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comparison nxn_clustering.xml @ 7:0d88631bb7de draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:32:50 -0400
parents 70b071de9bee
children 198b1e30c739
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6:e3a7d6cc87af 7:0d88631bb7de
1 <tool id="ctb_chemfp_nxn_clustering" name="NxN Clustering" version="0.4"> 1 <tool id="ctb_chemfp_nxn_clustering" name="NxN clustering" version="1.5">
2 <description>of molecular fingerprints</description> 2 <description>of molecular fingerprints</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.1p1">chemfp</requirement> 4 <requirement type="package" version="1.5">chemfp</requirement>
5 <requirement type="package" version="2">python</requirement> 5 <requirement type="package" version="2.2.3">matplotlib</requirement>
6 <requirement type="package" version="2.0.2">matplotlib</requirement> 6 <requirement type="package" version="1.2.1">scipy</requirement>
7 <requirement type="package" version="0.19.0">scipy</requirement>
8 <requirement type="package" version="2.4.1">openbabel</requirement> 7 <requirement type="package" version="2.4.1">openbabel</requirement>
9 </requirements> 8 </requirements>
10 <command detect_errors="exit_code"> 9 <command detect_errors="exit_code">
11 <![CDATA[ 10 <![CDATA[
12 python '$__tool_directory__/nxn_clustering.py' 11 python '$__tool_directory__/nxn_clustering.py'
14 -t $threshold 13 -t $threshold
15 #if str($output_files) in ['both', 'image']: 14 #if str($output_files) in ['both', 'image']:
16 --cluster '$image' 15 --cluster '$image'
17 #end if 16 #end if
18 #if str($output_files) in ['both', 'matrix']: 17 #if str($output_files) in ['both', 'matrix']:
19 --smatrix '$smilarity_matrix' 18 --smatrix '$similarity_matrix'
20 #end if 19 #end if
21 --oformat '$oformat' 20 --oformat '$oformat'
22 ]]> 21 ]]>
23 </command> 22 </command>
24 <inputs> 23 <inputs>
25 <param name="infile" type="data" format="fps" label="Finperprint dataset" help="Dataset missing? See TIP below"/> 24 <param name="infile" type="data" format="fps" label="Fingerprint dataset" help="Dataset missing? See TIP below"/>
26 <param name='threshold' type='float' value='0.0' /> 25 <param name='threshold' label='Threshold' type='float' value='0.0' />
27 <param name='oformat' type='select' format='text' label="Format of the resulting picture"> 26 <param name='oformat' type='select' format='text' label="Format of the resulting picture">
28 <option value='png'>PNG</option> 27 <option value='png'>PNG</option>
29 <option value='svg'>SVG</option> 28 <option value='svg'>SVG</option>
30 </param> 29 </param>
31 <param name='output_files' type='select' format='text' label="Output options"> 30 <param name='output_files' type='select' format='text' label="Output options">
32 <option value='both'>NxN matrix and Image</option> 31 <option value='both'>NxN matrix and image</option>
33 <option value='image'>Image</option> 32 <option value='image'>Image</option>
34 <option value='matrix'>NxN Matrix</option> 33 <option value='matrix'>NxN ḿatrix</option>
35 </param> 34 </param>
36 35
37 </inputs> 36 </inputs>
38 <outputs> 37 <outputs>
39 <data name="image" format="svg" label="${tool.name} on ${on_string} - Cluster Image"> 38 <data name="image" format="svg" label="${tool.name} on ${on_string} - Dendrogram Image">
40 <filter>output_files == "both" or output_files == "image"</filter> 39 <filter>output_files == "both" or output_files == "image"</filter>
41 <change_format> 40 <change_format>
42 <when input="oformat" value="png" format="png"/> 41 <when input="oformat" value="png" format="png"/>
43 </change_format> 42 </change_format>
44 </data> 43 </data>
45 <data name="smilarity_matrix" format="binary" label="${tool.name} on ${on_string} - Similarity Matrix"> 44 <data name="similarity_matrix" format="txt" label="${tool.name} on ${on_string} - Similarity Matrix">
46 <filter>output_files == "both" or output_files == "matrix"</filter> 45 <filter>output_files == "both" or output_files == "matrix"</filter>
47 </data> 46 </data>
48 </outputs> 47 </outputs>
49 <tests> 48 <tests>
50 <test> 49 <test>
51 <param name="infile" ftype="fps" value="targets.fps" /> 50 <param name="infile" ftype="fps" value="targets.fps" />
52 <param name='treshold' value='0.75' /> 51 <param name='threshold' value='0.75' />
53 <param name='oformat' value='svg' /> 52 <param name='oformat' value='svg' />
54 <param name='output_files' value='image' /> 53 <param name='output_files' value='both' />
55 <output name="image" file='NxN_Clustering_on_q.svg' ftype="svg" compare="sim_size"/> 54 <output name="image" file='NxN_Clustering_on_q.svg' ftype="svg"/>
55 <output name="similarity_matrix" file='NxN_Clustering_on_q.txt' ftype="txt"/>
56 </test> 56 </test>
57 </tests> 57 </tests>
58 <help> 58 <help>
59 <![CDATA[ 59 <![CDATA[
60 60
61 .. class:: infomark 61 .. class:: infomark
62 62
63 **What this tool does** 63 **What this tool does**
64 64
65 Generating hierarchical clusters and visualizing clusters with dendrograms. 65 Based on a set of fingerprints, generates a square self-similarity (NxN) matrix, as well as a dendrogram visualizing the clusters derived from it using hierarchical clustering. For the clustering and the fingerprint handling the chemfp_ project is used.
66 For the clustering and the fingerprint handling the chemfp_ project is used.
67 66
68 .. _chemfp: http://chemfp.com/ 67 .. _chemfp: http://chemfp.com/
69 68
70 ----- 69 -----
71 70
72 .. class:: warningmark 71 .. class:: warningmark
73 72
74 **Hint** 73 **Hint**
75 74
76 The plotting of the cluster image is sensible only with a small dataset. 75 The plotting of the dendrogram is sensible only with a small dataset - if more than around 20 fingerprints are used the plot will be unreadable.
77 76
78 ----- 77 -----
79 78
80 .. class:: infomark 79 .. class:: infomark
81 80