| Previous changeset 0:1a5960636405 (2019-10-07) Next changeset 2:5642f48f5698 (2019-11-20) |
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Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 10f45d117e34624bceb32442742ae0b8eb2dae30" |
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modified:
macros.xml sim.xml |
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added:
test-data/index.ndx |
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| diff -r 1a5960636405 -r ec3f665cca3e macros.xml --- a/macros.xml Mon Oct 07 12:48:44 2019 -0400 +++ b/macros.xml Wed Oct 30 13:34:07 2019 -0400 |
| b |
| @@ -1,5 +1,5 @@ <macros> - <token name="@VERSION@">2019.1.1</token> + <token name="@VERSION@">2019.1.2</token> <xml name="requirements"> <requirements> <requirement type="package" version="2019.1">gromacs</requirement> |
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| diff -r 1a5960636405 -r ec3f665cca3e sim.xml --- a/sim.xml Mon Oct 07 12:48:44 2019 -0400 +++ b/sim.xml Wed Oct 30 13:34:07 2019 -0400 |
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| @@ -23,6 +23,10 @@ ln -s '$cpt_inp.cpt_in' ./inp.cpt && #end if + #if $ndx_inp.ndx_bool == "yes": + ln -s '$ndx_inp.ndx_in' ./index.ndx && + #end if + gmx grompp -f ./md.mdp -c ./inp.gro @@ -32,6 +36,9 @@ #if $posres.posres_bool == "true": -r ./inp.gro #end if + #if $ndx_inp.ndx_bool == "true": + -n ./index.ndx + #end if -p ./top_input.top -o outp.tpr &>> verbose.txt && @@ -138,6 +145,18 @@ <when value="false"/> </conditional> + <conditional name="ndx_inp"> + <param name="ndx_bool" type="select" label="Use a custom index (ndx) file" help="Use an index file specifying custom atom groups."> + <option value="yes">Use custom index file</option> + <option value="no" selected="true">Use default generated group</option> + </param> + <when value="yes"> + <param argument="ndx_in" type="data" format='txt' label="Index file"/> + </when> + <when value="no"/> + </conditional> + + <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)"> <option value="nvt">Isothermal-isochoric ensemble (NVT)</option> <option value="npt">Isothermal-isobaric ensemble (NPT)</option> @@ -175,6 +194,7 @@ <param name="cpt_in" value="npt.cpt" /> <param name="mdpfile" value="custom" /> <param name="mdp_input" value="md.mdp" /> + <param name="ndx_bool" value="no" /> <param name="traj" value="trr"/> <param name="str" value="gro"/> <param name="ensemble" value="npt" /> @@ -188,6 +208,24 @@ <param name="top_input" value="topol_solv.top" /> <param name="cpt_bool" value="yes" /> <param name="cpt_in" value="npt.cpt" /> + <param name="ndx_bool" value="no" /> + <param name="traj" value="trr"/> + <param name="str" value="both"/> + <expand macro="test_params"/> + <param name="ensemble" value="npt" /> + <param name="posres_bool" value="false" /> + <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/> + <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/> + <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/> + </test> + + <test> + <param name="gro_input" value="npt.gro" /> + <param name="top_input" value="topol_solv.top" /> + <param name="cpt_bool" value="yes" /> + <param name="cpt_in" value="npt.cpt" /> + <param name="ndx_bool" value="yes" /> + <param name="ndx_in" value="index.ndx" /> <param name="traj" value="trr"/> <param name="str" value="both"/> <expand macro="test_params"/> @@ -205,6 +243,7 @@ <param name="itp_inp" value="posres.itp" /> <param name="cpt_bool" value="no" /> <param name="cpt_out" value="true" /> + <param name="ndx_bool" value="no" /> <param name="traj" value="xtc"/> <param name="str" value="pdb"/> <param name="ensemble" value="nvt" /> |
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| diff -r 1a5960636405 -r ec3f665cca3e test-data/index.ndx --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/index.ndx Wed Oct 30 13:34:07 2019 -0400 |
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| b'@@ -0,0 +1,13162 @@\n+[ System ]\n+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15\n+ 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30\n+ 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45\n+ 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60\n+ 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75\n+ 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90\n+ 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105\n+ 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120\n+ 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135\n+ 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150\n+ 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165\n+ 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180\n+ 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195\n+ 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210\n+ 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225\n+ 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240\n+ 241 242 243 244 245 246 247 248 249 250 251 252 253 254 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