Mercurial > repos > chemteam > md_converter
diff md_converter.xml @ 11:d7ec25187599 draft default tip
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit e21dacffada5e1405279ac09e41119508f48f63d"
author | chemteam |
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date | Tue, 30 Nov 2021 15:30:25 +0000 |
parents | be3cb628aa3e |
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--- 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>