Mercurial > repos > chemteam > bio3d_dccm

changeset 2:c9ae0c833ded draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author chemteam
date Mon, 07 Oct 2019 12:44:45 -0400
parents 18440ff54f63
children
files dccm.xml macros.xml
diffstat 2 files changed, 18 insertions(+), 18 deletions(-) [+]
line wrap: on
line diff
--- a/dccm.xml	Wed Apr 03 15:44:43 2019 -0400
+++ b/dccm.xml	Mon Oct 07 12:44:45 2019 -0400
@@ -1,10 +1,10 @@
 <tool id="bio3d_dccm" name="DCCM analysis" version="@VERSION@">
-    <description>Dynamical Cross-Correlation Maps using Bio3D (DCCM)</description>
+    <description>- Dynamical Cross-Correlation Maps using Bio3D (DCCM)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="0.20_35">r-lattice</requirement>
+        <requirement type="package" version="0.20_38">r-lattice</requirement>
     </expand>
     <command detect_errors="exit_code">
 <![CDATA[ 
@@ -59,16 +59,16 @@
         <expand macro="analysis_inputs"/>
         <conditional name="dccm">
            <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"/>
@@ -78,13 +78,13 @@
            <when value="ligand"/>
            <when value="nucleic"/>
            <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>
@@ -105,7 +105,7 @@
 **What it does**
         
 The extent to which the atomic fluctuations/displacements of a system are correlated with one another can be assessed by examining the magnitude of all pairwise cross-correlation coefficients.
-The DCCM Analysis tool can plot the atom-wise cross-correlations using the Bio3D package. The negative values (negative correlation) indicate the atoms moves in opposite directions and the positive values (positive correlation) indicate the atoms moves in same directions.
+The DCCM Analysis tool can plot the atom-wise cross-correlations using the Bio3D package. Negative values (negative correlation) indicate the atoms move in opposite directions, while positive values (positive correlation) indicate the atoms move in the same direction.
       
 _____
 
@@ -115,7 +115,7 @@
 **Input**
 
        - Input file in PDB format
-       - Input file in dcd format
+       - Input file in DCD format
 
 _____
 
@@ -124,7 +124,7 @@
 
 **Output**
 
-       - Image (as PNG) of the dccm plot
+       - Image (as PNG) of the DCCM plot
        - Tab-separated file of raw data
 
     ]]></help>
--- a/macros.xml	Wed Apr 03 15:44:43 2019 -0400
+++ b/macros.xml	Mon Oct 07 12:44:45 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">