Mercurial > repos > chemteam > gmx_trj
comparison trj.xml @ 1:e9cc595562b8 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit e40a6ea54592a2c6e40e44bbad52985fcdcaddb3"
| author | chemteam |
|---|---|
| date | Thu, 13 Feb 2020 03:51:40 -0500 |
| parents | bb0053c4e4f2 |
| children | 9363254ef848 |
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| 0:bb0053c4e4f2 | 1:e9cc595562b8 |
|---|---|
| 42 #end if | 42 #end if |
| 43 | 43 |
| 44 -b '$time.b' | 44 -b '$time.b' |
| 45 -dt '$time.dt' | 45 -dt '$time.dt' |
| 46 -o ./output.${output_format} && | 46 -o ./output.${output_format} && |
| 47 | 47 &>> verbose.txt && |
| 48 mv ./output.${output_format} '$output' | 48 mv ./output.${output_format} '$output' |
| 49 | 49 |
| 50 ]]></command> | 50 ]]></command> |
| 51 | 51 |
| 52 <inputs> | 52 <inputs> |
| 75 <option value="cluster">cluster</option> | 75 <option value="cluster">cluster</option> |
| 76 <option value="whole">whole</option> | 76 <option value="whole">whole</option> |
| 77 </param> | 77 </param> |
| 78 <param name="ur" type="select" label="Unit cell representation" > | 78 <param name="ur" type="select" label="Unit cell representation" > |
| 79 <option value="rect">rect</option> | 79 <option value="rect">rect</option> |
| 80 <option value="tric" selected="true">tric</option> | 80 <option value="tric">tric</option> |
| 81 <option value="zero">zero</option> | 81 <option value="compact">compact</option> |
| 82 </param> | 82 </param> |
| 83 <param name="boxcenter" type="select" label="Center for PBC and centering treatment" > | 83 <param name="boxcenter" type="select" label="Center for PBC and centering treatment" > |
| 84 <option value="rect">rect</option> | 84 <option value="rect">rect</option> |
| 85 <option value="tric">tric</option> | 85 <option value="tric" selected="true">tric</option> |
| 86 <option value="compact">compact</option> | 86 <option value="zero">zero</option> |
| 87 </param> | 87 </param> |
| 88 </when> | 88 </when> |
| 89 <when value="trjcat"> | 89 <when value="trjcat"> |
| 90 <param name="trj_input" type="data" format='xtc,trr' label="Input trajectories" help="In XTC or TRR format, but please do not mix the two. Please note this tool does not currently take order into account when concatenating." multiple="true"/> | 90 <param name="trj_input" type="data" format='xtc,trr' label="Input trajectories" help="In XTC or TRR format, but please do not mix the two. Please note this tool does not currently take order into account when concatenating." multiple="true"/> |
| 91 <param name="cat" type="boolean" label="Do not discard double time frames" truevalue="-cat" falsevalue="-nocat"/> | 91 <param name="cat" type="boolean" label="Do not discard double time frames" truevalue="-cat" falsevalue="-nocat"/> |
| 107 <outputs> | 107 <outputs> |
| 108 <data name="output" format="xtc"> | 108 <data name="output" format="xtc"> |
| 109 <change_format> | 109 <change_format> |
| 110 <when input="output_format" value="trr" format="trr"/> | 110 <when input="output_format" value="trr" format="trr"/> |
| 111 <when input="output_format" value="xtc" format="xtc"/> | 111 <when input="output_format" value="xtc" format="xtc"/> |
| 112 <when input="output_format" value="gro" format="dcd"/> | 112 <when input="output_format" value="gro" format="gro"/> |
| 113 <when input="output_format" value="pdb" format="pdb"/> | 113 <when input="output_format" value="pdb" format="pdb"/> |
| 114 </change_format> | 114 </change_format> |
| 115 </data> | 115 </data> |
| 116 </outputs> | 116 </outputs> |
| 117 <tests> | 117 <tests> |