Mercurial > repos > chemteam > mdanalysis_extract_rmsd
comparison extract_rmsd.xml @ 1:8f6ad93973cb draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 45fe75a3a8ca80f799c85e194429c4c7f38bb5f6"
author | chemteam |
---|---|
date | Wed, 28 Oct 2020 21:41:04 +0000 |
parents | 743bd6aa3c7a |
children | 589f8ef21e58 |
comparison
equal
deleted
inserted
replaced
0:743bd6aa3c7a | 1:8f6ad93973cb |
---|---|
1 <tool id="mdanalysis_extract_rmsd" name="Extract RMSD distance matrix data" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> | 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> | 2 <description>from MD ensemble with MDAnalysis</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 <token name="@GALAXY_VERSION@">0</token> | 5 <token name="@GALAXY_VERSION@">1</token> |
6 </macros> | 6 </macros> |
7 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
9 #for t in $strs: | 9 #for t in $strs: |
10 echo $t &>> ./strs.txt && | 10 echo $t &>> ./strs.txt && |
14 #end for | 14 #end for |
15 | 15 |
16 python '$__tool_directory__/extract_rmsd.py' | 16 python '$__tool_directory__/extract_rmsd.py' |
17 --trajs trajs.txt | 17 --trajs trajs.txt |
18 --strs strs.txt | 18 --strs strs.txt |
19 --ref-str '$refstr' | |
20 --traj-format '$trajs[0].ext' | 19 --traj-format '$trajs[0].ext' |
21 --str-format '$strs[0].ext' | 20 --str-format '$strs[0].ext' |
22 --ref-str-format '${refstr.ext}' | |
23 --outfile '$output' | 21 --outfile '$output' |
24 --group '$group' | 22 --group '$group' |
25 --fitting '$fitting' | |
26 --start '$start' | 23 --start '$start' |
27 --end '$end' | 24 --end '$end' |
28 --step '$step' | 25 --step '$step' |
29 | 26 |
30 ]]></command> | 27 ]]></command> |
31 <inputs> | 28 <inputs> |
32 <param type="data_collection" name="strs" label="Input structures" format="pdb,gro"/> | 29 <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"/> | 30 <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' /> | 31 <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" /> | 32 <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" /> | 33 <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" /> | 34 <param name="step" type="integer" min="1" value="1" label="Frequency of trajectory frame sampling for RMSD calculation" /> |
40 </inputs> | 35 </inputs> |
41 <outputs> | 36 <outputs> |
54 <element name="traj1" ftype="xtc" value="test.xtc" /> | 49 <element name="traj1" ftype="xtc" value="test.xtc" /> |
55 <element name="traj2" ftype="xtc" value="test.xtc" /> | 50 <element name="traj2" ftype="xtc" value="test.xtc" /> |
56 </collection> | 51 </collection> |
57 </param> | 52 </param> |
58 | 53 |
59 <param name="refstr" ftype="pdb" value="test.pdb" /> | |
60 <param name="fitting" value="protein" /> | |
61 <param name="group" value="resname BGLC" /> | 54 <param name="group" value="resname BGLC" /> |
62 <param name="start" value="0" /> | 55 <param name="start" value="0" /> |
63 <param name="end" value="15" /> | 56 <param name="end" value="15" /> |
64 <param name="step" value="1" /> | 57 <param name="step" value="1" /> |
65 <output name="output"> | 58 <output name="output"> |
66 <assert_contents> | 59 <assert_contents> |
67 <has_text text="0.0" n="20"/> | 60 <has_text text="0.0" n="20"/> |
68 <has_size value="1588" /> | 61 <has_size value="1126" /> |
69 <has_n_lines n="74" /> | 62 <has_n_lines n="74" /> |
70 </assert_contents> | 63 </assert_contents> |
71 </output> | 64 </output> |
72 </test> | 65 </test> |
73 </tests> | 66 </tests> |
78 | 71 |
79 This tool takes collections of MD structures and trajectories and inputs and performs the following steps: | 72 This tool takes collections of MD structures and trajectories and inputs and performs the following steps: |
80 - aligns them to a reference structure | 73 - 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 | 74 - 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. | 75 - returns RMSD data as a three-dimensional tensor. |
76 | |
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'. | |
83 | 78 |
84 _____ | 79 _____ |
85 | 80 |
86 | 81 |
87 .. class:: infomark | 82 .. class:: infomark |