Mercurial > repos > chemteam > bio3d_pca
changeset 5:24867ab16f36 draft default tip
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
| author | chemteam |
|---|---|
| date | Mon, 07 Oct 2019 12:45:05 -0400 |
| parents | 994c509873db |
| children | |
| files | macros.xml pca.xml |
| diffstat | 2 files changed, 19 insertions(+), 19 deletions(-) [+] |
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--- a/macros.xml Wed Apr 03 15:44:21 2019 -0400 +++ b/macros.xml Mon Oct 07 12:45:05 2019 -0400 @@ -1,14 +1,14 @@ <macros> - <token name="@VERSION@">2.3</token> + <token name="@VERSION@">2.3.4</token> <xml name="requirements"> <requirements> - <requirement type="package" version="2.3_3">r-bio3d</requirement> + <requirement type="package" version="2.3_4">r-bio3d</requirement> <yield/> </requirements> </xml> <xml name="analysis_inputs"> - <param format="dcd" name="dcdin" type="data" label="dcd trajectory input"/> - <param format="pdb" name="pdbin" type="data" label="pdb input"/> + <param format="dcd" name="dcdin" type="data" label="DCD trajectory input"/> + <param format="pdb" name="pdbin" type="data" label="PDB input"/> <yield/> </xml> <xml name="tests_inputs">
--- a/pca.xml Wed Apr 03 15:44:21 2019 -0400 +++ b/pca.xml Mon Oct 07 12:45:05 2019 -0400 @@ -1,5 +1,5 @@ <tool id="bio3d_pca" name="PCA" version="@VERSION@"> - <description>Principle component analysis using Bio3D</description> + <description>- principal component analysis using Bio3D</description> <macros> <import>macros.xml</import> </macros> @@ -62,16 +62,16 @@ label="Use singular value decomposition (SVD) instead of default eigenvalue decomposition ?" help="Default: No" /> <conditional name="pca"> <param name="sele" type="select" label="Select domains"> - <option value="calpha">Calpha</option> - <option value="cbeta">Cbeta</option> + <option value="calpha">C-alpha</option> + <option value="cbeta">C-beta</option> <option value="backbone">Backbone</option> <option value="sidechain">Sidechain</option> <option value="protein">Protein</option> <option value="ligand">Ligand</option> - <option value="nucleic">Nucleic Acids</option> - <option value="elety">Atom Names</option> - <option value="resid">Resid</option> - <option value="segid">Segid</option> + <option value="nucleic">Nucleic acids</option> + <option value="elety">Atom names</option> + <option value="resid">Residue ID</option> + <option value="segid">Segment ID</option> </param> <when value="calpha"> </when> @@ -88,13 +88,13 @@ <when value="nucleic"> </when> <when value="elety"> - <param name="elety" type="text" value="CA" label="Atom Name"/> + <param name="elety" type="text" value="CA" label="Atom name"/> </when> <when value="resid"> - <param name="resid" type="text" value="BGLC" label="Resid"/> + <param name="resid" type="text" value="BGLC" label="Residue ID"/> </when> <when value="segid"> - <param name="segid" type="text" value="SUBS" label="Segid"/> + <param name="segid" type="text" value="SUBS" label="Segment ID"/> </when> </conditional> </inputs> @@ -122,7 +122,7 @@ **What it does** -PCA can be used to determine the relationship between statistically meaningful conformations (major global motions) +Principal component analysis (PCA) can be used to determine the relationship between statistically meaningful conformations (major global motions) sampled during the trajectory. _____ @@ -133,7 +133,7 @@ **Input** - Input file in PDB format - - Input file in dcd format + - Input file in DCD format _____ @@ -142,9 +142,9 @@ **Output** - - Image (as PNG) of the pca plot - - Image (as PNG) of the pca clusterd plot - - Image (as PNG) of the PC1 plotted on RMSF + - Image (as PNG) of the PCA plot + - Image (as PNG) of the PCA clustered plot + - Image (as PNG) of the first principal component plotted on RMSF - Tab-separated file of raw data ]]></help>