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comparison rmsd_clustering.xml @ 0:f45b010339f6 draft default tip

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
author chemteam
date Mon, 24 Aug 2020 10:06:27 +0000
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1 <tool id="biomd_rmsd_clustering" name="Hierarchical clustering" version="0.@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <description>from MD RMSD matrix data</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.5.2</token>
5 <token name="@GALAXY_VERSION@">0</token>
6 </macros>
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">scipy</requirement>
9 <requirement type="package" version="1.19.1">numpy</requirement>
10 <requirement type="package" version="3.3.1">matplotlib</requirement>
11 </requirements>
12 <command detect_errors="aggressive"><![CDATA[
13 python '$__tool_directory__/rmsd_clustering.py'
14 #if $inp.ext == 'json':
15 --json '$inp'
16 --outp-mat '$outp_mat'
17 #elif $inp.ext == 'tabular':
18 --mat '$inp'
19 #end if
20 --Z '$Z'
21 #if $dendrogram:
22 --dendrogram '$dend'
23 --clustering-method '$clustering_method'
24 #end if
25 #if $heatmap:
26 --heatmap '$hmap'
27 --cmap '$cmap'
28 #end if
29 --start '$start'
30 --end '$end'
31 '$normalize'
32 ]]></command>
33 <inputs>
34 <param label="JSON or tabular input file" type="data" format="json,tabular" name="inp" argument="--json"/>
35 <param label="First trajectory frame to calculate distance matrix" value="0" type="integer" name="start" argument="--start"/>
36 <param label="Last trajectory frame to calculate distance matrix" value="-1" type="integer" name="end" argument="--end"/>
37 <param label="Normalize the RMSD variation over the trajectories before averaging." checked="false" type="boolean" name="normalize" argument="--normalize" truevalue="--normalize" falsevalue=""/>
38 <param label="Output dendrogram?" type="boolean" name="dendrogram" argument="--dendrogram" />
39 <param label="Output distance matrix file?" type="boolean" name="heatmap" argument="--heatmap"/>
40 <param label="Method to use for clustering." type="select" name="clustering_method" argument="--clustering-method">
41 <option selected="true" value="average">average</option>
42 <option value="centroid">centroid</option>
43 <option value="complete">complete</option>
44 <option value="median">median</option>
45 <option value="single">single</option>
46 <option value="ward">ward</option>
47 <option value="weighted">weighted</option>
48 </param>
49 <param label="Matplotlib colormap to use for plotting distance matrix." value="plasma" type="text" name="cmap" argument="--cmap"/>
50 </inputs>
51 <outputs>
52 <data label="Tabular output file" format="tabular" name="outp_mat">
53 <filter>inp.ext == 'json'</filter>
54 </data>
55 <data label="Dendrogram" format="png" name="dend">
56 <filter>dendrogram</filter>
57 </data>
58 <data label="Heatmap" format="png" name="hmap">
59 <filter>heatmap</filter>
60 </data>
61 <data label="File for cluster linkage array" format="tabular" name="Z"/>
62 </outputs>
63 <tests>
64 <test expect_num_outputs="4">
65 <param name="inp" value="inp.json"/>
66 <param name="dendrogram" value="true"/>
67 <param name="heatmap" value="true"/>
68 <param name="clustering_method" value="average"/>
69 <param name="cmap" value="plasma"/>
70 <param name="start" value="0"/>
71 <param name="end" value="-1"/>
72 <param name="normalize" value="true"/>
73 <output name="outp_mat" value="outp_mat.tabular"/>
74 <output name="dend" value="dendrogram.png"/>
75 <output name="hmap" value="heatmap.png"/>
76 <output name="Z" value="Z.tabular"/>
77 </test>
78 </tests>
79 <help><![CDATA[
80 .. class:: infomark
81
82 **What it does**
83
84 This tool takes the three-dimensional tensor file (in JSON format) produced by the 'Extract RMSD distance matrix data' tool and flattens it along the time axix to give a two-dimensional distance matrix.
85
86 Optionally, it also plots the distance matrix as a heatmap with matplotlib, performs hierarchical clustering with scipy, and plots the corresponding dendrogram.
87
88 _____
89
90
91 .. class:: infomark
92
93 **Input**
94
95 - Three-dimensional tensor (JSON).
96 - User selection of desired outputs, clustering method and other parameters
97
98 _____
99
100
101 .. class:: infomark
102
103 **Output**
104
105 - Tabular file containing a two-dimensional N x N distance matrix, where N is the number of MD trajectories
106 - Optional: a heatmap representing the distance matrix.
107 - Optional: a tabular file containing the cluster linkage array produced by hierarchical clustering of the distance matrix
108 - Optional: A dendrogram representing the hierarchical clustering.
109 ]]></help>
110 <citations>
111 <citation type="doi">10.1038/s41592-019-0686-2</citation>
112 <citation type="doi">{10.1109/MCSE.2007.55</citation>
113 </citations>
114 </tool>