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comparison 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
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-1:000000000000 0:743bd6aa3c7a
1 <tool id="mdanalysis_extract_rmsd" name="Extract RMSD distance matrix data" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <description>from MD ensemble with MDAnalysis</description>
3 <macros>
4 <import>macros.xml</import>
5 <token name="@GALAXY_VERSION@">0</token>
6 </macros>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9 #for t in $strs:
10 echo $t &>> ./strs.txt &&
11 #end for
12 #for t in $trajs:
13 echo $t &>> ./trajs.txt &&
14 #end for
15
16 python '$__tool_directory__/extract_rmsd.py'
17 --trajs trajs.txt
18 --strs strs.txt
19 --ref-str '$refstr'
20 --traj-format '$trajs[0].ext'
21 --str-format '$strs[0].ext'
22 --ref-str-format '${refstr.ext}'
23 --outfile '$output'
24 --group '$group'
25 --fitting '$fitting'
26 --start '$start'
27 --end '$end'
28 --step '$step'
29
30 ]]></command>
31 <inputs>
32 <param type="data_collection" name="strs" label="Input structures" format="pdb,gro"/>
33 <param type="data_collection" name="trajs" label="Input trajectories" format="xtc,dcd,trr"/>
34 <param name="refstr" type="data" format="pdb,gro" label="Reference structure" help="Structure for aligning all trajectories against."/>
35 <param name='group' type='text' label='Group for RMSD calculation' />
36 <param name='fitting' type='text' label='Group for alignment prior to RMSD calculation' />
37 <param name="start" type="integer" min="0" value="0" label="First trajectory frame for RMSD calculation" />
38 <param name="end" type="integer" min="0" value="0" label="End trajectory frame for RMSD calculation" />
39 <param name="step" type="integer" min="1" value="1" label="Frequency of trajectory frame sampling for RMSD calculation" />
40 </inputs>
41 <outputs>
42 <data name="output" format="json" />
43 </outputs>
44 <tests>
45 <test>
46 <param name="strs">
47 <collection type="list">
48 <element name="str1" ftype="gro" value="test.gro" />
49 <element name="str2" ftype="gro" value="test.gro" />
50 </collection>
51 </param>
52 <param name="trajs">
53 <collection type="list">
54 <element name="traj1" ftype="xtc" value="test.xtc" />
55 <element name="traj2" ftype="xtc" value="test.xtc" />
56 </collection>
57 </param>
58
59 <param name="refstr" ftype="pdb" value="test.pdb" />
60 <param name="fitting" value="protein" />
61 <param name="group" value="resname BGLC" />
62 <param name="start" value="0" />
63 <param name="end" value="15" />
64 <param name="step" value="1" />
65 <output name="output">
66 <assert_contents>
67 <has_text text="0.0" n="20"/>
68 <has_size value="1588" />
69 <has_n_lines n="74" />
70 </assert_contents>
71 </output>
72 </test>
73 </tests>
74 <help><![CDATA[
75 .. class:: infomark
76
77 **What it does**
78
79 This tool takes collections of MD structures and trajectories and inputs and performs the following steps:
80 - aligns them to a reference structure
81 - calculates RMSD differences for a selected group of atoms between all possible pairs of trajectories at all time points
82 - returns RMSD data as a three-dimensional tensor.
83
84 _____
85
86
87 .. class:: infomark
88
89 **Input**
90
91 - Collection of structure files (PDB, GRO).
92 - Collection of trajectory files (DCD, XTC, TRR).
93 - Single structure file for alignment.
94 - User selection of fitting group, alignment group, start and end frames of the trajectory, and a frame step for the calculation.
95
96 _____
97
98
99 .. class:: infomark
100
101 **Output**
102
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.
104
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.
106
107 ]]></help>
108 <expand macro="citations" />
109 </tool>