Mercurial > repos > bgruening > ctb_im_cluster_butina_matrix
comparison cluster_butina_matrix.xml @ 0:0332c2ff19f2 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
author | bgruening |
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date | Tue, 21 Jul 2020 05:25:09 -0400 |
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-1:000000000000 | 0:0332c2ff19f2 |
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1 <tool id="ctb_im_cluster_butina_matrix" name="Butina Cluster Matrix" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> | |
2 <description>using RDKit</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 <token name="@GALAXY_VERSION@">0</token> | |
6 </macros> | |
7 <expand macro="requirements" /> | |
8 <command detect_errors="exit_code"><![CDATA[ | |
9 cluster_butina_matrix | |
10 -i '$infile' | |
11 -if sdf | |
12 -t '$threshold' | |
13 -mt '$matrix_threshold' | |
14 -d '$descriptor_opts' | |
15 -m '$metric_opts' | |
16 --meta | |
17 -o outp | |
18 -of tsv &>> $logfile && | |
19 cat outp_metrics.txt &>> $logfile && | |
20 gzip -d outp.tsv.gz | |
21 ]]></command> | |
22 <inputs> | |
23 <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF format"/> | |
24 <param name="threshold" min="0" max="1" type="float" value="0.7" label="Threshold" help="Similarity clustering threshold (1.0 means identical)"/> | |
25 <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)"/> | |
26 | |
27 <param name="descriptor_opts" type="select" label="Descriptor Options" help="Descriptor or fingerprint type (default rdkit)"> | |
28 <option value="rdkit" selected="true">rdkit</option> | |
29 <option value="maccs">maccs</option> | |
30 <option value="morgan2">morgan2</option> | |
31 <option value="morgan3">morgan3</option> | |
32 </param> | |
33 | |
34 <param name="metric_opts" type="select" label="Similarity metric" help="Default is the Tanimoto coefficient"> | |
35 <option value="tanimoto" selected="true">tanimoto</option> | |
36 <option value="asymmetric">asymmetric</option> | |
37 <option value="braunblanquet">braunblanquet</option> | |
38 <option value="cosine">cosine</option> | |
39 <option value="dice">dice</option> | |
40 <option value="kulczynski">kulczynski</option> | |
41 <option value="mcconnaughey">mcconnaughey</option> | |
42 <option value="rogotgoldberg">rogotgoldberg</option> | |
43 <option value="russel">russel</option> | |
44 <option value="sokal">sokal</option> | |
45 </param> | |
46 </inputs> | |
47 | |
48 <expand macro="outputs" output_format="tsv" filetype="tabular"/> | |
49 | |
50 <tests> | |
51 <test> | |
52 <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/> | |
53 <param name="descriptor_opts" value="rdkit"/> | |
54 <param name="metric_opts" value="tanimoto"/> | |
55 <param name="threshold" value="0.6"/> | |
56 <param name="matrix_threshold" value="0.5"/> | |
57 <output name="outfile" ftype="tabular" file="cluster_butina_matrix_output1.tsv"/> | |
58 <output name="logfile"> | |
59 <assert_contents> | |
60 <has_text text="Found 30 clusters"/> | |
61 </assert_contents> | |
62 </output> | |
63 </test> | |
64 </tests> | |
65 <help><![CDATA[ | |
66 | |
67 .. class:: infomark | |
68 | |
69 **What this tool does** | |
70 | |
71 This tool performs Butina clustering for a set of input molecules, using the chemistry toolkit RDKit, and returns results in tabular format. | |
72 | |
73 | |
74 ----- | |
75 | |
76 .. class:: infomark | |
77 | |
78 **Input** | |
79 | |
80 | - Molecules in `SDF format`_ | |
81 | - A number of other parameters can be set, including the fingerprint type and the similarity metric to use. | |
82 | |
83 .. _SDF format: http://en.wikipedia.org/wiki/Chemical_table_file | |
84 | |
85 | |
86 ----- | |
87 | |
88 .. class:: infomark | |
89 | |
90 **Output** | |
91 | |
92 Tabular file containing clusters. | |
93 | |
94 ]]></help> | |
95 <expand macro="citations"/> | |
96 </tool> |