--- a/dihedrals.xml	Wed Apr 03 15:47:36 2019 -0400
+++ b/dihedrals.xml	Mon Oct 07 12:52:20 2019 -0400
@@ -7,8 +7,10 @@
     <command detect_errors="exit_code">
 <![CDATA[
     python '$__tool_directory__/dihedrals.py'
-        --idcd '$dcdin' 
-        --ipdb '$pdbin' 
+        --itraj '$trajin' 
+        --istr '$strin' 
+        --itrajext '$trajin.ext'
+        --istrext '$strin.ext'
         --isegid1 '$segid1' 
         --iresid1 '$resid1' 
         --iname1 '$name1' 
@@ -27,22 +29,22 @@
 ]]></command>
     <inputs>
         <expand macro="analysis_inputs"/>
-        <param name="segid1"  type="text" value="PRO" label="Segid of atom 1"/>
-        <param name="resid1"  type="text" value="212" label="Resid of atom 1"/>
+        <param name="segid1"  type="text" value="PRO" label="Segment ID of atom 1"/>
+        <param name="resid1"  type="text" value="212" label="Residue ID of atom 1"/>
         <param name="name1"  type="text" value="OE2" label="Atom name of atom 1"/>
-        <param name="segid2"  type="text" value="HET" label="Segid of atom 2"/>
-        <param name="resid2"  type="text" value="3" label="Resid of atom 2"/>
+        <param name="segid2"  type="text" value="HET" label="Segment ID of atom 2"/>
+        <param name="resid2"  type="text" value="3" label="Residue ID of atom 2"/>
         <param name="name2"  type="text" value="C1" label="Atom name of atom 2"/>
-        <param name="segid3"  type="text" value="HET" label="Segid of atom 3"/>
-        <param name="resid3"  type="text" value="3" label="Resid of atom 3"/>
+        <param name="segid3"  type="text" value="HET" label="Segment ID of atom 3"/>
+        <param name="resid3"  type="text" value="3" label="Residue ID of atom 3"/>
         <param name="name3"  type="text" value="C2" label="Atom name of atom 3"/>
-        <param name="segid4"  type="text" value="HET" label="Segid of atom 4"/>
-        <param name="resid4"  type="text" value="3" label="Resid of atom 4"/>
+        <param name="segid4"  type="text" value="HET" label="Segment ID of atom 4"/>
+        <param name="resid4"  type="text" value="3" label="Residue ID of atom 4"/>
         <param name="name4"  type="text" value="C3" label="Atom name of atom 4"/>
     </inputs>
     <outputs>
         <data format="tabular" name="output" label="Dihedral analysis raw data"/>
-        <data format="png" name="dihedral_plot" label="Dihedral Analysis Plot"/>
+        <data format="png" name="dihedral_plot" label="Dihedral analysis plot"/>
     </outputs>
     <tests>
         <test>
@@ -61,6 +63,29 @@
             <param name="name4" value="C3"/>
             <output name="output" file="Dihedral_analysis_raw_data.tabular" />
         </test>
+        <test>
+            <expand macro="tests_inputs_gmx"/>
+            <param name="segid1" value="SYSTEM"/>
+            <param name="resid1" value="212"/>
+            <param name="name1" value="OE2"/>
+            <param name="segid2" value="SYSTEM"/>
+            <param name="resid2" value="3"/>
+            <param name="name2" value="C1"/>
+            <param name="segid3" value="SYSTEM"/>
+            <param name="resid3" value="3"/>
+            <param name="name3" value="C2"/>
+            <param name="segid4" value="SYSTEM"/>
+            <param name="resid4" value="3"/>
+            <param name="name4" value="C3"/>
+            <output name="output">
+                <assert_contents>
+                    <has_n_columns n="2" />
+                    <has_line_matching expression="0\t-61.*" />
+                    <has_line_matching expression="12\t-76.*" />
+                    <has_line_matching expression="4\t-66.*" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 .. class:: infomark
@@ -78,8 +103,10 @@
 
        - Trajectory file  (DCD).
        - PDB file.
-       - Segids, resids and names of the four atoms to calculate dihedral angle.
-     
+       - Segment IDs, residue IDs and names of the four atoms to calculate the dihedral angle.
+
+Note that a MDAnalysis 'segment' is a larger organizational unit, for example one protein or all the solvent molecules or simply the whole system.
+
 _____
 
         
@@ -87,7 +114,7 @@
 
 **Output**
 
-       - Tab-separated file of raw data of the dihedral angle between two intersecting planes calculated for each frame.
+       - Tab-separated file of raw data of the dihedral angle calculated for each frame.
        - Image (as png) of the time series graph.
 
     ]]></help>