Mercurial > repos > bgruening > ctb_im_cluster_butina_matrix
view cluster_butina_matrix.xml @ 1:d804c6e6d5ad draft default tip
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit d1d0ec4ebc97b2274b18a0aab99f41addd5357ae"
author | bgruening |
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date | Mon, 27 Jul 2020 11:34:34 -0400 |
parents | 0332c2ff19f2 |
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<tool id="ctb_im_cluster_butina_matrix" name="Butina Cluster Matrix" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> <description>using RDKit</description> <macros> <import>macros.xml</import> <token name="@GALAXY_VERSION@">0</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ cluster_butina_matrix -i '$infile' -if sdf -t '$threshold' -mt '$matrix_threshold' -d '$descriptor_opts' -m '$metric_opts' --meta -o outp -of tsv &>> $logfile && cat outp_metrics.txt &>> $logfile && gzip -d outp.tsv.gz ]]></command> <inputs> <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF format"/> <param name="threshold" min="0" max="1" type="float" value="0.7" label="Threshold" help="Similarity clustering threshold (1.0 means identical)"/> <param name="matrix_threshold" min="0" max="1" type="float" value="0.5" label="Matrix threshold" help="Threshold for outputting values (1.0 means identical)"/> <param name="descriptor_opts" type="select" label="Descriptor Options" help="Descriptor or fingerprint type (default rdkit)"> <option value="rdkit" selected="true">rdkit</option> <option value="maccs">maccs</option> <option value="morgan2">morgan2</option> <option value="morgan3">morgan3</option> </param> <param name="metric_opts" type="select" label="Similarity metric" help="Default is the Tanimoto coefficient"> <option value="tanimoto" selected="true">tanimoto</option> <option value="asymmetric">asymmetric</option> <option value="braunblanquet">braunblanquet</option> <option value="cosine">cosine</option> <option value="dice">dice</option> <option value="kulczynski">kulczynski</option> <option value="mcconnaughey">mcconnaughey</option> <option value="rogotgoldberg">rogotgoldberg</option> <option value="russel">russel</option> <option value="sokal">sokal</option> </param> </inputs> <expand macro="outputs" output_format="tsv" filetype="tabular"/> <tests> <test> <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/> <param name="descriptor_opts" value="rdkit"/> <param name="metric_opts" value="tanimoto"/> <param name="threshold" value="0.6"/> <param name="matrix_threshold" value="0.5"/> <output name="outfile" ftype="tabular" file="cluster_butina_matrix_output1.tsv"/> <output name="logfile"> <assert_contents> <has_text text="Found 30 clusters"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ .. class:: infomark **What this tool does** This tool performs Butina clustering for a set of input molecules, using the chemistry toolkit RDKit, and returns results in tabular format. ----- .. class:: infomark **Input** | - Molecules in `SDF format`_ | - A number of other parameters can be set, including the fingerprint type and the similarity metric to use. .. _SDF format: http://en.wikipedia.org/wiki/Chemical_table_file ----- .. class:: infomark **Output** Tabular file containing clusters. ]]></help> <expand macro="citations"/> </tool>