Mercurial > repos > chemteam > biomd_extract_clusters

comparison get_clusters.xml @ 0:ad49025ba90d draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
author chemteam
date Mon, 24 Aug 2020 06:08:51 -0400
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1 <tool id="biomd_extract_clusters" name="Extract clusters of MD trajectories" version="0.@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <description>from linkage 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><![CDATA[
13 python '$__tool_directory__/get_clusters.py'
14 --Z '$Z'
15 --threshold '$threshold'
16 --min-members '$min_members'
17 --output '$output'
18 ]]></command>
19 <inputs>
20 <param label="Clustering linkage array" format="tabular" type="data" name="Z" argument="--Z"/>
21 <param label="Distance cutoff" value="0" type="integer" name="threshold" argument="--threshold"/>
22 <param label="Minimum number of members of the cluster" value="0" type="integer" name="min_members" argument="--min-members"/>
23 </inputs>
24 <outputs>
25 <data label="Cluster members (JSON)" format="json" name="output"/>
26 </outputs>
27 <tests>
28 <test>
29 <param name="Z" value="Z.tabular"/>
30 <param name="threshold" value="2"/>
31 <param name="min_members" value="2"/>
32 <output name="output" value="clusters.json"/>
33 </test>
34 </tests>
35 <help><![CDATA[
36 .. class:: infomark
37
38 **What it does**
39
40 This tool takes the hierarchical clustering linkage array (in tabular format) produced by the 'Hierarchical clustering' tool and returns a list of clusters and their members in JSON format.
41
42 _____
43
44
45 .. class:: infomark
46
47 **Input**
48
49 - Clustering linkage array.
50 - User-selected distance threshold for clustering and minimum number of members a cluster must have to be returned.
51
52 _____
53
54
55 .. class:: infomark
56
57 **Output**
58
59 - JSON file containing a list of clusters and their members.
60
61 ]]></help>
62 <citations>
63 <citation type="doi">10.1038/s41592-019-0686-2</citation>
64 <citation type="doi">{10.1109/MCSE.2007.55</citation>
65 </citations>
66 </tool>