Mercurial > repos > chemteam > alchemical_analysis
view alchemical_analysis/alchemical_analysis.xml @ 1:c1fa72716efc draft default tip
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit eefe89bfcd6c3e98f4e774e508ad0659dcc2f65c"
author | chemteam |
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date | Sun, 01 Dec 2019 09:47:52 -0500 |
parents | 5f136e371f44 |
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<tool id="alchemical_analysis" name="Alchemical Analysis" version="1.0.2"> <description>Analysis of alchemical free energy calculations</description> <requirements> <requirement type="package" version="1.0.2">alchemical-analysis</requirement> <requirement type="package" version="3.0.3">pymbar</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ ln -s '$datain' ./data.tar && tar xf ./data.tar && mkdir ./RESULTS/ && #if $skiplambda == "": alchemical_analysis -d data -o ./RESULTS -t '$temp' -s '$time' -c -q xvg -p '$prefix' -g -e -f 10 -w -u '$units' &>> '$output' #else: alchemical_analysis -d data -o ./RESULTS -t '$temp' -s '$time' -k '$skiplambda' -c -q xvg -p '$prefix' -g -e -f 10 -w -u '$units' &>> '$output' #end if ]]></command> <inputs> <param format="tar" name="datain" type="data" label="TI/FEP data output"/> <param name="prefix" type="text" value="md" label="Prefix for datafile sets" help="This should be md if you used the alchemical simulator tool"/> <param name="temp" type="integer" value="300" label="Temperature (K)"/> <param name="time" type="integer" value="0" label="Equilibration time (ps)" help="Discard data prior to this specified time as 'equilibration' data." /> <param name="units" type="select" label="Units to report energies" > <option value="kcal">kcal</option> <option value="kJ">kJ</option> <option value="kBT">kT</option> </param> <param name="skiplambda" type="text" label="Indices of lambda states to skip" help="Give a string of lambda indices separated by '-' (e.g. 2-3) and they will be removed from the analysis. Default: will use all the windows."> <validator type="regex" message="Only numeric values and '-' allowed">^[0-9-]*$</validator> </param> </inputs> <outputs> <data name="output" format="txt" label="output"> </data> <data name="results" format="txt" from_work_dir="./RESULTS/results.txt" label="Results"/> <data name="change" format="txt" from_work_dir="./RESULTS/dF_t.txt" label="Free energy change dF(t)"/> <data name="convergence" format="png" from_work_dir="./RESULTS/dF_t.png" label="Convergence Plot dF(t)"/> <data name="overlap" format="png" from_work_dir="./RESULTS/O_MBAR.png" label="Overlap Matrix"/> <data name="cfm" format="png" from_work_dir="./RESULTS/cfm.png" label="Curve Fitting Method (CFM) based consistency inspector"/> <data name="df_state" format="png" from_work_dir="./RESULTS/dF_state_long.png" label="Free energy change breakdown"/> <data name="ti_plot" format="png" from_work_dir="./RESULTS/dhdl_TI.png" label="Thermodynamic Integration plot"/> </outputs> <tests> <test> <param name="datain" value="data.tar" ftype="tar"/> <param name="prefix" value="md"/> <param name="temp" value="300"/> <param name="time" value="0"/> <param name="units" value="kcal"/> <param name="lambda" value="no"/> <output name="change" file="Free_energy_change_dF(t).txt" /> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** This tool can run analysis of alchemical free energy simulations. _____ .. class:: infomark **Input** - TAR archive file of the GROMACS XVG files from free energy simulations. Note that simulations should be at least 100 ps in length. _____ .. class:: infomark **Output** - Report and free energy outputs. - Overlap matrix of free energy windows (as PNG). - Convergence plot (as PNG). - Curve Fitting Method (CFM) based consistency inspector (as PNG). - Free energy change breakdown (as PNG). - Thermodynamic Integration plot (as PNG). ]]></help> <citations> <citation type="doi">10.1007/s10822-015-9840-9</citation> </citations> </tool>