| Next changeset 1:d9f8cc3258f9 (2020-08-24) |
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Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit ee29bbfa4e78dca11e2e06d0d35a434c063ab588" |
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added:
fastpca.xml test-data/contacts.dat test-data/contacts2.dat test-data/cov.dat test-data/proj.dat test-data/proj2.dat test-data/stats.dat test-data/val.dat test-data/val2.dat test-data/vec.dat |
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| diff -r 000000000000 -r dd195f7a791c fastpca.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastpca.xml Thu Jan 30 07:58:42 2020 -0500 |
| [ |
| @@ -0,0 +1,127 @@ +<tool id="fastpca" name="fastpca" version="@VERSION@"> + <description>- dimensionality reduction of MD simulations</description> + <macros> + <token name="@VERSION@">0.9.1</token> + </macros> + <requirements> + <requirement type="package" version="@VERSION@">fastpca</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + fastpca + -f '$input' + -p '$output_proj' + #if str($inputs.cov) == 'None': + -c '$output_cov' + #elif str($inputs.vec) == 'None': + -C '$inputs.cov' + #end if + #if str($inputs.vec) == 'None': + -v $output_vec + #else: + -V '$inputs.vec' + #end if + #if str($inputs.stats) == 'None': + -s '$output_stats' + #else: + -S '$inputs.stats' + #end if + -l '$output_val' + $norm + $periodic + $dynamic_shift + --verbose + + ]]></command> + <inputs> + <param format="tabular,xtc" name="input" type="data" label="Input data" help="Either a whitespace-separated tabular file or GROMACS XTC file."/> + <section name="inputs" title="Inputs" expanded="true" help="Use these (optional) inputs to project new data onto a previously computed principal space. If not set, the PCA will be computed from scratch and will not be comparable to previous runs." > + <param format="tabular" name="cov" type="data" label="Precomputed covariance/correlation matrix" optional="true"/> + <param format="tabular" name="vec" type="data" label="Precomputed eigenvectors" optional="true"/> + <param format="tabular" name="stats" type="data" label="Precomputed statistics (mean values, sigmas and boundary shifts)" optional="true"/> + </section> + + <param name="norm" type="select" label="How to normalize input:" help="Generally, normalization using the covariance matrix is appropriate when the variable scales are similar, and the correlation matrix is used when variables are on different scales." > + <option value="">Covariance</option> + <option value="-N">Correlation</option> + </param> + <param name="periodic" type="boolean" label="Compute covariance and PCA on a torus?" truevalue="-P" falsevalue="" value="false" help="Useful for computing PCA on periodic data - for example, dihedral angles."/> + <param name="dynamic_shift" type="boolean" label="Use dynamic shifting for periodic projection correction" truevalue="-D" falsevalue="" value="false" help="Default is fale, i.e. simply shift to region of lowest density"/> + </inputs> + <outputs> + <data name="output_proj" format="tabular"/> + <data name="output_cov" format="tabular"> + <filter>inputs["cov"] == None</filter> + </data> + <data name="output_vec" format="tabular"> + <filter>inputs["vec"] == None</filter> + </data> + <data name="output_stats" format="tabular"> + <filter>inputs["stats"] == None</filter> + </data> + <data name="output_val" format="tabular"/> + </outputs> + <tests> + <!-- fastpca -f contacts.dat -p proj.dat -c cov.dat -v vec.dat -s stats.dat -l val.dat -N --> + <test> + <param name="input" value="contacts.dat"/> + <param name="norm" value="-N"/> + <param name="periodic" value="false"/> + <param name="dynamic_shift" value="false"/> + <output name="output_proj" file="proj.dat"/> + <output name="output_cov" file="cov.dat"/> + <output name="output_vec" file="vec.dat"/> + <output name="output_stats" file="stats.dat"/> + <output name="output_val" file="val.dat"/> + </test> + <!-- fastpca -f contacts2.dat -p proj2.dat -C cov.dat -V vec.dat -S stats.dat -l val2.dat -N --> + <test> + <param name="input" value="contacts2.dat"/> + <param name="cov" value="cov.dat"/> + <param name="stats" value="stats.dat"/> + <param name="norm" value="-N"/> + <param name="periodic" value="false"/> + <param name="dynamic_shift" value="false"/> + <output name="output_proj" file="proj2.dat"/> + <output name="output_val" file="val2.dat"/> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + +**What it does** + +Dimensionality reduction of molecular dynamics trajectories. Data can be input as +tabular or GROMACS XTC files. In addition, data can be projected into a previously +computed coordinate space by providing precomputed eigenvectors, statistics and +a correlation/covariance matrix. + +Data can be normalized using the either the covariance or correlation matrix. Data +can also be calculated on a torus, which is useful for periodic data, such as protein +dihedral angles. + +_____ + + +.. class:: infomark + +**Input** + + - Tabular or XTC file + - If you want to project data into a previously calculated principal space, you can upload precomputed eigenvectors, statistics and correlation/covariance matrix. + +_____ + + +.. class:: infomark + +**Output** + + - Projected data (tabular file) with each column representing a principal component + - Eigenvectors, statistics and covariance/correlation matrix + + ]]></help> + <citations> + <citation type="doi">10.1063/1.4998259</citation> + </citations> +</tool> + |
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| diff -r 000000000000 -r dd195f7a791c test-data/contacts.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contacts.dat Thu Jan 30 07:58:42 2020 -0500 |
| b |
| b'@@ -0,0 +1,100 @@\n+1.935042715939207980e+01 1.997237540908500009e+01 2.578169160930507786e+01 2.662967434240173503e+01 2.140055638457945619e+01 2.186419820909153700e+01 2.138127281093456844e+01 2.450577396773067917e+01 2.344322452708901494e+01 2.052492021755178087e+01 2.498771361354259923e+01 7.287566146100804332e+00 9.674008889357175178e+00 1.097507993244919966e+01 8.876770539062370347e+00 5.585553189124439655e+00 8.057092627909513638e+00 6.343384160754197865e+00 5.416250355268554806e+00 8.648677395848054061e+00 1.153628403617782716e+01 8.996394069288133011e+00 7.306729640207964671e+00 8.305652835268356071e+00 4.644157037027860646e+00 7.186483368605500743e+00 9.334062186765249791e+00 7.466737103408760845e+00 7.342008913138132975e+00 1.221824200539302119e+01 1.166149015164001312e+01 1.064155789208259151e+01 8.299740524705329747e+00 1.042336849671943355e+01 1.019198518358406425e+01 6.793080657183581117e+00 7.701474375902781055e+00 1.087236025593441724e+01 9.539699414151193935e+00 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1.988520373183719414e+01 1.846851307360875438e+01 2.248594502026295316e+01\n' |
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| diff -r 000000000000 -r dd195f7a791c test-data/contacts2.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contacts2.dat Thu Jan 30 07:58:42 2020 -0500 |
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1.393081772440887001e+01 1.070700228444994373e+01 1.593277334165102488e+01\n' |
| b |
| diff -r 000000000000 -r dd195f7a791c test-data/cov.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cov.dat Thu Jan 30 07:58:42 2020 -0500 |
| b |
| b'@@ -0,0 +1,85 @@\n+ 1.000000e+00 2.431699e-01 1.386428e-01 6.964081e-02 6.975238e-03 -5.388288e-02 -1.235640e-01 -1.346290e-01 -1.657570e-01 -6.532789e-03 -2.100933e-01 -1.330822e-01 -1.863497e-01 -2.155688e-01 -2.228470e-01 -2.206246e-01 -2.077389e-01 -2.332197e-01 -9.386961e-02 1.107098e-01 1.323555e-01 2.574365e-01 2.232413e-01 2.843345e-01 4.133169e-01 2.622751e-01 4.049051e-01 3.536156e-01 2.328504e-01 3.108070e-01 2.433182e-01 1.575743e-01 3.261244e-03 -2.474522e-02 3.148077e-02 2.067967e-02 -1.405063e-01 -1.317355e-01 -8.014525e-02 -2.964913e-01 -8.128630e-02 9.711051e-02 -1.697372e-02 -1.095197e-01 3.564844e-02 8.265130e-02 -7.653294e-02 -1.418297e-02 2.034374e-01 7.059508e-02 1.540479e-01 1.701717e-01 1.459027e-01 1.503092e-01 1.931944e-01 1.748214e-01 1.308742e-01 1.890640e-01 1.915827e-01 1.601499e-01 1.731212e-01 8.456060e-02 1.267518e-01 2.551383e-01 1.981166e-01 1.412775e-01 2.275346e-01 2.275813e-01 3.065232e-01 3.161774e-01 2.865340e-01 3.042354e-01 3.414414e-01 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3.290460e-01 3.617804e-02 4.252153e-01 5.513016e-01 4.770550e-01 3.467639e-01 4.825747e-01 4.423651e-01 1.587508e-01 2.980973e-01 3.504779e-01 4.771593e-01 5.231477e-01 6.047992e-01 5.425960e-01 5.685804e-01 6.406140e-01 6.392886e-01 5.885057e-01 5.778499e-01 5.620948e-01 4.596908e-01 4.739304e-01 4.278824e-01 4.732158e-01 5.694002e-01 5.438157e-01 5.386405e-01 6.160199e-01 6.344648e-01 6.586365e-01 6.404534e-01 6.577830e-01 6.794926e-01 7.255451e-01 7.204965e-01 6.844592e-01 6.944836e-01 6.775051e-01 6.393428e-01 6.436974e-01 6.261895e-01 7.141637e-01 7.539583e-01 7.871885e-01 7.875350e-01 1.000000e+00\n' |
| b |
| diff -r 000000000000 -r dd195f7a791c test-data/proj.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/proj.dat Thu Jan 30 07:58:42 2020 -0500 |
| b |
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| b |
| diff -r 000000000000 -r dd195f7a791c test-data/proj2.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/proj2.dat Thu Jan 30 07:58:42 2020 -0500 |
| b |
| b'@@ -0,0 +1,100 @@\n+ -3.951473e+01 1.229162e+01 1.206066e+01 2.602058e+01 5.350080e+01 -4.808977e+01 -4.926673e+01 8.954220e+00 -5.727875e-01 -7.412464e+01 4.980059e+01 -3.046488e+01 3.056670e+01 -5.226328e+01 1.970306e+01 3.665741e+01 2.511060e+01 2.146784e+01 -5.583113e+01 2.273895e+01 -1.661368e+01 -3.942620e+01 -4.113052e+01 3.817784e+01 3.946857e-01 2.155028e+01 -1.798059e+01 4.603231e+00 1.008131e+00 -8.771671e+00 -2.372438e+01 3.479789e+00 5.602666e+00 -1.833383e+01 3.117855e+00 -4.087497e+00 1.390660e-01 -1.943008e+01 2.235639e+01 9.313805e+00 -1.604568e+01 3.013040e+01 -1.157131e+01 8.212835e+00 -1.539543e+00 4.215390e+00 -3.900767e+00 -4.186234e+00 2.149871e+00 1.088597e+01 -2.691122e+01 2.900292e+01 -2.833295e+01 4.443315e+00 -3.579413e+00 1.174783e+01 -7.310555e+00 6.865370e-01 -1.454794e+01 -8.661166e+00 5.022259e-01 -2.559092e+00 -9.534033e+00 -1.186941e+01 1.170849e+01 1.209516e+01 -9.753293e+00 2.081603e+01 -7.991579e+00 6.109249e+00 -4.830590e+00 -2.877154e-01 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| b |
| diff -r 000000000000 -r dd195f7a791c test-data/stats.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stats.dat Thu Jan 30 07:58:42 2020 -0500 |
| b |
| @@ -0,0 +1,85 @@ + 1.967497e+01 3.703805e-01 + 1.945682e+01 4.155976e-01 + 2.493662e+01 4.482403e-01 + 2.591100e+01 4.907198e-01 + 2.054311e+01 6.191418e-01 + 2.042238e+01 8.120932e-01 + 2.045441e+01 1.071626e+00 + 2.357741e+01 8.641369e-01 + 2.260843e+01 5.896767e-01 + 1.992950e+01 5.709322e-01 + 2.399211e+01 6.546606e-01 + 7.845941e+00 6.782487e-01 + 1.052719e+01 5.837915e-01 + 1.169832e+01 5.493730e-01 + 9.145760e+00 4.060450e-01 + 6.055308e+00 5.063536e-01 + 8.693517e+00 5.978220e-01 + 6.830967e+00 4.033432e-01 + 6.361173e+00 5.483321e-01 + 9.094970e+00 3.961013e-01 + 1.174759e+01 2.980387e-01 + 8.827140e+00 3.946120e-01 + 7.463399e+00 1.994348e-01 + 7.811651e+00 3.917859e-01 + 4.275341e+00 3.092223e-01 + 6.986056e+00 3.965528e-01 + 9.001224e+00 3.904505e-01 + 7.288267e+00 4.367149e-01 + 7.595355e+00 4.232301e-01 + 1.187438e+01 4.095508e-01 + 1.120698e+01 3.917284e-01 + 1.026656e+01 4.369231e-01 + 8.465002e+00 4.423827e-01 + 1.063072e+01 3.827076e-01 + 9.867346e+00 2.945949e-01 + 6.202634e+00 3.185203e-01 + 7.599270e+00 3.198939e-01 + 1.015873e+01 2.974711e-01 + 8.666472e+00 4.832279e-01 + 9.860568e+00 4.691489e-01 + 1.159276e+01 4.520981e-01 + 9.175733e+00 6.050901e-01 + 6.679121e+00 4.572131e-01 + 1.011808e+01 4.204646e-01 + 1.109328e+01 5.258842e-01 + 8.433053e+00 5.673694e-01 + 9.695981e+00 4.866417e-01 + 1.313777e+01 5.016506e-01 + 1.302361e+01 6.386153e-01 + 1.409427e+01 6.219133e-01 + 1.320250e+01 6.857931e-01 + 1.588558e+01 6.652152e-01 + 1.526147e+01 6.511772e-01 + 1.155960e+01 6.547106e-01 + 1.324390e+01 6.993882e-01 + 1.565683e+01 6.830393e-01 + 1.345531e+01 6.707395e-01 + 1.114576e+01 6.897825e-01 + 1.465040e+01 7.207709e-01 + 1.589369e+01 6.305320e-01 + 1.441524e+01 5.350904e-01 + 1.610456e+01 4.926006e-01 + 1.371388e+01 5.174074e-01 + 1.519495e+01 5.841832e-01 + 1.861954e+01 5.504953e-01 + 1.862698e+01 5.103952e-01 + 1.729435e+01 5.644140e-01 + 1.788582e+01 6.753580e-01 + 1.864438e+01 6.108037e-01 + 1.552720e+01 5.975017e-01 + 1.336845e+01 6.492108e-01 + 1.557286e+01 6.782724e-01 + 1.501091e+01 6.114845e-01 + 1.116047e+01 6.095425e-01 + 1.159290e+01 6.456012e-01 + 1.440479e+01 6.038611e-01 + 1.025204e+01 5.762923e-01 + 1.380680e+01 6.147225e-01 + 1.578026e+01 5.726969e-01 + 1.392271e+01 5.035768e-01 + 1.653598e+01 4.746090e-01 + 1.721792e+01 4.686125e-01 + 1.960588e+01 5.201088e-01 + 1.831822e+01 5.600042e-01 + 2.224398e+01 5.684325e-01 |
| b |
| diff -r 000000000000 -r dd195f7a791c test-data/val.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/val.dat Thu Jan 30 07:58:42 2020 -0500 |
| b |
| @@ -0,0 +1,85 @@ + 3.947222e+01 + 2.015408e+01 + 4.916455e+00 + 2.895004e+00 + 2.441851e+00 + 1.693793e+00 + 1.452903e+00 + 1.162406e+00 + 9.084163e-01 + 8.297056e-01 + 7.989324e-01 + 6.787932e-01 + 5.389385e-01 + 4.860497e-01 + 4.819947e-01 + 4.578189e-01 + 4.253657e-01 + 3.982626e-01 + 3.460761e-01 + 3.256565e-01 + 2.848984e-01 + 2.736597e-01 + 2.479534e-01 + 2.340745e-01 + 2.225551e-01 + 1.889215e-01 + 1.785513e-01 + 1.644114e-01 + 1.600505e-01 + 1.454533e-01 + 1.354044e-01 + 1.321860e-01 + 1.232544e-01 + 1.200232e-01 + 1.047262e-01 + 9.791054e-02 + 9.288343e-02 + 8.730712e-02 + 8.455886e-02 + 7.553146e-02 + 7.464053e-02 + 6.972549e-02 + 6.652490e-02 + 6.060531e-02 + 5.676623e-02 + 5.018758e-02 + 4.989483e-02 + 4.465919e-02 + 4.245154e-02 + 4.105765e-02 + 3.892739e-02 + 3.643910e-02 + 3.230759e-02 + 3.081278e-02 + 2.805245e-02 + 2.607806e-02 + 2.512062e-02 + 2.207873e-02 + 2.048675e-02 + 1.852247e-02 + 1.676865e-02 + 1.442674e-02 + 1.345403e-02 + 1.305317e-02 + 1.238466e-02 + 1.052215e-02 + 1.002042e-02 + 8.120974e-03 + 6.890932e-03 + 6.279938e-03 + 5.707040e-03 + 5.157449e-03 + 4.203168e-03 + 3.501119e-03 + 2.816421e-03 + 2.464797e-03 + 2.086617e-03 + 1.873654e-03 + 1.403892e-03 + 1.196570e-03 + 1.101350e-03 + 8.899093e-04 + 7.096377e-04 + 3.600828e-04 + 2.338050e-04 |
| b |
| diff -r 000000000000 -r dd195f7a791c test-data/val2.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/val2.dat Thu Jan 30 07:58:42 2020 -0500 |
| b |
| @@ -0,0 +1,85 @@ + 3.947222e+01 + 2.015408e+01 + 4.916455e+00 + 2.895004e+00 + 2.441851e+00 + 1.693793e+00 + 1.452903e+00 + 1.162406e+00 + 9.084164e-01 + 8.297056e-01 + 7.989324e-01 + 6.787932e-01 + 5.389385e-01 + 4.860497e-01 + 4.819947e-01 + 4.578189e-01 + 4.253657e-01 + 3.982626e-01 + 3.460761e-01 + 3.256565e-01 + 2.848984e-01 + 2.736597e-01 + 2.479534e-01 + 2.340746e-01 + 2.225550e-01 + 1.889216e-01 + 1.785514e-01 + 1.644114e-01 + 1.600505e-01 + 1.454532e-01 + 1.354044e-01 + 1.321860e-01 + 1.232545e-01 + 1.200232e-01 + 1.047262e-01 + 9.791049e-02 + 9.288340e-02 + 8.730713e-02 + 8.455885e-02 + 7.553143e-02 + 7.464052e-02 + 6.972550e-02 + 6.652490e-02 + 6.060527e-02 + 5.676623e-02 + 5.018758e-02 + 4.989473e-02 + 4.465916e-02 + 4.245147e-02 + 4.105768e-02 + 3.892737e-02 + 3.643909e-02 + 3.230761e-02 + 3.081277e-02 + 2.805252e-02 + 2.607810e-02 + 2.512066e-02 + 2.207874e-02 + 2.048678e-02 + 1.852242e-02 + 1.676865e-02 + 1.442676e-02 + 1.345409e-02 + 1.305316e-02 + 1.238469e-02 + 1.052216e-02 + 1.002041e-02 + 8.120949e-03 + 6.890981e-03 + 6.280023e-03 + 5.707032e-03 + 5.157477e-03 + 4.203180e-03 + 3.501140e-03 + 2.816480e-03 + 2.464769e-03 + 2.086600e-03 + 1.873642e-03 + 1.403898e-03 + 1.196546e-03 + 1.101421e-03 + 8.898859e-04 + 7.096480e-04 + 3.601291e-04 + 2.338039e-04 |
| b |
| diff -r 000000000000 -r dd195f7a791c test-data/vec.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vec.dat Thu Jan 30 07:58:42 2020 -0500 |
| b |
| b'@@ -0,0 +1,85 @@\n+ 3.597432e-02 2.692211e-02 2.817930e-01 8.201814e-02 -4.862062e-02 4.934469e-02 -5.074872e-03 -2.150250e-01 -1.988593e-01 -1.338510e-01 4.586823e-01 -8.329182e-03 -5.065555e-01 3.370271e-01 1.334040e-01 1.022590e-01 -1.449047e-01 1.035877e-01 1.174587e-01 9.936859e-02 -1.399434e-03 2.743653e-02 -1.961464e-02 6.141477e-02 7.851144e-03 3.421684e-02 -1.351951e-01 4.919332e-02 2.986516e-03 1.657092e-01 3.669791e-02 2.844914e-02 1.034812e-01 5.922159e-02 5.962049e-06 3.234775e-02 4.998555e-02 1.455689e-02 -3.058247e-02 1.714270e-02 3.528911e-02 8.575856e-02 -1.485020e-02 -4.939949e-02 5.514172e-02 5.081083e-02 8.656934e-03 -7.573655e-03 -8.480181e-02 3.290604e-02 -5.798370e-02 8.662148e-02 1.820673e-02 -2.277328e-03 -6.032412e-02 1.971969e-02 -3.662553e-02 3.839312e-02 -1.826046e-02 -2.437585e-02 -5.313370e-02 4.283162e-02 4.242042e-02 5.622661e-02 -2.380492e-02 -1.038485e-02 1.298166e-03 2.784345e-02 1.000499e-02 2.916464e-02 -3.485203e-03 -4.176440e-03 -1.341336e-02 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