Mercurial > repos > chemteam > mdanalysis_extract_rmsd
diff 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 |
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--- a/extract_rmsd.xml Mon Aug 24 16:41:41 2020 -0400 +++ b/extract_rmsd.xml Wed Oct 28 21:41:04 2020 +0000 @@ -2,7 +2,7 @@ <description>from MD ensemble with MDAnalysis</description> <macros> <import>macros.xml</import> - <token name="@GALAXY_VERSION@">0</token> + <token name="@GALAXY_VERSION@">1</token> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ @@ -16,13 +16,10 @@ python '$__tool_directory__/extract_rmsd.py' --trajs trajs.txt --strs strs.txt - --ref-str '$refstr' --traj-format '$trajs[0].ext' --str-format '$strs[0].ext' - --ref-str-format '${refstr.ext}' --outfile '$output' --group '$group' - --fitting '$fitting' --start '$start' --end '$end' --step '$step' @@ -31,9 +28,7 @@ <inputs> <param type="data_collection" name="strs" label="Input structures" format="pdb,gro"/> <param type="data_collection" name="trajs" label="Input trajectories" format="xtc,dcd,trr"/> - <param name="refstr" type="data" format="pdb,gro" label="Reference structure" help="Structure for aligning all trajectories against."/> <param name='group' type='text' label='Group for RMSD calculation' /> - <param name='fitting' type='text' label='Group for alignment prior to RMSD calculation' /> <param name="start" type="integer" min="0" value="0" label="First trajectory frame for RMSD calculation" /> <param name="end" type="integer" min="0" value="0" label="End trajectory frame for RMSD calculation" /> <param name="step" type="integer" min="1" value="1" label="Frequency of trajectory frame sampling for RMSD calculation" /> @@ -56,8 +51,6 @@ </collection> </param> - <param name="refstr" ftype="pdb" value="test.pdb" /> - <param name="fitting" value="protein" /> <param name="group" value="resname BGLC" /> <param name="start" value="0" /> <param name="end" value="15" /> @@ -65,7 +58,7 @@ <output name="output"> <assert_contents> <has_text text="0.0" n="20"/> - <has_size value="1588" /> + <has_size value="1126" /> <has_n_lines n="74" /> </assert_contents> </output> @@ -81,6 +74,8 @@ - calculates RMSD differences for a selected group of atoms between all possible pairs of trajectories at all time points - returns RMSD data as a three-dimensional tensor. +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'. + _____