diff rdf.xml @ 4:36babbdd7818 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"

--- a/rdf.xml	Wed Apr 03 15:47:16 2019 -0400
+++ b/rdf.xml	Mon Oct 07 12:51:57 2019 -0400
@@ -1,5 +1,5 @@
 <tool id="mdanalysis_rdf" name="RDF Analysis" version="@VERSION@">
-    <description>Radial Distribution Function between two atoms</description>
+    <description>- Radial Distribution Function between two atoms</description>
     <macros>
         <import>macros.xml</import>
     </macros>   
@@ -7,8 +7,10 @@
     <command detect_errors="exit_code">
 <![CDATA[
     python '$__tool_directory__/rdf.py' 
-        --idcd '$dcdin' 
-        --ipdb '$pdbin' 
+        --itraj '$trajin' 
+        --istr '$strin' 
+        --itrajext '$trajin.ext'
+        --istrext '$strin.ext'
         --isegid1 '$segid1'
         --iresid1 '$resid1'
         --iname1 '$name1' 
@@ -24,15 +26,17 @@
 ]]></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="nbins"  type="text" value="100" label="Number of bins in the histogram"/>
-        <param name="start"  type="text" value="0.0" label="Starting Point"/>
-        <param name="end"  type="text" value="5.0" label="End Point"/>
+        <param name="start"  type="text" min="0.0" value="0.0" label="Starting point (angstroms)"
+            help="Minimum value of r to calculate RDF for"/>
+        <param name="end"  type="text" value="15.0" label="End point (angstroms)"
+            help="Maximum value of r to calculate RDF for"/>
     </inputs>
     <outputs>
         <data format="tabular" name="output" label="RDF raw data"/>
@@ -58,13 +62,32 @@
               </assert_contents>
             </output>
         </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="nbins" value="100"/>
+            <param name="start" value="0.0"/>
+            <param name="end" value="5.0"/>
+            <output name="output">
+              <assert_contents>
+                <has_n_columns n="2" />
+                <not_has_text text="nan" />
+                <has_line_matching expression="3.275\s+6336.*" />
+              </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 .. class:: infomark
 
 **What it does**
         
-The Radial Distribution Function (RDF) , g(r), also called pair distribution function or pair correlation function function can be used to find how density varies as a function of distance from a reference atom. 
+The Radial Distribution Function (RDF), g(r), also called pair distribution function or pair correlation function, can be used to find how density varies as a function of distance from a reference atom. 
 
 _____
 
@@ -73,10 +96,13 @@
 
 **Input**
 
-       - Trajectory file  (DCD).
+       - Trajectory file (DCD).
        - PDB file.
-       - Segids, resids and names of two atoms to calculate distances.
-     
+       - Segment IDs, residue IDs and names of two atoms to calculate RDF values.
+
+Note that a MDAnalysis 'segment' is a larger organizational unit, for example one protein or all the solvent molecules or simply the whole system.
+
+Other parameters can also be specified: the number of bins in the RDF histogram, and the start and end points for the calculation (i.e. the values of r between which RDF will be calculated).
 _____