Mercurial > repos > chemteam > mdanalysis_extract_rmsd

annotate extract_rmsd.xml @ 0:743bd6aa3c7a 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 16:41:41 -0400
parents
children 8f6ad93973cb
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1 <tool id="mdanalysis_extract_rmsd" name="Extract RMSD distance matrix data" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description>from MD ensemble with MDAnalysis</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <token name="@GALAXY_VERSION@">0</token>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 #for t in $strs:
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10 echo $t &>> ./strs.txt &&
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11 #end for
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12 #for t in $trajs:
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13 echo $t &>> ./trajs.txt &&
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14 #end for
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15
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16 python '$__tool_directory__/extract_rmsd.py'
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17 --trajs trajs.txt
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18 --strs strs.txt
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19 --ref-str '$refstr'
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20 --traj-format '$trajs[0].ext'
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21 --str-format '$strs[0].ext'
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22 --ref-str-format '${refstr.ext}'
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23 --outfile '$output'
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24 --group '$group'
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25 --fitting '$fitting'
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26 --start '$start'
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27 --end '$end'
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28 --step '$step'
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29
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30 ]]></command>
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31 <inputs>
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32 <param type="data_collection" name="strs" label="Input structures" format="pdb,gro"/>
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33 <param type="data_collection" name="trajs" label="Input trajectories" format="xtc,dcd,trr"/>
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34 <param name="refstr" type="data" format="pdb,gro" label="Reference structure" help="Structure for aligning all trajectories against."/>
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35 <param name='group' type='text' label='Group for RMSD calculation' />
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36 <param name='fitting' type='text' label='Group for alignment prior to RMSD calculation' />
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37 <param name="start" type="integer" min="0" value="0" label="First trajectory frame for RMSD calculation" />
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38 <param name="end" type="integer" min="0" value="0" label="End trajectory frame for RMSD calculation" />
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39 <param name="step" type="integer" min="1" value="1" label="Frequency of trajectory frame sampling for RMSD calculation" />
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40 </inputs>
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41 <outputs>
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42 <data name="output" format="json" />
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43 </outputs>
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44 <tests>
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45 <test>
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46 <param name="strs">
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47 <collection type="list">
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48 <element name="str1" ftype="gro" value="test.gro" />
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49 <element name="str2" ftype="gro" value="test.gro" />
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50 </collection>
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51 </param>
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52 <param name="trajs">
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53 <collection type="list">
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54 <element name="traj1" ftype="xtc" value="test.xtc" />
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55 <element name="traj2" ftype="xtc" value="test.xtc" />
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56 </collection>
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57 </param>
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58
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59 <param name="refstr" ftype="pdb" value="test.pdb" />
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60 <param name="fitting" value="protein" />
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61 <param name="group" value="resname BGLC" />
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62 <param name="start" value="0" />
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63 <param name="end" value="15" />
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64 <param name="step" value="1" />
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65 <output name="output">
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66 <assert_contents>
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67 <has_text text="0.0" n="20"/>
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68 <has_size value="1588" />
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69 <has_n_lines n="74" />
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70 </assert_contents>
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71 </output>
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72 </test>
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73 </tests>
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74 <help><![CDATA[
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75 .. class:: infomark
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76
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77 **What it does**
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78
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79 This tool takes collections of MD structures and trajectories and inputs and performs the following steps:
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80 - aligns them to a reference structure
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81 - calculates RMSD differences for a selected group of atoms between all possible pairs of trajectories at all time points
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82 - returns RMSD data as a three-dimensional tensor.
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83
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84 _____
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85
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86
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87 .. class:: infomark
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88
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89 **Input**
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90
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91 - Collection of structure files (PDB, GRO).
743bd6aa3c7a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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92 - Collection of trajectory files (DCD, XTC, TRR).
743bd6aa3c7a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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93 - Single structure file for alignment.
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94 - User selection of fitting group, alignment group, start and end frames of the trajectory, and a frame step for the calculation.
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95
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96 _____
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97
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98
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99 .. class:: infomark
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100
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101 **Output**
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102
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103 The output consists of a three-dimensional numpy array saved in JSON format, with dimensions N x N x t, where N is the number of trajectories and t is the number of time frames. Thus, the file effectively contains multiple distance matrices (one for each time step) representing the RMSD between all pairs of trajectories for a chosen group of atoms.
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104
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105 It may be more useful to flatten the tensor to a two-dimensional matrix by averaging or slicing on the time axis; this can be achieved using the 'Hierarchical clustering' tool.
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106
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107 ]]></help>
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108 <expand macro="citations" />
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109 </tool>