Mercurial > repos > chemteam > bio3d_pca_visualize
diff visualize_pc.xml @ 3:f61a718993fd 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 12:44:04 -0400 |
| parents | 65bfd1b90b96 |
| children |
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--- a/visualize_pc.xml Wed Apr 03 15:45:52 2019 -0400 +++ b/visualize_pc.xml Mon Oct 07 12:44:04 2019 -0400 @@ -1,5 +1,5 @@ <tool id="bio3d_pca_visualize" name="PCA visualization" version="@VERSION@"> - <description>Generate trajectories of principle components of motions</description> + <description>- generate trajectories of principal components of atomic motion</description> <macros> <import>macros.xml</import> </macros> @@ -60,36 +60,44 @@ 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 value="cbeta"/> - <when value="backbone"/> - <when value="sidechain"/> - <when value="protein"/> - <when value="ligand"/> - <when value="nucleic"/> - <when value="elety"> - <param name="elety" type="text" value="CA" label="Atom Name"/> - </when> - <when value="resid"> - <param name="resid" type="text" value="BGLC" label="Resid"/> - </when> - <when value="segid"> - <param name="segid" type="text" value="SUBS" label="Segid"/> - </when> + <when value="calpha"> + </when> + <when value="cbeta"> + </when> + <when value="backbone"> + </when> + <when value="sidechain"> + </when> + <when value="protein"> + </when> + <when value="ligand"> + </when> + <when value="nucleic"> + </when> + <when value="elety"> + <param name="elety" type="text" value="CA" label="Atom name"/> + </when> + <when value="resid"> + <param name="resid" type="text" value="BGLC" label="Residue ID"/> + </when> + <when value="segid"> + <param name="segid" type="text" value="SUBS" label="Segment ID"/> + </when> </conditional> - <param name="pc_id" type="integer" value="1" label="Principle component id"/> + <param name="pc_id" type="integer" value="1" label="Principal component ID"/> </inputs> + <outputs> <data format="pdb" name="pdbout" label="PCA_${pc_id}.pdb"/> </outputs> @@ -107,7 +115,7 @@ **What it does** -This tool can generate small trajectories of a given principle component. +This tool can generate small trajectories of a given principal component. _____ @@ -117,7 +125,7 @@ **Input** - Input file in PDB format - - Input file in dcd format + - Input file in DCD format _____ @@ -126,7 +134,7 @@ **Output** - - A short trajectory (as PDB) of the given priciple component id. + - A short trajectory (as PDB) of the given principal component ID. ]]></help>