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comparison sim.xml @ 1:ec3f665cca3e draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 10f45d117e34624bceb32442742ae0b8eb2dae30"
author chemteam
date Wed, 30 Oct 2019 13:34:07 -0400
parents 1a5960636405
children 5642f48f5698
comparison
equal deleted inserted replaced
0:1a5960636405 1:ec3f665cca3e
21 21
22 #if $cpt_inp.cpt_bool == "yes": 22 #if $cpt_inp.cpt_bool == "yes":
23 ln -s '$cpt_inp.cpt_in' ./inp.cpt && 23 ln -s '$cpt_inp.cpt_in' ./inp.cpt &&
24 #end if 24 #end if
25 25
26 #if $ndx_inp.ndx_bool == "yes":
27 ln -s '$ndx_inp.ndx_in' ./index.ndx &&
28 #end if
29
26 gmx grompp 30 gmx grompp
27 -f ./md.mdp 31 -f ./md.mdp
28 -c ./inp.gro 32 -c ./inp.gro
29 #if $cpt_inp.cpt_bool == "yes": 33 #if $cpt_inp.cpt_bool == "yes":
30 -t ./inp.cpt 34 -t ./inp.cpt
31 #end if 35 #end if
32 #if $posres.posres_bool == "true": 36 #if $posres.posres_bool == "true":
33 -r ./inp.gro 37 -r ./inp.gro
38 #end if
39 #if $ndx_inp.ndx_bool == "true":
40 -n ./index.ndx
34 #end if 41 #end if
35 -p ./top_input.top 42 -p ./top_input.top
36 -o outp.tpr &>> verbose.txt && 43 -o outp.tpr &>> verbose.txt &&
37 44
38 45
136 <param argument="itp_inp" type="data" format='itp' label="Position restraint (ITP) file"/> 143 <param argument="itp_inp" type="data" format='itp' label="Position restraint (ITP) file"/>
137 </when> 144 </when>
138 <when value="false"/> 145 <when value="false"/>
139 </conditional> 146 </conditional>
140 147
148 <conditional name="ndx_inp">
149 <param name="ndx_bool" type="select" label="Use a custom index (ndx) file" help="Use an index file specifying custom atom groups.">
150 <option value="yes">Use custom index file</option>
151 <option value="no" selected="true">Use default generated group</option>
152 </param>
153 <when value="yes">
154 <param argument="ndx_in" type="data" format='txt' label="Index file"/>
155 </when>
156 <when value="no"/>
157 </conditional>
158
159
141 <param name="ensemble" label="Ensemble" type="select" help="NVT ensemble (constant number of particles, volume and temperature) or NPT ensemble (constant number of particles, pressure and temperature)"> 160 <param name="ensemble" label="Ensemble" type="select" help="NVT ensemble (constant number of particles, volume and temperature) or NPT ensemble (constant number of particles, pressure and temperature)">
142 <option value="nvt">Isothermal-isochoric ensemble (NVT)</option> 161 <option value="nvt">Isothermal-isochoric ensemble (NVT)</option>
143 <option value="npt">Isothermal-isobaric ensemble (NPT)</option> 162 <option value="npt">Isothermal-isobaric ensemble (NPT)</option>
144 </param> 163 </param>
145 164
173 <param name="top_input" value="topol_solv.top" /> 192 <param name="top_input" value="topol_solv.top" />
174 <param name="cpt_bool" value="yes" /> 193 <param name="cpt_bool" value="yes" />
175 <param name="cpt_in" value="npt.cpt" /> 194 <param name="cpt_in" value="npt.cpt" />
176 <param name="mdpfile" value="custom" /> 195 <param name="mdpfile" value="custom" />
177 <param name="mdp_input" value="md.mdp" /> 196 <param name="mdp_input" value="md.mdp" />
197 <param name="ndx_bool" value="no" />
178 <param name="traj" value="trr"/> 198 <param name="traj" value="trr"/>
179 <param name="str" value="gro"/> 199 <param name="str" value="gro"/>
180 <param name="ensemble" value="npt" /> 200 <param name="ensemble" value="npt" />
181 <param name="posres_bool" value="false" /> 201 <param name="posres_bool" value="false" />
182 <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/> 202 <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/>
186 <test> 206 <test>
187 <param name="gro_input" value="npt.gro" /> 207 <param name="gro_input" value="npt.gro" />
188 <param name="top_input" value="topol_solv.top" /> 208 <param name="top_input" value="topol_solv.top" />
189 <param name="cpt_bool" value="yes" /> 209 <param name="cpt_bool" value="yes" />
190 <param name="cpt_in" value="npt.cpt" /> 210 <param name="cpt_in" value="npt.cpt" />
211 <param name="ndx_bool" value="no" />
191 <param name="traj" value="trr"/> 212 <param name="traj" value="trr"/>
192 <param name="str" value="both"/> 213 <param name="str" value="both"/>
193 <expand macro="test_params"/> 214 <expand macro="test_params"/>
194 <param name="ensemble" value="npt" /> 215 <param name="ensemble" value="npt" />
195 <param name="posres_bool" value="false" /> 216 <param name="posres_bool" value="false" />
197 <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/> 218 <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/>
198 <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/> 219 <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/>
199 </test> 220 </test>
200 221
201 <test> 222 <test>
223 <param name="gro_input" value="npt.gro" />
224 <param name="top_input" value="topol_solv.top" />
225 <param name="cpt_bool" value="yes" />
226 <param name="cpt_in" value="npt.cpt" />
227 <param name="ndx_bool" value="yes" />
228 <param name="ndx_in" value="index.ndx" />
229 <param name="traj" value="trr"/>
230 <param name="str" value="both"/>
231 <expand macro="test_params"/>
232 <param name="ensemble" value="npt" />
233 <param name="posres_bool" value="false" />
234 <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/>
235 <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/>
236 <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/>
237 </test>
238
239 <test>
202 <param name="gro_input" value="em.gro" /> 240 <param name="gro_input" value="em.gro" />
203 <param name="top_input" value="topol_solv.top" /> 241 <param name="top_input" value="topol_solv.top" />
204 <param name="posres_bool" value="true" /> 242 <param name="posres_bool" value="true" />
205 <param name="itp_inp" value="posres.itp" /> 243 <param name="itp_inp" value="posres.itp" />
206 <param name="cpt_bool" value="no" /> 244 <param name="cpt_bool" value="no" />
207 <param name="cpt_out" value="true" /> 245 <param name="cpt_out" value="true" />
246 <param name="ndx_bool" value="no" />
208 <param name="traj" value="xtc"/> 247 <param name="traj" value="xtc"/>
209 <param name="str" value="pdb"/> 248 <param name="str" value="pdb"/>
210 <param name="ensemble" value="nvt" /> 249 <param name="ensemble" value="nvt" />
211 <expand macro="test_params"/> 250 <expand macro="test_params"/>
212 251