Mercurial > repos > bgruening > autodock_vina_prepare_box
changeset 2:73c2c9774c2d draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
| author | bgruening |
|---|---|
| date | Wed, 02 Oct 2019 12:49:11 -0400 |
| parents | 4f7c5cad3377 |
| children | 908880455b2d |
| files | calc_vina_box_params.py prepare_box.xml test-data/box_params.txt test-data/box_params_1.txt test-data/box_params_2.txt |
| diffstat | 5 files changed, 43 insertions(+), 34 deletions(-) [+] |
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--- a/calc_vina_box_params.py Tue May 07 13:31:59 2019 -0400 +++ b/calc_vina_box_params.py Wed Oct 02 12:49:11 2019 -0400 @@ -28,9 +28,13 @@ # optionally add buffers in each direction - expansion box_dims = [dims[0] + options.bufx, dims[1] + options.bufy, dims[2] + options.bufz] - # if no seed set, then randomly generate one between 0 and 2**31 - if options.seed == None: - options.seed = randint(0, 2147483647) + optionalvals = "" + + + if options.seed != None: + optionalvals += "seed = " + str(options.seed) + "\n" + if options.exhaustiveness != None: + optionalvals += "exhaustiveness = " + str(options.exhaustiveness) + "\n" with open(options.output, 'w') as f: f.write( @@ -41,12 +45,7 @@ center_x = {} center_y = {} center_z = {} -num_modes = 9999 -energy_range = 9999 -exhaustiveness = {} -cpu = 4 -seed = {} - """.format(box_dims[0], box_dims[1], box_dims[2], center[0], center[1], center[2], options.exhaustiveness, options.seed) +{}""".format(box_dims[0], box_dims[1], box_dims[2], center[0], center[1], center[2], optionalvals) ) @@ -61,8 +60,7 @@ """) parser.add_argument('--ligand', dest='ligand_path', help='The input ligand (mol file)') parser.add_argument('--config', dest='output', help='The output file containing calculated params (txt)') - parser.add_argument('--exh', dest='exhaustiveness', default=10, type=int, help='The number of poses ' - 'to return from docking job') + parser.add_argument('--exh', dest='exhaustiveness', type=int, help='Exhaustiveness of global search') parser.add_argument('--bufx', dest='bufx', default=0, type=float, help='the buffer in the x direction ' '(float - in angs.)') parser.add_argument('--bufy', dest='bufy', default=0, type=float, help='the buffer in the y direction '
--- a/prepare_box.xml Tue May 07 13:31:59 2019 -0400 +++ b/prepare_box.xml Wed Oct 02 12:49:11 2019 -0400 @@ -6,18 +6,20 @@ </requirements> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/calc_vina_box_params.py' - --ligand '$input1' - --config '$output1' + --ligand '$ligand' + --config '$output' --bufx '$bufx' --bufy '$bufy' --bufz '$bufz' - --exh '$exh' + #if $exh: + --exh '$exh' + #end if #if $seed_value: --seed '$seed_value' #end if ]]></command> <inputs> - <param type="data" name="input1" format="mol" label="Input ligand" + <param type="data" name="ligand" format="mol" label="Input ligand" help="The input ligand (mol file)"/> <param name="bufx" type="float" value="0" label="x-axis buffer" help="Buffer in the x direction (in angs.)"/> @@ -25,24 +27,30 @@ help="Buffer in the y direction (in angs.)"/> <param name="bufz" type="float" value="0" label="z-axis buffer" help="Buffer in the z direction (in angs.)"/> - <param name="exh" type="integer" value="0" label="Exhaustiveness" - help="Number of poses to return from docking job"/> - <!-- <param name="seed" type="boolean" label="Specify random seed for simulation reproducibility?"/> --> + <param name="exh" type="integer" optional="true" label="Exhaustiveness (optional)" + help="Exhaustiveness of global search (optional, default = 8)"/> <param type="integer" name="seed_value" optional="true" label="Random seed (optional)" help="Choose a seed value; if none is selected, a seed will be chosen randomly"/> </inputs> <outputs> - <data name="output1" format="txt" /> + <data name="output" format="txt" /> </outputs> <tests> <test> - <param name="input1" value="NUDT5A-x0114_2.mol" /> + <param name="ligand" value="NUDT5A-x0114_2.mol" /> + <param name="bufx" value="1" /> + <param name="bufy" value="2" /> + <param name="bufz" value="3" /> + <output name="output" file="box_params_1.txt" /> + </test> + <test> + <param name="ligand" value="NUDT5A-x0114_2.mol" /> <param name="bufx" value="1" /> <param name="bufy" value="2" /> <param name="bufz" value="3" /> <param name="exh" value="10" /> <param name="seed_value" value="1" /> - <output name="output1" file="box_params.txt" /> + <output name="output" file="box_params_2.txt" /> </test> </tests> <help>
--- a/test-data/box_params.txt Tue May 07 13:31:59 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ - -size_x = 12.443000000000001 -size_y = 11.888 -size_z = 9.290999999999997 -center_x = -29.8395 -center_y = 4.364 -center_z = -64.5925 -num_modes = 9999 -energy_range = 9999 -exhaustiveness = 10 -cpu = 4 -seed = 1 - \ No newline at end of file