diff md_converter.xml @ 9:ba83f0923369 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/md_converter.xml	Wed Jul 14 11:15:09 2021 +0000
@@ -0,0 +1,89 @@
+<tool id="md_converter" name="MDTraj file converter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
+    <description>- interconvert between MD trajectory file formats.</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.9.6</token>
+        <token name="@GALAXY_VERSION@">0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">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,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>
+
+    <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"/>
+                <when input="output_format" value="netcdf" format="netcdf"/>
+            </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>
+        <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, dcd and netcdf.
+
+_____
+
+
+.. class:: infomark
+
+**Input**
+
+       - Trajectory file (trr, xtc, dcd, netcdf)
+
+_____
+
+
+.. class:: infomark
+
+**Output**
+
+       - Trajectory file (trr, xtc, dcd, netcdf)
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1016/j.bpj.2015.08.015</citation>
+    </citations>
+</tool>