| Previous changeset 4:85fad59f8168 (2020-04-06) Next changeset 6:55ac04db36aa (2020-07-28) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit c35334ca80c87a5078da1a6df85b34e23b80d837" |
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modified:
sucos_max.py sucos_max.xml |
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| diff -r 85fad59f8168 -r d4c67ced6abc sucos_max.py --- a/sucos_max.py Mon Apr 06 09:12:07 2020 -0400 +++ b/sucos_max.py Wed Apr 15 09:26:07 2020 -0400 |
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| @@ -39,7 +39,7 @@ from rdkit import Chem -def process(inputfilename, clusterfilenames, outputfilename): +def process(inputfilename, clusterfilenames, outputfilename, filter_value, filter_field): all_clusters = {} for filename in clusterfilenames: cluster = [] @@ -120,7 +120,13 @@ mol.SetDoubleProp("Cum_SuCOS_FeatureMap_Score", scores_cum[1] if scores_cum[1] > 0 else 0) mol.SetDoubleProp("Cum_SuCOS_Protrude_Score", scores_cum[2] if scores_cum[2] > 0 else 0) - writer.write(mol) + if filter_value and filter_field: + if mol.HasProp(filter_field): + val = mol.GetDoubleProp(filter_field) + if val > filter_value: + writer.write(mol) + else: + writer.write(mol) input_file.close() writer.flush() @@ -137,11 +143,13 @@ parser.add_argument('-i', '--input', help='Input file to score in SDF format. Can be gzipped (*.gz).') parser.add_argument('-o', '--output', help='Output file in SDF format. Can be gzipped (*.gz).') parser.add_argument('clusters', nargs='*', help="One or more SDF files with the clustered hits") + parser.add_argument('--filter-value', type=float, help='Filter out values with scores less than this.') + parser.add_argument('--filter-field', help='Field to use to filter values.') args = parser.parse_args() utils.log("Max SuCOS Args: ", args) - process(args.input, args.clusters, args.output) + process(args.input, args.clusters, args.output, args.filter_value, args.filter_field) if __name__ == "__main__": |
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| diff -r 85fad59f8168 -r d4c67ced6abc sucos_max.xml --- a/sucos_max.xml Mon Apr 06 09:12:07 2020 -0400 +++ b/sucos_max.xml Wed Apr 15 09:26:07 2020 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="sucos_max_score" name="Max SuCOS score" version="0.2.2"> +<tool id="sucos_max_score" name="Max SuCOS score" version="0.2.3"> <description>- determine maximum SuCOS score of ligands against clustered fragment hits</description> <macros> <import>sucos_macros.xml</import> @@ -8,6 +8,9 @@ python '$__tool_directory__/sucos_max.py' -i '$input' -o '$output' + #if $filter_field and $filter_value + --filter-field '$filter_field' --filter-value $filter_value + #end if #for $cluster in $clusters '$cluster' #end for @@ -15,6 +18,17 @@ <inputs> <param name="input" type="data" format="sdf" label="Ligands to be scored" help="Input in SDF format." /> <param name="clusters" type="data" format="sdf" multiple="true" label="Set of clusters to score against" help="Clusters in SDF format." /> + <param name="filter_field" type="text" label="Filter field" optional="true" + help="Filter output using this field's values. (e.g. Max_SuCOS_Score or Cum_SuCOS_Score)"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"/> + </sanitizer> + </param> + <param name="filter_value" type="float" label="Filter value" optional="true" + help="Filter out scores less than this value."/> </inputs> <outputs> <data format="sdf" name="output" label="The scored ligands"/> @@ -27,6 +41,20 @@ <assert_contents> <has_text text="Max_SuCOS_Score" /> <has_text text="Cum_SuCOS_Score" /> + <has_n_lines n="2224" /> + </assert_contents> + </output> + </test> + <test> + <param name="input" ftype="sdf" value="sucos_cluster.sdf"/> + <param name="clusters" ftype="sdf" value="cluster1.sdf,cluster2.sdf,cluster3.sdf,cluster4.sdf,cluster5.sdf,cluster6.sdf"/> + <param name="filter_field" value="Cum_SuCOS_Score"/> + <param name="filter_value" value="15"/> + <output name="output" ftype="sdf"> + <assert_contents> + <has_text text="Max_SuCOS_Score" /> + <has_text text="Cum_SuCOS_Score" /> + <has_n_lines n="686" /> </assert_contents> </output> </test> @@ -54,6 +82,10 @@ The clustered reference compounds are likely to have been generated using the "Cluster ligands using SuCOS" tool and will comprise a SDF format file for each cluster. The ligands to be scored are supplied in a SDF file. +Optional filtering of the output is possible, for instance to retain only records with SuCOS scores greater that a +certain value. Use the optional 'Filter field' and 'Filter value' parameters. The 'Filter field' would typically +be one of the properties listed below. + .. class:: infomark **Output** |