Mercurial > repos > tduigou > retropath2
changeset 2:8a04f97b785d draft
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
| author | tduigou |
|---|---|
| date | Mon, 07 Feb 2022 15:20:35 +0000 |
| parents | d3f66245c4a6 |
| children | 8e56fc458ca5 |
| files | retropath2.xml test-data/results_retropath2.csv |
| diffstat | 2 files changed, 76 insertions(+), 175 deletions(-) [+] |
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--- 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 @@ -<tool id="retropath2" name="RetroPath2.0" version="2.0.5"> +<tool id="retropath2" name="RetroPath2.0" version="2.3.0"> <description>Build a reaction network from a set of source compounds to a set of sink compounds</description> <requirements> - <requirement type="package" version="2.0.5">retropath2_wrapper</requirement> + <requirement type="package" version="2.3.0">retropath2_wrapper</requirement> </requirements> <stdio> <exit_code range="1" level="fatal" description="Source has been found in the sink" /> @@ -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 ]]></command> <inputs> - <param name="rulesfile" type="data" format="csv" label="Rules File" /> - <param name="sinkfile" type="data" format="csv" label="Sink File" /> - <param name="source_inchi" type="text" label="Source InChI" optional="false" > - <validator type="empty_field" message="You must provide the InChI key" /> - </param> - <param name="source_name" type="text" value="target" optional="true" label="Source name" /> + <param name="rulesfile" type="data" format="csv" label="Rules File"/> + <param name="sinkfile" type="data" format="csv" label="Sink File"/> + <conditional name="source_inchi_type"> + <param name="inchi_type" type="select" label="InChI type"> + <!-- <option value="name" selected="true">By name</option> --> + <option value="string">By string</option> + </param> + <when value="string"> + <param name="source_inchi" type="text" label="Source InChI" optional="false"> + <validator type="empty_field" message="You must provide the InChI string"/> + </param> + </when> + </conditional> + <param name="source_name" type="text" value="target" optional="true" label="Source name"/> <section name="adv" title="Advanced Options" expanded="false"> - <param name="max_steps" type="integer" value="3" label="Maximal Pathway length" /> + <param name="version" type="select" label="Workflow version"> + <option value="v9">v9</option> + <option value="r20210127">r20210127</option> + <option value="r20220104" selected="true">r20220104</option> + </param> + <param name="max_steps" type="integer" value="3" label="Maximal Pathway length" /> <param name="topx" type="integer" value="100" label="TopX" /> <param name="dmin" type="integer" value="0" label="Minimum rule diameter" /> <param name="dmax" type="integer" value="1000" label="Maximum rule diameter" /> @@ -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<option value=\\""$6"\\"\\>" "["$1"]\\t " $2 "</option>"}' | 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 ]]></help>
--- 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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