diff md_converter.xml @ 11:d7ec25187599 draft default tip

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit e21dacffada5e1405279ac09e41119508f48f63d"

--- a/md_converter.xml	Tue Nov 30 09:55:06 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,89 +0,0 @@
-<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@">1.9.7</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>