Mercurial > repos > chemteam > biomd_neqgamma

annotate 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
parents
children afcb925def69
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4f3222cb5cf6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
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1 <tool id="biomd_neqgamma" name="dcTMD friction correction" version="0.@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>for calculating friction and free energy profiles from TMD ensembles</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.5.2</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">scipy</requirement>
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9 <requirement type="package" version="1.19.1">numpy</requirement>
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10 <requirement type="package" version="1.1.2">pandas</requirement>
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11 </requirements>
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12 <command><![CDATA[
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13 #for t in $xvgs:
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14 echo $t &>> ./xvgs.txt &&
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15 #end for
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16
4f3222cb5cf6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
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17 python '$__tool_directory__/NEQGamma.py'
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18 -i ./xvgs.txt
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19 -o outp.txt
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20 -ofrict ofrict.txt
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21 -vel '$vel'
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22 -T '$T'
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23 -av '$av'
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24 -sigma '$sigma'
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25 #if $json:
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26 -json '$json'
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27 #end if
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28
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29 ]]></command>
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30 <inputs>
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31 <param type="data_collection" name="xvgs" label="XVG constraint force files" format="xvg" help="XVG files generated by GROMACS"/>
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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."/>
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33 <param label="Pull velocity in nm/ps of the TMD simulations" value="0.001" min="0" type="float" name="vel" argument="-vel"/>
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34 <param label="Temperature in K" value="300" min="0" type="float" name="T" argument="-T"/>
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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."/>
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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."/>
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37 </inputs>
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38 <outputs>
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39 <collection name="outp_col" type="list" label="Free energy data">
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40 <discover_datasets pattern="(?P&lt;designation&gt;^cluster\d+)_outp\.txt$" ext="txt"/>
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41 <filter>json</filter>
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42 </collection>
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43 <collection name="outp_frict_col" type="list" label="Friction data">
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44 <discover_datasets pattern="(?P&lt;designation&gt;^cluster\d+)_ofrict\.txt$" ext="txt"/>
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45 <filter>json</filter>
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46 </collection>
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47 <data name="outp" from_work_dir="outp.txt" format="tabular" label="Free energy data">
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48 <filter>not json</filter>
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49 </data>
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50 <data name="outp_frict" from_work_dir="ofrict.txt" format="tabular" label="Friction data">
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51 <filter>not json</filter>
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52 </data>
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53 </outputs>
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54 <tests>
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55 <test>
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56 <param name="xvgs">
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57 <collection type="list">
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58 <element name="pull1" ftype="xvg" value="pull1.xvg" />
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59 <element name="pull2" ftype="xvg" value="pull2.xvg" />
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60 <element name="pull3" ftype="xvg" value="pull3.xvg" />
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61 </collection>
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62 </param>
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63 <param name="vel" value="0.001" />
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64 <param name="T" value="300" />
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65 <param name="av" value="20" />
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66 <param name="sigma" value="20" />
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67 <output name="outp" value="NEQGamma_outp.txt" />
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68 <output name="outp_frict" value="NEQGamma_ofrict.txt" />
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69 </test>
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70 <test>
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71 <param name="xvgs">
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72 <collection type="list">
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73 <element name="pull1" ftype="xvg" value="pull1.xvg" />
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74 <element name="pull2" ftype="xvg" value="pull2.xvg" />
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75 <element name="pull3" ftype="xvg" value="pull3.xvg" />
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76 </collection>
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77 </param>
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78 <param name="json" value="NEQGamma_clusters.json" />
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79 <param name="vel" value="0.001" />
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80 <param name="T" value="300" />
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81 <param name="av" value="20" />
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82 <param name="sigma" value="20" />
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83 <output_collection name="outp_col" type="list">
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84 <element name="cluster0" file="NEQGamma_outp1.txt"/>
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85 <element name="cluster1" file="NEQGamma_outp2.txt"/>
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86 </output_collection>
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87 <output_collection name="outp_frict_col" type="list">
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88 <element name="cluster0" file="NEQGamma_ofrict1.txt"/>
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89 <element name="cluster1" file="NEQGamma_ofrict2.txt"/>
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90 </output_collection>
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91 </test>
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92
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93 </tests>
4f3222cb5cf6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 79589d149a8ff2791d4f71d28b155011672db827"
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94 <help><![CDATA[
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95
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96 .. class:: infomark
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97
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98 **What it does**
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99
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100 Perform dcTMD friction correction from an ensemble of XVG files generated by GROMACS targeted molecular dynamics (TMD) simulations.
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101
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102 _____
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103
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104
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105 .. class:: infomark
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106
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107 **Input**
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108
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109 - Ensemble of XVG files from TMD simulations
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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.
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111
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112 _____
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113
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114
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115 .. class:: infomark
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116
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117 **Output**
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118
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119 - Tab-separated files containing free energy and friction data.
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120 ]]></help>
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121 <citations>
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122 <citation type="doi">10.1021/acs.jctc.8b00835</citation>
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123 </citations>
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124 </tool>
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125