Mercurial > repos > bgruening > sucos_max_score
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
author | bgruening |
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date | Wed, 02 Oct 2019 12:57:54 -0400 |
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children | 8eab6d2b7bdf |
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<tool id="sucos_max_score" name="Max SuCOS score" version="0.1"> <description>- determine maximum SuCOS score of ligands against clustered fragment hits</description> <macros> <import>sucos_macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="aggressive"><![CDATA[ python '$__tool_directory__/sucos_max.py' -i '$input' -o '$output' -m $mode #for $cluster in $clusters '$cluster' #end for ]]></command> <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="mode" type="select" value="max" label="Mode"> <option value="max">Max score</option> <option value="cum">Cumulative score</option> </param> </inputs> <outputs> <data format="sdf" name="output" label="The scored ligands"/> </outputs> <tests> <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="mode" value="max"/> <output name="output" ftype="sdf"> <assert_contents> <has_text text="Max_SuCOS_Score" /> </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="mode" value="cum"/> <output name="output" ftype="sdf"> <assert_contents> <has_text text="Cum_SuCOS_Score" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** This tool determines the maximum SuCOS score of ligands, presumed to be potential follow on compounds, compared to a set of clustered reference compounds, presumed to be fragment screening hits. Each ligand to be scored is compared to all of the reference compounds with the highest score being recorded, along with the cluster it came from and the index of the molecule within that cluster. The original SuCOS code is on GitHub_ under a MIT license. The SuCOS work is described here_. .. _GitHub: https://github.com/susanhleung/SuCOS .. _here: https://chemrxiv.org/articles/SuCOS_is_Better_than_RMSD_for_Evaluating_Fragment_Elaboration_and_Docking_Poses/8100203 .. class:: infomark **Input** 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. .. class:: infomark **Output** The same SD file as the input ligands with a "Max_SuCOS_Score" property added containing the best (maximum) SuCOS score along with the "Max_SuCOS_FeatureMap_Score" and "Max_SuCOS_Tanimoto_Score" of that comparison. In addition, the "Max_SuCOS_Cluster" field shows the name of the cluster file that contained the molecule with this best score and the "Max_SuCOS_Index" shows the index (first record is index 1) of that molecule in the file. ]]></help> <expand macro="citations"/> </tool>