourcefile**\ : (string) Path to the source file * **-max_steps**\ : (integer) Maximal number of steps * **-rulesfile**\ : (string) Path to the rules file * **-rulesfile_format**\ : (string) Valid Options: tar, csv. Format of the rules file +The InChI source DB entries are obtained by the following command: + +`cat chem_prop.tsv | awk -F'\\t' '{print "\\t\\t\\t\\t\\t"}' | sed 's/\\&/\\&/g'` + +where `chem_prop.tsv` has been downloaded on MetaNetX. + Advanced options: - * **-topx**\ : (integer, default: 100) For each iteration, number of rules * **-dmin**\ : (integer, default: 0) * **-dmax**\ : (integer, default: 1000) @@ -93,20 +109,13 @@ Output ------ - * **-scope_csv**\ : (string) Path to the output scope csv file -Version -------- - -v2.0.4 - Authors ------- - -* **Melchior du Lac** -* Joan Hérisson +* **Joan Hérisson** +* Melchior du Lac License ------- @@ -116,7 +125,6 @@ Acknowledgments --------------- - * Thomas Duigou ]]> diff -r d3f66245c4a6 -r 8a04f97b785d test-data/results_retropath2.csv --- a/test-data/results_retropath2.csv Mon Dec 20 15:24:52 2021 +0000 +++ b/test-data/results_retropath2.csv Mon Feb 07 15:20:35 2022 +0000 @@ -1,150 +1,43 @@ -"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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