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comparison NEQGamma.xml @ 0:4f3222cb5cf6 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
author chemteam
date Fri, 11 Sep 2020 21:54:45 +0000
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-1:000000000000 0:4f3222cb5cf6
1 <tool id="biomd_neqgamma" name="dcTMD friction correction" version="0.@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>for calculating friction and free energy profiles from TMD ensembles</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.5.2</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros>
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">scipy</requirement>
9 <requirement type="package" version="1.19.1">numpy</requirement>
10 <requirement type="package" version="1.1.2">pandas</requirement>
11 </requirements>
12 <command><![CDATA[
13 #for t in $xvgs:
14 echo $t &>> ./xvgs.txt &&
15 #end for
16
17 python '$__tool_directory__/NEQGamma.py'
18 -i ./xvgs.txt
19 -o outp.txt
20 -ofrict ofrict.txt
21 -vel '$vel'
22 -T '$T'
23 -av '$av'
24 -sigma '$sigma'
25 #if $json:
26 -json '$json'
27 #end if
28
29 ]]></command>
30 <inputs>
31 <param type="data_collection" name="xvgs" label="XVG constraint force files" format="xvg" help="XVG files generated by GROMACS"/>
32 <param type="data" name="json" optional="true" label="Ensemble subgroups" format="json" help="Optional: list of sub-ensembles in JSON format (e.g. produced by the 'Extract clusters' tool). If not specified, results will be calculated for the entire ensemble."/>
33 <param label="Pull velocity in nm/ps of the TMD simulations" value="0.001" min="0" type="float" name="vel" argument="-vel"/>
34 <param label="Temperature in K" value="300" min="0" type="float" name="T" argument="-T"/>
35 <param label="Size of averaging window for displaying Gamma(x)" value="0" min="0" type="integer" name="av" argument="-av" help="Recommended: 4 to 20 per 100 data points."/>
36 <param label="Sigma value for Gauss filter for displaying Gamma(x)" value="0" min="0" type="integer" name="sigma" argument="-sigma" help="Recommended: 4 per 100 data points."/>
37 </inputs>
38 <outputs>
39 <collection name="outp_col" type="list" label="Free energy data">
40 <discover_datasets pattern="(?P&lt;designation&gt;^cluster\d+)_outp\.txt$" ext="txt"/>
41 <filter>json</filter>
42 </collection>
43 <collection name="outp_frict_col" type="list" label="Friction data">
44 <discover_datasets pattern="(?P&lt;designation&gt;^cluster\d+)_ofrict\.txt$" ext="txt"/>
45 <filter>json</filter>
46 </collection>
47 <data name="outp" from_work_dir="outp.txt" format="tabular" label="Free energy data">
48 <filter>not json</filter>
49 </data>
50 <data name="outp_frict" from_work_dir="ofrict.txt" format="tabular" label="Friction data">
51 <filter>not json</filter>
52 </data>
53 </outputs>
54 <tests>
55 <test>
56 <param name="xvgs">
57 <collection type="list">
58 <element name="pull1" ftype="xvg" value="pull1.xvg" />
59 <element name="pull2" ftype="xvg" value="pull2.xvg" />
60 <element name="pull3" ftype="xvg" value="pull3.xvg" />
61 </collection>
62 </param>
63 <param name="vel" value="0.001" />
64 <param name="T" value="300" />
65 <param name="av" value="20" />
66 <param name="sigma" value="20" />
67 <output name="outp" value="NEQGamma_outp.txt" />
68 <output name="outp_frict" value="NEQGamma_ofrict.txt" />
69 </test>
70 <test>
71 <param name="xvgs">
72 <collection type="list">
73 <element name="pull1" ftype="xvg" value="pull1.xvg" />
74 <element name="pull2" ftype="xvg" value="pull2.xvg" />
75 <element name="pull3" ftype="xvg" value="pull3.xvg" />
76 </collection>
77 </param>
78 <param name="json" value="NEQGamma_clusters.json" />
79 <param name="vel" value="0.001" />
80 <param name="T" value="300" />
81 <param name="av" value="20" />
82 <param name="sigma" value="20" />
83 <output_collection name="outp_col" type="list">
84 <element name="cluster0" file="NEQGamma_outp1.txt"/>
85 <element name="cluster1" file="NEQGamma_outp2.txt"/>
86 </output_collection>
87 <output_collection name="outp_frict_col" type="list">
88 <element name="cluster0" file="NEQGamma_ofrict1.txt"/>
89 <element name="cluster1" file="NEQGamma_ofrict2.txt"/>
90 </output_collection>
91 </test>
92
93 </tests>
94 <help><![CDATA[
95
96 .. class:: infomark
97
98 **What it does**
99
100 Perform dcTMD friction correction from an ensemble of XVG files generated by GROMACS targeted molecular dynamics (TMD) simulations.
101
102 _____
103
104
105 .. class:: infomark
106
107 **Input**
108
109 - Ensemble of XVG files from TMD simulations
110 - Optional: JSON file containing subgroups of trajectories from the ensemble. If this option is used, the dcTMD calculation will be performed separately for each sub-ensemble.
111
112 _____
113
114
115 .. class:: infomark
116
117 **Output**
118
119 - Tab-separated files containing free energy and friction data.
120 ]]></help>
121 <citations>
122 <citation type="doi">10.1021/acs.jctc.8b00835</citation>
123 </citations>
124 </tool>
125