Mercurial > repos > chemteam > gmx_merge_topology_files
comparison merge_top.xml @ 0:33ed3c26b8c2 draft
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7ba07c3130a2170e8f91acc4a81f5626563a79eb
| author | chemteam |
|---|---|
| date | Thu, 28 Mar 2019 10:12:00 -0400 |
| parents | |
| children | f2faba46d680 |
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| -1:000000000000 | 0:33ed3c26b8c2 |
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| 1 <tool id="gmx_merge_topology_files" name="Merge GROMACS topologies" version="0.1.0"> | |
| 2 <description>for example, for protein and ligand files</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <command detect_errors="exit_code"><![CDATA[ | |
| 7 ln -s '$top_input' ./top_input.top && | |
| 8 #for $itp_input in $itp_inputs | |
| 9 ln -s '$itp_input' ./$itp_input.element_identifier && | |
| 10 echo '$itp_input.element_identifier' >> ./itps.txt && | |
| 11 #end for | |
| 12 | |
| 13 python '$__tool_directory__/merge_top.py' top_input.top itps.txt | |
| 14 ]]></command> | |
| 15 <inputs> | |
| 16 <param argument="top_input" type="data" format='top' label="Topology (TOP) file"/> | |
| 17 <param argument="itp_inputs" type="data" format='itp' multiple="true" label="Position restraint file"/> | |
| 18 </inputs> | |
| 19 <outputs> | |
| 20 <data name="output" format="top" from_work_dir="top_output.top"/> | |
| 21 </outputs> | |
| 22 <tests> | |
| 23 <test> | |
| 24 <param name="top_input" value="topol.top" /> | |
| 25 <param name="itp_inputs" value="posres.itp" /> | |
| 26 <output name="output" file="top_output.top" ftype="top" /> | |
| 27 </test> | |
| 28 </tests> | |
| 29 <help><![CDATA[ | |
| 30 Use this tool to combine GROMACS topologies - for example, the topology files for a ligand and protein. | |
| 31 ]]></help> | |
| 32 <expand macro="citations" /> | |
| 33 </tool> |