Mercurial > repos > chemteam > biomd_rmsd_clustering

annotate rmsd_clustering.xml @ 0:ee1f38eb220e 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 06:08:17 -0400
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children b9c46dbe9605
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1 <tool id="biomd_rmsd_clustering" name="Hierarchical clustering" version="0.@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description>from MD RMSD matrix data</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.5.2</token>
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5 <token name="@GALAXY_VERSION@">0</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">scipy</requirement>
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9 <requirement type="package" version="1.19.1">numpy</requirement>
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10 <requirement type="package" version="3.3.1">matplotlib</requirement>
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11 </requirements>
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12 <command detect_errors="aggressive"><![CDATA[
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13 python '$__tool_directory__/rmsd_clustering.py'
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14 #if $inp.ext == 'json':
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15 --json '$inp'
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16 --outp-mat '$outp_mat'
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17 #elif $inp.ext == 'tabular':
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18 --mat '$inp'
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19 #end if
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20 --Z '$Z'
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21 #if $dendrogram:
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22 --dendrogram '$dend'
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23 --clustering-method '$clustering_method'
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24 #end if
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25 #if $heatmap:
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26 --heatmap '$hmap'
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27 --cmap '$cmap'
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28 #end if
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29 --start '$start'
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30 --end '$end'
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31 '$normalize'
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32 ]]></command>
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33 <inputs>
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34 <param label="JSON or tabular input file" type="data" format="json,tabular" name="inp" argument="--json"/>
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35 <param label="First trajectory frame to calculate distance matrix" value="0" type="integer" name="start" argument="--start"/>
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36 <param label="Last trajectory frame to calculate distance matrix" value="-1" type="integer" name="end" argument="--end"/>
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37 <param label="Normalize the RMSD variation over the trajectories before averaging." checked="false" type="boolean" name="normalize" argument="--normalize" truevalue="--normalize" falsevalue=""/>
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38 <param label="Output dendrogram?" type="boolean" name="dendrogram" argument="--dendrogram" />
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39 <param label="Output distance matrix file?" type="boolean" name="heatmap" argument="--heatmap"/>
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40 <param label="Method to use for clustering." type="select" name="clustering_method" argument="--clustering-method">
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41 <option selected="true" value="average">average</option>
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42 <option value="centroid">centroid</option>
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43 <option value="complete">complete</option>
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44 <option value="median">median</option>
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45 <option value="single">single</option>
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46 <option value="ward">ward</option>
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47 <option value="weighted">weighted</option>
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48 </param>
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49 <param label="Matplotlib colormap to use for plotting distance matrix." value="plasma" type="text" name="cmap" argument="--cmap"/>
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50 </inputs>
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51 <outputs>
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52 <data label="Tabular output file" format="tabular" name="outp_mat">
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53 <filter>inp.ext == 'json'</filter>
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54 </data>
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55 <data label="Dendrogram" format="png" name="dend">
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56 <filter>dendrogram</filter>
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57 </data>
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58 <data label="Heatmap" format="png" name="hmap">
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59 <filter>heatmap</filter>
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60 </data>
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61 <data label="File for cluster linkage array" format="tabular" name="Z"/>
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62 </outputs>
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63 <tests>
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64 <test expect_num_outputs="4">
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65 <param name="inp" value="inp.json"/>
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66 <param name="dendrogram" value="true"/>
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67 <param name="heatmap" value="true"/>
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68 <param name="clustering_method" value="average"/>
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69 <param name="cmap" value="plasma"/>
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70 <param name="start" value="0"/>
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71 <param name="end" value="-1"/>
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72 <param name="normalize" value="true"/>
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73 <output name="outp_mat" value="outp_mat.tabular"/>
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74 <output name="dend" value="dendrogram.png"/>
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75 <output name="hmap" value="heatmap.png"/>
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76 <output name="Z" value="Z.tabular"/>
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77 </test>
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78 </tests>
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79 <help><![CDATA[
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80 .. class:: infomark
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81
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82 **What it does**
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83
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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.
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85
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86 Optionally, it also plots the distance matrix as a heatmap with matplotlib, performs hierarchical clustering with scipy, and plots the corresponding dendrogram.
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87
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88 _____
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89
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90
ee1f38eb220e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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91 .. class:: infomark
ee1f38eb220e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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92
ee1f38eb220e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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93 **Input**
ee1f38eb220e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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94
ee1f38eb220e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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95 - Three-dimensional tensor (JSON).
ee1f38eb220e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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96 - User selection of desired outputs, clustering method and other parameters
ee1f38eb220e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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97
ee1f38eb220e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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98 _____
ee1f38eb220e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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99
ee1f38eb220e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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100
ee1f38eb220e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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101 .. class:: infomark
ee1f38eb220e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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102
ee1f38eb220e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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103 **Output**
ee1f38eb220e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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104
ee1f38eb220e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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105 - Tabular file containing a two-dimensional N x N distance matrix, where N is the number of MD trajectories
ee1f38eb220e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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106 - Optional: a heatmap representing the distance matrix.
ee1f38eb220e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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107 - Optional: a tabular file containing the cluster linkage array produced by hierarchical clustering of the distance matrix
ee1f38eb220e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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108 - Optional: A dendrogram representing the hierarchical clustering.
ee1f38eb220e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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109 ]]></help>
ee1f38eb220e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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110 <citations>
ee1f38eb220e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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111 <citation type="doi">10.1038/s41592-019-0686-2</citation>
ee1f38eb220e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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112 <citation type="doi">{10.1109/MCSE.2007.55</citation>
ee1f38eb220e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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113 </citations>
ee1f38eb220e "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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114 </tool>