Mercurial > repos > chemteam > gmx_trj

comparison trj.xml @ 1:e9cc595562b8 draft

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"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
comparison
equal deleted inserted replaced
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>