# HG changeset patch
# User chemteam
# Date 1570466705 14400
# Node ID 24867ab16f369a718e73b6717b02a3e77f96dbc5
# Parent  994c509873db276d02dbeb858415fc2b8189d17a
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"

diff -r 994c509873db -r 24867ab16f36 macros.xml
--- 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">
diff -r 994c509873db -r 24867ab16f36 pca.xml
--- 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>