diff md_converter.xml @ 4:1c25c23ff450 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/md_converter.xml	Wed Nov 20 11:16:29 2019 -0500
@@ -0,0 +1,75 @@
+<tool id="md_converter" name="MDTraj file converter" version="1.9.3.1">
+
+    <description>- interconvert between MD trajectory file formats.</description>
+
+    <requirements>
+        <requirement type="package" version="1.9.3">mdtraj</requirement>
+    </requirements>
+
+    <command detect_errors="exit_code"><![CDATA[
+
+        ln -s '$input_file' ./input.$input_file.ext &&
+        mdconvert ./input.$input_file.ext -o ./output.${output_format} &&
+        cp ./output.${output_format} $output
+
+    ]]></command>
+    <inputs>
+        <param argument="input_file" type="data" format='xtc, trr, dcd' 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>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data name="output">
+            <change_format>
+                <when input="output_format" value="trr" format="trr"/>
+                <when input="output_format" value="xtc" format="xtc"/>
+                <when input="output_format" value="dcd" format="dcd"/>
+            </change_format>
+        </data>
+    </outputs> 
+
+    <tests>
+        <test>
+            <param name="conversion" value="traj" />
+            <param name="output_format" value="dcd" />
+            <param name="input_file" value="traj.xtc" ftype="xtc"/>
+            <output name="output" file="traj.dcd" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="conversion" value="traj" />
+            <param name="output_format" value="trr" />
+            <param name="input_file" value="traj.dcd" ftype="dcd"/>
+            <output name="output" file="traj.trr"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+        
+This tool interconverts between MD trajectory file formats: xtc, trr and dcd.
+
+_____
+
+
+.. class:: infomark
+
+**Input**
+
+       - Trajectory file (trr, xtc, dcd)
+     
+_____
+
+        
+.. class:: infomark
+
+**Output**
+
+       - Trajectory file (trr, xtc, dcd)
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1016/j.bpj.2015.08.015</citation>
+    </citations>
+</tool>