Mercurial > repos > chemteam > alchemical_analysis
comparison alchemical_analysis/alchemical_analysis.xml @ 0:5f136e371f44 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit 4c75f8d26505d221d4144f4ae7d2fb7698fbe4ab"
author | chemteam |
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date | Mon, 18 Nov 2019 09:52:20 -0500 |
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1 <tool id="alchemical_analysis" name="Alchemical Analysis" version="1.0.2"> | |
2 <description>Analysis of alchemical free energy calculations</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.0.2">alchemical-analysis</requirement> | |
5 <requirement type="package" version="3.0.3">pymbar</requirement> | |
6 </requirements> | |
7 <command detect_errors="exit_code"><![CDATA[ | |
8 ln -s '$datain' ./data.tar && | |
9 tar xf ./data.tar && | |
10 mkdir ./RESULTS/ && | |
11 #if $skiplambda == "": | |
12 alchemical_analysis -d data -o ./RESULTS -t '$temp' -s '$time' -c -q xvg -p '$prefix' -g -e -f 10 -w -u '$units' &>> '$output' | |
13 #else: | |
14 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' | |
15 #end if | |
16 ]]></command> | |
17 <inputs> | |
18 <param format="tar" name="datain" type="data" label="TI/FEP data output"/> | |
19 <param name="prefix" type="text" value="md" label="Prefix for datafile sets" help="This should be md if you used the alchemical simulator tool"/> | |
20 <param name="temp" type="integer" value="300" label="Temperature (K)"/> | |
21 <param name="time" type="integer" value="0" label="Equilibration time (ps)" help="Discard data prior to this specified time as 'equilibration' data." /> | |
22 <param name="units" type="select" label="Units to report energies" > | |
23 <option value="kcal">kcal</option> | |
24 <option value="kJ">kJ</option> | |
25 <option value="kBT">kT</option> | |
26 </param> | |
27 <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."> | |
28 <validator type="regex" message="Only numeric values and '-' allowed">^[0-9-]*$</validator> | |
29 </param> | |
30 </inputs> | |
31 <outputs> | |
32 <data name="output" format="txt" label="output"> | |
33 </data> | |
34 <data name="results" format="txt" from_work_dir="./RESULTS/results.txt" label="Results"/> | |
35 <data name="change" format="txt" from_work_dir="./RESULTS/dF_t.txt" label="Free energy change dF(t)"/> | |
36 <data name="convergence" format="png" from_work_dir="./RESULTS/dF_t.png" label="Convergence Plot dF(t)"/> | |
37 <data name="overlap" format="png" from_work_dir="./RESULTS/O_MBAR.png" label="Overlap Matrix"/> | |
38 <data name="cfm" format="png" from_work_dir="./RESULTS/cfm.png" label="Curve Fitting Method (CFM) based consistency inspector"/> | |
39 <data name="df_state" format="png" from_work_dir="./RESULTS/dF_state_long.png" label="Free energy change breakdown"/> | |
40 <data name="ti_plot" format="png" from_work_dir="./RESULTS/dhdl_TI.png" label="Thermodynamic Integration plot"/> | |
41 </outputs> | |
42 <tests> | |
43 <test> | |
44 <param name="datain" value="data.tar" ftype="tar"/> | |
45 <param name="prefix" value="md"/> | |
46 <param name="temp" value="300"/> | |
47 <param name="time" value="0"/> | |
48 <param name="units" value="kcal"/> | |
49 <param name="lambda" value="no"/> | |
50 <output name="change" file="Free_energy_change_dF(t).txt" /> | |
51 </test> | |
52 </tests> | |
53 <help><![CDATA[ | |
54 .. class:: infomark | |
55 | |
56 **What it does** | |
57 | |
58 | |
59 This tool can run analysis of alchemical free energy simulations. | |
60 | |
61 _____ | |
62 | |
63 | |
64 .. class:: infomark | |
65 | |
66 **Input** | |
67 | |
68 - TAR archive file of the GROMACS XVG files from free energy simulations. Note that simulations should be at least 100 ps in length. | |
69 | |
70 _____ | |
71 | |
72 | |
73 .. class:: infomark | |
74 | |
75 **Output** | |
76 | |
77 - Report and free energy outputs. | |
78 - Overlap matrix of free energy windows (as PNG). | |
79 - Convergence plot (as PNG). | |
80 - Curve Fitting Method (CFM) based consistency inspector (as PNG). | |
81 - Free energy change breakdown (as PNG). | |
82 - Thermodynamic Integration plot (as PNG). | |
83 | |
84 ]]></help> | |
85 <citations> | |
86 <citation type="doi">10.1007/s10822-015-9840-9</citation> | |
87 </citations> | |
88 </tool> |