Mercurial > repos > chemteam > mdanalysis_extract_rmsd

annotate extract_rmsd.xml @ 2:589f8ef21e58 draft default tip

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
author chemteam
date Fri, 13 Nov 2020 19:44:09 +0000
parents 8f6ad93973cb
children
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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>
2
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5 <token name="@GALAXY_VERSION@">2</token>
0
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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 --traj-format '$trajs[0].ext'
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20 --str-format '$strs[0].ext'
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21 --outfile '$output'
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22 --group '$group'
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23 --start '$start'
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24 --end '$end'
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25 --step '$step'
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26
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27 ]]></command>
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28 <inputs>
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29 <param type="data_collection" name="strs" label="Input structures" format="pdb,gro"/>
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30 <param type="data_collection" name="trajs" label="Input trajectories" format="xtc,dcd,trr"/>
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31 <param name='group' type='text' label='Group for RMSD calculation' />
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32 <param name="start" type="integer" min="0" value="0" label="First trajectory frame for RMSD calculation" />
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33 <param name="end" type="integer" min="0" value="0" label="End trajectory frame for RMSD calculation" />
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34 <param name="step" type="integer" min="1" value="1" label="Frequency of trajectory frame sampling for RMSD calculation" />
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35 </inputs>
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36 <outputs>
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37 <data name="output" format="json" />
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38 </outputs>
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39 <tests>
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40 <test>
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41 <param name="strs">
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42 <collection type="list">
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43 <element name="str1" ftype="gro" value="test.gro" />
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44 <element name="str2" ftype="gro" value="test.gro" />
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45 </collection>
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46 </param>
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47 <param name="trajs">
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48 <collection type="list">
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49 <element name="traj1" ftype="xtc" value="test.xtc" />
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50 <element name="traj2" ftype="xtc" value="test.xtc" />
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51 </collection>
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52 </param>
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53
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54 <param name="group" value="resname BGLC" />
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55 <param name="start" value="0" />
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56 <param name="end" value="15" />
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57 <param name="step" value="1" />
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58 <output name="output">
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59 <assert_contents>
2
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60 <has_text text="0.0" n="60"/>
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61 <has_size value="1126" />
0
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62 <has_n_lines n="74" />
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63 </assert_contents>
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64 </output>
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65 </test>
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66 </tests>
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67 <help><![CDATA[
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68 .. class:: infomark
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69
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70 **What it does**
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71
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72 This tool takes collections of MD structures and trajectories and inputs and performs the following steps:
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73 - aligns them to a reference structure
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74 - calculates RMSD differences for a selected group of atoms between all possible pairs of trajectories at all time points
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75 - returns RMSD data as a three-dimensional tensor.
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76
1
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77 Note: in an older version of this tool trajectories were aligned to a reference group prior to RMSD calculation. This is no longer supported; you should perform alignment yourself using a more efficient tool such as 'Modify/convert GROMACS trajectories'.
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78
0
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79 _____
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80
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81
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82 .. class:: infomark
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83
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84 **Input**
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85
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86 - Collection of structure files (PDB, GRO).
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87 - Collection of trajectory files (DCD, XTC, TRR).
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88 - Single structure file for alignment.
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89 - 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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90
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91 _____
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94 .. class:: infomark
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96 **Output**
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98 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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99
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100 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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101
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102 ]]></help>
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103 <expand macro="citations" />
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104 </tool>