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Changeset 1:057daf00ca31 (2019-01-13)

Previous changeset 0:e838317708a6 (2018-10-08) Next changeset 2:50a2b87784b5 (2019-02-26)

Commit message:
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d commit 8e1fece3eaef36823e90f5d10f8bb8b809544c55

modified:
rmsf.xml

added:
test-data/PCA_raw_data.tabular
test-data/RMSD_raw_data.tabular
test-data/rmsf_raw_data.tabular

removed:
test-data/PC1_PDB.pdb
test-data/PCA_raw_data.csv
test-data/RMSD_raw_data.csv
test-data/dccm_plot.png
test-data/dccm_raw_data.csv
test-data/rmsf_raw_data.csv

diff -r e838317708a6 -r 057daf00ca31 rmsf.xml
--- a/rmsf.xml Mon Oct 08 12:50:23 2018 -0400
+++ b/rmsf.xml Sun Jan 13 03:21:33 2019 -0500

[

@@ -132,11 +132,7 @@
         <test>
             <expand macro="tests_inputs"/>
             <param name="sele" value="calpha"/>
-            <output name="output">
-              <assert_contents>
-                <has_n_columns n="2" />
-              </assert_contents>
-            </output>
+            <output name="output" file="rmsf_raw_data.tabular" />
         </test>
     </tests>
     <help><![CDATA[

diff -r e838317708a6 -r 057daf00ca31 test-data/PC1_PDB.pdb
--- a/test-data/PC1_PDB.pdb Mon Oct 08 12:50:23 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,14791 +0,0 @@\n-MODEL 1\n-ATOM 1 CA ALA 1 24.197 5.292 5.774 1.00 0.05 \n-ATOM 2 CA ALA 2 23.445 7.891 3.028 1.00 0.04 \n-ATOM 3 CA ALA 3 24.995 9.213 -0.229 1.00 0.04 \n-ATOM 4 CA ALA 4 24.439 12.164 -2.595 1.00 0.05 \n-ATOM 5 CA ALA 5 25.954 11.194 -5.963 1.00 0.08 \n-ATOM 6 CA ALA 6 22.514 11.125 -7.630 1.00 0.05 \n-ATOM 7 CA ALA 7 20.153 14.073 -7.862 1.00 0.08 \n-ATOM 8 CA ALA 8 17.482 13.463 -5.205 1.00 0.04 \n-ATOM 9 CA ALA 9 14.490 15.817 -5.576 1.00 0.02 \n-ATOM 10 CA ALA 10 11.052 14.708 -4.396 1.00 0.07 \n-ATOM 11 CA ALA 11 8.198 15.513 -6.896 1.00 0.02 \n-ATOM 12 CA ALA 12 5.822 18.263 -5.514 1.00 0.04 \n-ATOM 13 CA ALA 13 2.245 17.206 -4.720 1.00 0.05 \n-ATOM 14 CA ALA 14 -0.383 19.619 -3.321 1.00 0.04 \n-ATOM 15 CA ALA 15 -3.326 18.616 -1.169 1.00 0.03 \n-ATOM 16 CA ALA 16 -6.175 20.200 0.820 1.00 0.02 \n-ATOM 17 CA ALA 17 -6.648 20.354 4.596 1.00 0.01 \n-ATOM 18 CA ALA 18 -10.198 21.285 5.623 1.00 0.04 \n-ATOM 19 CA ALA 19 -11.428 22.994 8.812 1.00 0.05 \n-ATOM 20 CA ALA 20 -14.240 22.210 11.307 1.00 0.04 \n-ATOM 21 CA ALA 21 -15.968 25.339 9.926 1.00 0.04 \n-ATOM 22 CA ALA 22 -16.143 23.831 6.418 1.00 0.03 \n-ATOM 23 CA ALA 23 -13.303 25.671 4.682 1.00 0.02 \n-ATOM 24 CA ALA 24 -10.421 23.993 2.844 1.00 0.01 \n-ATOM 25 CA ALA 25 -6.811 25.245 2.494 1.00 0.01 \n-ATOM 26 CA ALA 26 -4.007 24.119 0.146 1.00 0.03 \n-ATOM 27 CA ALA 27 -1.040 22.400 1.855 1.00 0.02 \n-ATOM 28 CA ALA 28 2.156 21.854 -0.155 1.00 0.06 \n-ATOM 29 CA ALA 29 4.028 18.533 0.065 1.00 0.06 \n-ATOM 30 CA ALA 30 6.117 16.163 -2.035 1.00 0.04 \n-ATOM 31 CA ALA 31 6.368 12.391 -2.616 1.00 0.03 \n-ATOM 32 CA ALA 32 9.409 10.160 -1.944 1.00 0.01 \n-ATOM 33 CA ALA 33 10.183 6.647 -3.273 1.00 0.01 \n-ATOM 34 CA ALA 34 10.995 3.651 -1.004 1.00 0.01 \n-ATOM 35 CA ALA 35 14.535 2.434 -0.203 1.00 0.03 \n-ATOM 36 CA ALA 36 13.984 -0.881 -2.019 1.00 0.05 \n-ATOM 37 CA ALA 37 13.549 0.773 -5.456 1.00 0.03 \n-ATOM 38 CA ALA 38 16.787 2.795 -4.941 1.00 0.04 \n-ATOM 39 CA ALA 39 20.345 1.757 -5.847 1.00 0.07 \n-ATOM 40 CA ALA 40 22.321 0.268 -2.894 1.00 0.05 \n-ATOM 41 CA ALA 41 26.077 0.879 -3.164 1.00 0.03 \n-ATOM 42 CA ALA 42 29.273 1.550 -1.211 1.00 0.03 \n-ATOM 43 CA ALA 43 29.818 4.986 0.448 1.00 0.04 \n-ATOM 44 CA ALA 44 33.171 5.621 -1.259 1.00 0.02 \n-ATOM 45 CA ALA 45 32.479 4.215 -4.713 1.00 0.06 \n-ATOM 46 CA ALA 46 29.962 3.090 -7.378 1.00 0.04 \n-ATOM 47 CA ALA 47 30.361 -0.512 -6.123 1.00 0.03 \n-ATOM 48 CA ALA 48 27.092 -2.453 -5.754 1.00 0.05 \n-ATOM 49 CA ALA 49'..b'.271 -23.421 -6.056 1.00 0.05 \n-ATOM 386 CA ALA 386 -18.831 -20.648 -6.522 1.00 0.07 \n-ATOM 387 CA ALA 387 -20.917 -22.335 -3.781 1.00 0.07 \n-ATOM 388 CA ALA 388 -18.422 -21.355 -1.011 1.00 0.09 \n-ATOM 389 CA ALA 389 -19.049 -17.938 0.678 1.00 0.11 \n-ATOM 390 CA ALA 390 -16.213 -15.339 0.421 1.00 0.09 \n-ATOM 391 CA ALA 391 -14.237 -17.392 -2.120 1.00 0.05 \n-ATOM 392 CA ALA 392 -15.125 -15.344 -5.236 1.00 0.04 \n-ATOM 393 CA ALA 393 -13.819 -11.735 -5.068 1.00 0.04 \n-ATOM 394 CA ALA 394 -14.186 -10.779 -8.753 1.00 0.04 \n-ATOM 395 CA ALA 395 -14.563 -11.904 -12.357 1.00 0.03 \n-ATOM 396 CA ALA 396 -10.865 -12.326 -13.334 1.00 0.02 \n-ATOM 397 CA ALA 397 -9.716 -15.776 -14.545 1.00 0.02 \n-ATOM 398 CA ALA 398 -7.731 -18.105 -12.223 1.00 0.03 \n-ATOM 399 CA ALA 399 -5.424 -18.609 -15.234 1.00 0.04 \n-ATOM 400 CA ALA 400 -4.283 -14.973 -14.844 1.00 0.02 \n-ATOM 401 CA ALA 401 -2.147 -13.312 -12.122 1.00 0.04 \n-ATOM 402 CA ALA 402 1.155 -13.783 -13.925 1.00 0.02 \n-ATOM 403 CA ALA 403 3.548 -10.722 -13.835 1.00 0.02 \n-ATOM 404 CA ALA 404 5.405 -11.613 -17.064 1.00 0.04 \n-ATOM 405 CA ALA 405 2.104 -11.975 -18.956 1.00 0.04 \n-ATOM 406 CA ALA 406 0.828 -8.568 -17.766 1.00 0.02 \n-ATOM 407 CA ALA 407 4.203 -6.980 -18.675 1.00 0.08 \n-ATOM 408 CA ALA 408 3.835 -8.287 -22.218 1.00 0.11 \n-ATOM 409 CA ALA 409 0.169 -7.322 -22.591 1.00 0.07 \n-ATOM 410 CA ALA 410 -0.257 -4.001 -20.729 1.00 0.04 \n-ATOM 411 CA ALA 411 3.174 -2.365 -19.968 1.00 0.03 \n-ATOM 412 CA ALA 412 2.097 1.289 -20.212 1.00 0.03 \n-ATOM 413 CA ALA 413 -0.758 0.762 -17.730 1.00 0.01 \n-ATOM 414 CA ALA 414 -0.921 3.400 -15.002 1.00 0.02 \n-ATOM 415 CA ALA 415 -2.788 4.441 -11.864 1.00 0.01 \n-ATOM 416 CA ALA 416 -3.627 8.153 -11.551 1.00 0.02 \n-ATOM 417 CA ALA 417 -4.688 9.952 -8.356 1.00 0.04 \n-ATOM 418 CA ALA 418 -5.878 13.552 -7.876 1.00 0.03 \n-ATOM 419 CA ALA 419 -7.870 15.831 -5.583 1.00 0.03 \n-ATOM 420 CA ALA 420 -6.649 14.822 -2.057 1.00 0.02 \n-ATOM 421 CA ALA 421 -8.791 16.537 0.622 1.00 0.02 \n-ATOM 422 CA ALA 422 -8.475 15.737 4.352 1.00 0.02 \n-ATOM 423 CA ALA 423 -10.483 17.155 7.299 1.00 0.03 \n-ATOM 424 CA ALA 424 -13.106 16.563 10.015 1.00 0.05 \n-ATOM 425 CA ALA 425 -16.080 14.342 8.995 1.00 0.05 \n-ATOM 426 CA ALA 426 -18.451 16.404 6.797 1.00 0.03 \n-ATOM 427 CA ALA 427 -15.858 18.916 5.559 1.00 0.01 \n-ATOM 428 CA ALA 428 -14.438 17.551 2.262 1.00 0.01 \n-ATOM 429 CA ALA 429 -17.527 18.224 0.113 1.00 0.03 \n-ATOM 430 CA ALA 430 -16.755 21.948 0.408 1.00 0.01 \n-ATOM 431 CA ALA 431 -14.705 23.937 -2.210 1.00 0.07 \n-ATOM 432 CA ALA 432 -10.871 23.713 -2.349 1.00 0.04 \n-ATOM 433 CA ALA 433 -8.634 26.639 -1.246 1.00 0.00 \n-ENDMDL\n-END \n'

diff -r e838317708a6 -r 057daf00ca31 test-data/PCA_raw_data.csv
--- a/test-data/PCA_raw_data.csv Mon Oct 08 12:50:23 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,433 +0,0 @@\n-1\t0.047054686094184\t0.037444554009466\t0.0436373752498419\n-2\t0.0374612726835819\t0.0421940084118394\t0.0502594227984125\n-3\t0.0433756675554919\t0.0317325933130716\t0.0403625943915308\n-4\t0.0510257056296009\t0.0259167010959584\t0.0487038482874812\n-5\t0.0821599928173458\t0.0202843453895025\t0.0931097380090753\n-6\t0.0495229453182157\t0.0616870132943792\t0.036931846383537\n-7\t0.0772757510667949\t0.0547389711016673\t0.0480543163817793\n-8\t0.0406747587442514\t0.0302119768147152\t0.0399769016585532\n-9\t0.0244890463095143\t0.0319116007219823\t0.0684655636732839\n-10\t0.0672579099651296\t0.0548076048097413\t0.0256285115378148\n-11\t0.0153664392267895\t0.0310733561698423\t0.0426444512162961\n-12\t0.0394817828863475\t0.0254723443384889\t0.0434776653788169\n-13\t0.0464865338274322\t0.0281998031316707\t0.0465643919700792\n-14\t0.0393419705791136\t0.0141199609384353\t0.0396447853702283\n-15\t0.026577889009673\t0.0135787186184255\t0.0328220260483191\n-16\t0.0219563438480857\t0.0421017494399764\t0.0302159395225704\n-17\t0.010975439689373\t0.0466064360934659\t0.0288272078407575\n-18\t0.0378138617975345\t0.0291106157136003\t0.0370454227703895\n-19\t0.0453853224772918\t0.0618658932548866\t0.0635807430837699\n-20\t0.0447758169855008\t0.0650820018722237\t0.122445871065834\n-21\t0.0388549235037704\t0.049403731732436\t0.0870138170165552\n-22\t0.0336632944632125\t0.15224904615837\t0.0846243821293733\n-23\t0.0234394606993052\t0.0660872099476867\t0.0473701102445529\n-24\t0.0145374953929588\t0.0437544709819327\t0.0372129797260203\n-25\t0.010248927935897\t0.0438068166081511\t0.0509677856490063\n-26\t0.0257643545423895\t0.0250676685037629\t0.0197800056202805\n-27\t0.0207498391119746\t0.0289113732877244\t0.0364473822536388\n-28\t0.0633574041489475\t0.0457624637907477\t0.0529484434030222\n-29\t0.0645264877783871\t0.0477434075674047\t0.0503393907553271\n-30\t0.0410543407824722\t0.0249707111202241\t0.056811946592756\n-31\t0.0329757183257431\t0.030529215455093\t0.0536359083287068\n-32\t0.0144768356314732\t0.0177762751352106\t0.0453713695228114\n-33\t0.00726235095718219\t0.014261882074373\t0.0217449550026648\n-34\t0.0115220248525844\t0.0183520262566761\t0.0173333732448174\n-35\t0.0343241145755693\t0.0174075910107145\t0.0266918760863228\n-36\t0.0460967573167652\t0.0233117921023779\t0.0192836721988975\n-37\t0.0340477144614674\t0.0268811760903813\t0.0353523585857448\n-38\t0.0354838097634601\t0.0212717321724172\t0.0525788512954211\n-39\t0.0690927323596705\t0.024969641785531\t0.0572005729718226\n-40\t0.0463401191673253\t0.0325739188502574\t0.0329354032350865\n-41\t0.033174992285762\t0.0299562299100976\t0.04849667162213\n-42\t0.0264325837736703\t0.0447085213379716\t0.0631332272839774\n-43\t0.0393618181854106\t0.0643630926612786\t0.047804796332516\n-44\t0.0154811052245312\t0.0888687402615369\t0.0355853673063155\n-45\t0.064203471305564\t0.0765191765217101\t0.056198612978836\n-46\t0.0398882307716378\t0.0534938725605389\t0.0523234525710228\n-47\t0.0337023863657773\t0.0125466270484919\t0.0403951002118661\n-48\t0.0512773347051046\t0.040980620761514\t0.0302537197494746\n-49\t0.0228762626643446\t0.0402695948573052\t0.0239460067368674\n-50\t0.0210164143116124\t0.0330384356463391\t0.0377750222564115\n-51\t0.0748447983498102\t0.0261362865381843\t0.0302444007400203\n-52\t0.0765216044363644\t0.0213581472795363\t0.0422974641922236\n-53\t0.038978707133341\t0.0262095613876111\t0.0630473365984147\n-54\t0.030385231909456\t0.0148950386779584\t0.0208081923767633\n-55\t0.0170325089028514\t0.0289904933590215\t0.0385860865803793\n-56\t0.0174383083383827\t0.0327798756568667\t0.0582594808854083\n-57\t0.0729809247575406\t0.0313483736871799\t0.0580061220949384\n-58\t0.0365484250313067\t0.0294509740166702\t0.0650665779931943\n-59\t0.024940913778825\t0.0588711265407226\t0.056242124797916\n-60\t0.0316430002100229\t0.0656525903169871\t0.05484061772312\n-61\t0.0685781041404429\t0.0799180910725266\t0.064081414730569\n-62\t0.0540679155817946\t0.0711834012480137\t0.0387292757722466\n-63\t0.0312844314977701\t0.0718039204477457\t0.0448057288741991\n-64\t0.0375636384696563\t0.102316385127181\t0.0407807427161319\n-65\t0.0487776964513693\t0.0944104026562651\t0.033032449709766\n-66\t0.0276642561352783\t0.0619172488252132\t0.0402257175'..b'6436\n-369\t0.0327067131348003\t0.0328514117412749\t0.0483068384808962\n-370\t0.0816451813634065\t0.0723589840447464\t0.0616419739570862\n-371\t0.0960242593301912\t0.0810213957123859\t0.0808261977757139\n-372\t0.0461077257973784\t0.0738574826706993\t0.095353001882528\n-373\t0.0290577868076998\t0.0396272970077043\t0.0753018355132944\n-374\t0.0451968471555777\t0.0235398962413966\t0.0408964457449849\n-375\t0.0632417117857562\t0.0299977544119108\t0.015922295863419\n-376\t0.0443888944771728\t0.0378394062391532\t0.037717982209393\n-377\t0.0208424921286551\t0.0205999207631271\t0.0352763295099375\n-378\t0.0236608400511204\t0.019675594397584\t0.0231004084789437\n-379\t0.0328782999122257\t0.0191059376075217\t0.0413185391747002\n-380\t0.0711437620367174\t0.0606041809509478\t0.0176377481547067\n-381\t0.104728053682563\t0.0378088892769319\t0.0371901129287555\n-382\t0.1079251849944\t0.044319340008037\t0.0423660430600816\n-383\t0.0791940160605305\t0.0374620044832845\t0.0405331449376568\n-384\t0.0605847854808395\t0.0250279247665912\t0.00685094030254738\n-385\t0.0477040868024281\t0.0332461826945654\t0.0393598149490871\n-386\t0.0737317194472677\t0.0498408318751618\t0.0272081865917124\n-387\t0.0745937771588014\t0.0452948345972303\t0.0474973468036219\n-388\t0.0930549517890915\t0.0598724881718477\t0.0328824779203484\n-389\t0.108886714895057\t0.060602649742014\t0.035469707899227\n-390\t0.0886210296923761\t0.0774452993915426\t0.0299896515399513\n-391\t0.0496932895058497\t0.0505855867362092\t0.0294763715056123\n-392\t0.0394115139853251\t0.0188322834866273\t0.0425536221510137\n-393\t0.0408208611524245\t0.0189470834290675\t0.0247693884875928\n-394\t0.0359347192914615\t0.032344593595802\t0.04932943561198\n-395\t0.033239373437095\t0.0324534714405929\t0.0368709563392347\n-396\t0.0185481331779979\t0.0304281379343391\t0.0510045165968631\n-397\t0.0246244036756985\t0.0582805842428899\t0.0436328911983327\n-398\t0.0283440109211938\t0.0245063233020521\t0.0369206993133835\n-399\t0.0387534015280088\t0.0737543765352868\t0.0767375558799032\n-400\t0.0164052346042237\t0.0399881095383189\t0.0733484738643714\n-401\t0.03608907142737\t0.0981507293542106\t0.150760195706147\n-402\t0.0243457400079534\t0.108107208348457\t0.0461236327183582\n-403\t0.0162969652691559\t0.079585543961126\t0.0578500863219819\n-404\t0.0405858212948549\t0.0941089614876254\t0.0713559549657677\n-405\t0.0433068150674698\t0.113551956264355\t0.0765452682115934\n-406\t0.0203479429422323\t0.0949389517814371\t0.0409312542349892\n-407\t0.0800944593519408\t0.0947042955466688\t0.060320125909439\n-408\t0.112820429608844\t0.0956209512151558\t0.10108774859435\n-409\t0.0722540486276906\t0.0882383084346954\t0.0490804655516016\n-410\t0.038046664574931\t0.062428383748833\t0.0251013672688867\n-411\t0.0284157799548429\t0.0661154626468726\t0.0231932633930966\n-412\t0.0281380487260166\t0.0827417970197115\t0.023788142534469\n-413\t0.0116064831564034\t0.0367444132435296\t0.0224441453772377\n-414\t0.0180616746581932\t0.0575489485636574\t0.0244537928927198\n-415\t0.0089709109877673\t0.0597034920804175\t0.011921828102604\n-416\t0.0163098768970852\t0.0503826188984707\t0.0232502170709251\n-417\t0.043169677266108\t0.126561096573347\t0.0360124102914864\n-418\t0.0259562839115752\t0.12381339192599\t0.0321617881394841\n-419\t0.029333561584791\t0.0404093238303602\t0.0350569045418453\n-420\t0.0238023706224343\t0.0172532357096332\t0.0243415866836097\n-421\t0.0164438338814252\t0.0119691449440208\t0.0272949331623209\n-422\t0.0190336245458057\t0.00902530660663473\t0.0544177863967794\n-423\t0.0311032554955338\t0.0176935885261446\t0.0321799203879992\n-424\t0.045563297295363\t0.0077311559432036\t0.0241315913252779\n-425\t0.0472012002073129\t0.0155440465089401\t0.0293494258944502\n-426\t0.032817520238095\t0.016278927780019\t0.0434651774259206\n-427\t0.0112784656676895\t0.00867506860267379\t0.0352806367969836\n-428\t0.0121221989805735\t0.0360467510884142\t0.0418156392437459\n-429\t0.032992657167336\t0.0692534224643054\t0.0526550268956959\n-430\t0.0135480387672979\t0.0591678975954087\t0.0525335361508873\n-431\t0.0660904820855133\t0.0724506585196891\t0.032569322190446\n-432\t0.0428224468098853\t0.0691213159641431\t0.0513939503573059\n-433\t0.00162790530191714\t0.0713694808434317\t0.0554225883342971\n'

diff -r e838317708a6 -r 057daf00ca31 test-data/PCA_raw_data.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/PCA_raw_data.tabular Sun Jan 13 03:21:33 2019 -0500

b'@@ -0,0 +1,433 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diff -r e838317708a6 -r 057daf00ca31 test-data/RMSD_raw_data.csv
--- a/test-data/RMSD_raw_data.csv Mon Oct 08 12:50:23 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,15 +0,0 @@
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diff -r e838317708a6 -r 057daf00ca31 test-data/RMSD_raw_data.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RMSD_raw_data.tabular Sun Jan 13 03:21:33 2019 -0500

@@ -0,0 +1,15 @@
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diff -r e838317708a6 -r 057daf00ca31 test-data/dccm_plot.png

Binary file test-data/dccm_plot.png has changed

diff -r e838317708a6 -r 057daf00ca31 test-data/dccm_raw_data.csv
--- a/test-data/dccm_raw_data.csv Mon Oct 08 12:50:23 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r e838317708a6 -r 057daf00ca31 test-data/rmsf_raw_data.csv
--- a/test-data/rmsf_raw_data.csv Mon Oct 08 12:50:23 2018 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

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diff -r e838317708a6 -r 057daf00ca31 test-data/rmsf_raw_data.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rmsf_raw_data.tabular Sun Jan 13 03:21:33 2019 -0500

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