diff md_converter.xml @ 0:acce5039ece7 draft

planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 8aeaf3f199cccb1bbb26a29628e7bb75abaf189d

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/md_converter.xml	Sun Oct 14 05:31:36 2018 -0400
@@ -0,0 +1,115 @@
+<tool id="md_converter" name="MDTraj file converter" version="1.9.1">
+
+    <description>- interconvert between MD trajectory or structure file formats.</description>
+
+    <requirements>
+        <requirement type="package" version="1.9.1">mdtraj</requirement>
+        <requirement type="package" version="2018.2">gromacs</requirement>
+    </requirements>
+
+    <command detect_errors="exit_code"><![CDATA[
+
+        #if $input.conversion == 'str':
+            ln -s '$input_file' ./input.$input_file.ext &&
+            gmx editconf -f ./input.$input_file.ext -o ./output.${input.output_format} &&
+            cp ./output.${input.output_format} $output
+        #end if
+
+        #if $input.conversion == 'traj':
+            ln -s '$input_file' ./input.$input_file.ext &&
+            mdconvert ./input.$input_file.ext -o ./output.${input.output_format} &&
+            cp ./output.${input.output_format} $output
+    
+        #end if
+
+    ]]></command>
+    <inputs>
+        <conditional name="input">
+            <param argument="conversion" type="select" label="Type of conversion">
+                <option value="traj">Trajectory file</option>
+                <option value="str">Structure file</option>
+            </param>
+            <when value="traj">
+                <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>
+            </when>
+            <when value="str">
+                <param argument="input_file" type="data" format='gro, pdb' label="Input file for conversion"/>
+                <param argument="output_format" type="select" label="Output format">
+                    <option value="gro">GRO file</option>
+                    <option value="pdb">PDB file</option>
+                </param>
+            </when>
+        </conditional>
+    </inputs>
+
+    <outputs>
+        <data name="output" format="text">
+            <change_format>
+                <when input="output_format" value="gro" format="gro"/>
+                <when input="output_format" value="pdb" format="pdb"/>
+                <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" />
+            <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" />
+            <output name="output" file="traj.trr"/>
+        </test>
+        <test>
+            <param name="conversion" value="str" />
+            <param name="output_format" value="gro" />
+            <param name="input_file" value="str.pdb" ftype="pdb"/>
+            <output name="output" file="str.gro" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="conversion" value="str" />
+            <param name="output_format" value="pdb" />
+            <param name="input_file" value="str.gro" ftype="gro"/>
+            <output name="output" file="str2.pdb" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+        
+This tool interconverts between MD file formats: xtc, trr and dcd (trajectory formats) and pdb and gro (structure formats).
+
+_____
+
+
+.. class:: infomark
+
+**Input**
+
+       - Trajectory file (trr, xtc, dcd) or structure file (pdb, gro)
+     
+_____
+
+        
+.. class:: infomark
+
+**Output**
+
+       - Trajectory file (trr, xtc, dcd) or structure file (pdb, gro)
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1016/j.bpj.2015.08.015</citation>
+        <citation type="doi">10.1016/j.softx.2015.06.001</citation>
+    </citations>
+</tool>
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