Mercurial > repos > chemteam > bio3d_pca_visualize

changeset 3:f61a718993fd draft default tip

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"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 7ac6900f4790
children
files macros.xml visualize_pc.xml
diffstat 2 files changed, 39 insertions(+), 31 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Wed Apr 03 15:45:52 2019 -0400
+++ b/macros.xml	Mon Oct 07 12:44:04 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/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>