Mercurial > repos > chemteam > md_converter

changeset 5:79e8ab8f1e81 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 3a9e92e1bcca2d2dc9b4f1bf6a4fcf94838f43f4"
author chemteam
date Mon, 24 Feb 2020 13:46:47 -0500
parents 1c25c23ff450
children 795e3abe95f0
files md_converter.xml
diffstat 1 files changed, 21 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/md_converter.xml	Wed Nov 20 11:16:29 2019 -0500
+++ b/md_converter.xml	Mon Feb 24 13:46:47 2020 -0500
@@ -1,4 +1,4 @@
-<tool id="md_converter" name="MDTraj file converter" version="1.9.3.1">
+<tool id="md_converter" name="MDTraj file converter" version="1.9.3.2">
 
     <description>- interconvert between MD trajectory file formats.</description>
 
@@ -14,11 +14,12 @@
 
     ]]></command>
     <inputs>
-        <param argument="input_file" type="data" format='xtc, trr, dcd' label="Input file for conversion"/>
+        <param argument="input_file" type="data" format='xtc,trr,dcd,netcdf' label="Input file for conversion"/>
         <param argument="output_format" type="select" label="Output format">
             <option value="trr">TRR file</option>
             <option value="xtc">XTC file</option>
             <option value="dcd">DCD file</option>
+            <option value="netcdf">NETCDF file</option>
         </param>
     </inputs>
 
@@ -28,9 +29,10 @@
                 <when input="output_format" value="trr" format="trr"/>
                 <when input="output_format" value="xtc" format="xtc"/>
                 <when input="output_format" value="dcd" format="dcd"/>
+                <when input="output_format" value="netcdf" format="netcdf"/>
             </change_format>
         </data>
-    </outputs> 
+    </outputs>
 
     <tests>
         <test>
@@ -45,11 +47,21 @@
             <param name="input_file" value="traj.dcd" ftype="dcd"/>
             <output name="output" file="traj.trr"/>
         </test>
+        <test>
+            <param name="conversion" value="traj" />
+            <param name="output_format" value="netcdf" />
+            <param name="input_file" value="traj.trr" ftype="trr"/>
+            <output name="output">
+              <assert_contents>
+                  <has_size value="461416" delta="6000"/>
+              </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**
-        
-This tool interconverts between MD trajectory file formats: xtc, trr and dcd.
+
+This tool interconverts between MD trajectory file formats: xtc, trr, dcd and netcdf.
 
 _____
 
@@ -58,16 +70,16 @@
 
 **Input**
 
-       - Trajectory file (trr, xtc, dcd)
-     
+       - Trajectory file (trr, xtc, dcd, netcdf)
+
 _____
 
-        
+
 .. class:: infomark
 
 **Output**
 
-       - Trajectory file (trr, xtc, dcd)
+       - Trajectory file (trr, xtc, dcd, netcdf)
     ]]></help>
     <citations>
         <citation type="doi">10.1016/j.bpj.2015.08.015</citation>