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Commit message:
planemo upload for repository https://github.com/chamaelj/tools-artbio/tree/master/tools/basicplot commit 09c37709000f22d9fb378ec1a4ec0e8f46e6bf73-dirty |
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basicplot.xml test-data/basicplot.pdf test-data/data.tab |
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| diff -r 000000000000 -r da8c70a64f0c basicplot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/basicplot.xml Fri Mar 31 07:23:53 2017 -0400 |
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| @@ -0,0 +1,89 @@ +<tool id="Basicplot" name="basicplot" version="0.9.0"> + <description>Basic plot</description> + <requirements> + <requirement type="package" version="3.1.2">R</requirement> + </requirements> + <command><![CDATA[ + Rscript '$basicplot' "\${GALAXY_SLOTS:-1}" + ]]></command> + <configfiles> + <configfile name="basicplot"> + <![CDATA[ + ## Setup R error handling to go to stderr + options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + options(warn=-1) + Table = read.delim("${input}", header=TRUE) + pdf("${output}") + pairs(Table[ ,-1], main="${title}", log="xy", pch = 20) + dev.off() + ]]> + </configfile> + </configfiles> + <inputs> + <param name="input" type="data" format="tabular" label="tabular file"/> + <param name="title" type="text" size="25" value="Title" label="Main Title"/> + </inputs> + <outputs> + <data name="output" format="pdf" label="plot" /> + </outputs> +<tests> + <test> + <param name="input" value="data.tab" ftype="tabular"/> + <param name="title" value="Title"/> + <output name="output" file="basicplot.pdf" ftype="pdf"/> + </test> +</tests> +<help> + +**What it does** + +Take on tabular file of numerical data as input and produces pairwise plots of numerical data, in log-log scale. +The first column of the data frame is ignored. + +Example of input data: + +<![CDATA[ + +gene sample1 sample2 sample3 sample4 sample5 sample6 + +tRNA:Ala-AGC-2-3 4407 4506 2267 2423 2736 1153 + +tRNA:Asp-GTC-1-10 2111 2931 3302 3499 3809 1682 + +tRNA:Asp-GTC-1-11 2099 2936 3349 3556 4124 1629 + +tRNA:Glu-TTC-1-6 1095 1376 1189 1162 1120 561 + +tRNA:Glu-TTC-1-5 1022 1415 1156 1081 1120 578 + +tRNA:Glu-TTC-1-4 1047 1336 1156 1182 1127 602 + +tRNA:Glu-CTC-3-4 3613 3414 8161 9021 9776 5248 + +tRNA:Glu-CTC-3-5 3741 3292 7893 8845 9833 5074 + +tRNA:Glu-CTC-3-6 3619 3379 7663 8737 9513 5021 + +tRNA:Glu-CTC-3-8 7249 5809 80760 39479 62652 27404 + +tRNA:Glu-CTC-3-9 3770 3367 8007 8969 9976 5100 + +]]> + + +</help> +<citations> + <citation type="bibtex"> +@Manual{, + title = {R: A Language and Environment for Statistical Computing}, + author = {{R Core Team}}, + organization = {R Foundation for Statistical Computing}, + address = {Vienna, Austria}, + year = {2014}, + url = {http://www.R-project.org/}, + } + </citation> + </citations> + +</tool> + |
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| diff -r 000000000000 -r da8c70a64f0c test-data/data.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/data.tab Fri Mar 31 07:23:53 2017 -0400 |
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| b'@@ -0,0 +1,315 @@\n+gene\tsample1\tsample2\tsample3\tsample4\tsample5\tsample6\n+tRNA:Ala-AGC-2-3\t4407\t4506\t2267\t2423\t2736\t1153\n+tRNA:Asp-GTC-1-10\t2111\t2931\t3302\t3499\t3809\t1682\n+tRNA:Asp-GTC-1-11\t2099\t2936\t3349\t3556\t4124\t1629\n+tRNA:Glu-TTC-1-6\t1095\t1376\t1189\t1162\t1120\t561\n+tRNA:Glu-TTC-1-5\t1022\t1415\t1156\t1081\t1120\t578\n+tRNA:Glu-TTC-1-4\t1047\t1336\t1156\t1182\t1127\t602\n+tRNA:Glu-CTC-3-4\t3613\t3414\t8161\t9021\t9776\t5248\n+tRNA:Glu-CTC-3-5\t3741\t3292\t7893\t8845\t9833\t5074\n+tRNA:Glu-CTC-3-6\t3619\t3379\t7663\t8737\t9513\t5021\n+tRNA:Glu-CTC-3-8\t7249\t5809\t80760\t39479\t62652\t27404\n+tRNA:Glu-CTC-3-9\t3770\t3367\t8007\t8969\t9976\t5100\n+tRNA:Phe-GAA-1-8\t643\t2989\t666\t739\t587\t174\n+tRNA:Gly-GCC-1-1\t12814\t13201\t7120\t6420\t6356\t2666\n+tRNA:Gly-GCC-1-2\t12633\t12847\t7030\t6383\t6387\t2620\n+tRNA:Gly-GCC-1-3\t13025\t13045\t7068\t6367\t6502\t2571\n+tRNA:Gly-GCC-1-4\t12714\t13076\t7009\t6563\t6620\t2579\n+tRNA:Gly-GCC-1-5\t12888\t13220\t7231\t6513\t6421\t2657\n+tRNA:Gly-GCC-1-6\t12852\t13061\t7109\t6334\t6481\t2593\n+tRNA:Gly-GCC-1-7\t12573\t13053\t7078\t6511\t6714\t2590\n+tRNA:Gly-GCC-2-1\t12819\t12784\t6973\t6305\t6276\t2635\n+tRNA:Gly-GCC-1-8\t12868\t13112\t7401\t6246\t6379\t2617\n+tRNA:Gly-GCC-1-9\t13095\t13221\t6971\t6442\t6614\t2714\n+tRNA:Gly-GCC-1-10\t12709\t12973\t7233\t6402\t6510\t2584\n+tRNA:Gly-GCC-1-11\t12883\t13180\t7172\t6437\t6656\t2657\n+tRNA:Gly-GCC-1-12\t13002\t13101\t6948\t6451\t6491\t2579\n+tRNA:Gly-GCC-1-13\t12571\t13071\t7121\t6446\t6448\t2613\n+tRNA:His-GTG-1-4\t7316\t10889\t3975\t3530\t4804\t1844\n+tRNA:Ala-TGC-2-1\t4718\t6157\t2509\t2117\t3548\t837\n+tRNA:Ile-AAT-1-1\t152\t713\t108\t151\t92\t27\n+tRNA:Ile-AAT-1-3\t145\t690\t101\t149\t80\t42\n+tRNA:Ile-AAT-1-4\t140\t663\t86\t129\t88\t35\n+tRNA:Ile-AAT-1-5\t111\t747\t86\t155\t106\t28\n+tRNA:Ile-AAT-1-6\t140\t750\t96\t173\t96\t27\n+tRNA:Ile-AAT-1-7\t137\t710\t116\t145\t81\t27\n+tRNA:Lys-CTT-1-4\t5121\t10210\t4309\t3995\t4380\t1508\n+tRNA:Lys-CTT-1-3\t5311\t13055\t4776\t4514\t4681\t1614\n+tRNA:Lys-CTT-1-2\t5213\t10390\t4334\t3842\t4550\t1547\n+tRNA:Lys-CTT-1-5\t5154\t9982\t4220\t3890\t4377\t1439\n+tRNA:Lys-CTT-1-1\t5235\t10006\t4220\t3813\t4409\t1551\n+tRNA:Lys-CTT-1-6\t5287\t10212\t4337\t3938\t4466\t1599\n+tRNA:Lys-CTT-1-7\t5169\t10143\t4079\t3978\t4515\t1485\n+tRNA:Lys-CTT-1-8\t5340\t10445\t4331\t4013\t4450\t1551\n+tRNA:Lys-CTT-1-9\t5245\t9909\t4270\t3891\t4485\t1485\n+tRNA:Lys-CTT-1-10\t5218\t10293\t4289\t3878\t4558\t1546\n+tRNA:Lys-CTT-1-11\t5275\t9977\t4499\t4043\t4385\t1530\n+tRNA:Lys-TTT-1-1\t3266\t10276\t2311\t2703\t2140\t871\n+tRNA:Lys-TTT-2-4\t9595\t20989\t8440\t10144\t7801\t3391\n+tRNA:Lys-TTT-2-5\t9686\t21288\t8283\t10019\t7970\t3200\n+tRNA:Leu-CAG-1-1\t2684\t3413\t974\t861\t1189\t539\n+tRNA:Leu-CAA-2-1\t2443\t3406\t1048\t885\t1204\t614\n+tRNA:Leu-CAA-1-1\t2421\t3383\t978\t816\t1147\t620\n+tRNA:Met-CAT-1-1\t237\t470\t327\t285\t661\t204\n+tRNA:Met-CAT-1-2\t79\t244\t205\t167\t364\t105\n+tRNA:Met-CAT-1-5\t53\t193\t114\t99\t208\t89\n+tRNA:iMet-CAT-2-1\t1494\t17755\t1947\t2718\t1286\t989\n+tRNA:iMet-CAT-1-4\t1566\t17948\t2023\t2628\t1280\t981\n+tRNA:iMet-CAT-1-5\t1589\t18065\t2003\t2738\t1416\t1046\n+tRNA:Asn-GTT-1-6\t94\t335\t59\t77\t77\t33\n+tRNA:Asn-GTT-1-5\t93\t319\t82\t62\t72\t38\n+tRNA:Asn-GTT-1-4\t77\t339\t53\t65\t56\t23\n+tRNA:Asn-GTT-1-8\t103\t326\t69\t74\t65\t32\n+tRNA:Asn-GTT-1-7\t99\t351\t59\t79\t55\t38\n+tRNA:Asn-GTT-1-3\t94\t347\t68\t85\t83\t25\n+tRNA:Asn-GTT-1-2\t108\t319\t53\t79\t75\t32\n+tRNA:Asn-GTT-1-1\t96\t317\t56\t87\t82\t26\n+tRNA:Pro-TGG-1-1\t2231\t2569\t1055\t896\t1356\t752\n+tRNA:Pro-TGG-1-2\t2230\t2573\t1031\t925\t1385\t739\n+tRNA:Arg-TCG-3-1\t67\t69\t64\t50\t61\t24\n+tRNA:Arg-TCG-3-2\t62\t98\t50\t38\t53\t17\n+tRNA:Arg-TCG-3-3\t65\t98\t44\t54\t50\t26\n+tRNA:Arg-TCG-3-4\t52\t83\t40\t41\t59\t17\n+tRNA:Arg-TCG-2-1\t73\t116\t109\t96\t82\t22\n+tRNA:Arg-TCG-1-1\t70\t277\t68\t102\t76\t41\n+tRNA:Arg-TCG-2-2\t51\t110\t58\t59\t54\t29\n+tRNA:Arg-ACG-1-5\t124\t804\t173\t217\t168\t96\n+tRNA:Arg-ACG-1-3\t164\t850\t185\t226\t153\t111\n+tRNA:Arg-ACG-1-2\t179\t820\t209\t226\t189\t107\n+tRNA:Arg-ACG-1-1\t151\t832\t205\t226\t210\t99\n+tRNA:Arg-ACG-1-10\t155\t817\t203\t251\t224\t120\n+tRNA:Arg-ACG-1-9\t174\t818\t213\t260\t274\t207\n+tRNA:Arg-ACG-1-8\t184\t850\t618\t455\t835\t170\n+tRNA:Arg-ACG-1-7\t183\t820\t217\t258\t192\t101\n+tRNA:Arg-ACG-1-6\t176\t848\t210\t283\t229\t96\n+tRNA:Arg-TCG-4-1\t757\t670\t35\t59\t32\t18\n+tRNA:Arg-TCG-2-3\t58\t91\t63\t58\t70\t24\n+tRNA:Ser-GCT-2-1\t3684\t22180\t2738\t3202\t2952\t1093\n+tRNA:Ser-GCT-2-2\t3619\t21784\t2711\t3100\t2895\t1062\n+tRNA:Ser-AGA-1-1\t911\t1415\t4'..b'31\t2728\t1182\n+tRNA:Ala-AGC-2-5\t4519\t4523\t2200\t2499\t2693\t1138\n+tRNA:Ala-AGC-2-2\t4305\t4412\t2310\t2457\t2788\t1199\n+tRNA:Pro-TGG-1-3\t2191\t2699\t1003\t973\t1451\t719\n+tRNA:Ala-AGC-2-9\t4348\t4524\t2217\t2339\t2646\t1127\n+tRNA:Ala-AGC-2-10\t4388\t4539\t2204\t2425\t2714\t1204\n+tRNA:Ala-AGC-1-1\t4400\t4636\t2294\t2326\t2648\t1073\n+tRNA:Pro-TGG-1-4\t2128\t2567\t1058\t938\t1355\t747\n+tRNA:Ala-AGC-2-7\t4460\t4494\t2192\t2383\t2647\t1100\n+tRNA:Ala-AGC-2-8\t4456\t4497\t2254\t2401\t2709\t1128\n+tRNA:Asn-GTT-1-10\t93\t345\t59\t62\t90\t30\n+tRNA:Phe-GAA-1-6\t626\t3000\t689\t774\t654\t223\n+tRNA:Val-AAC-1-2\t2022\t3326\t1374\t474\t836\t72\n+tRNA:Asp-GTC-1-6\t2037\t2889\t3162\t3454\t3843\t1636\n+tRNA:Asp-GTC-1-5\t2059\t2941\t3257\t3425\t3794\t1664\n+tRNA:Asp-GTC-1-4\t2092\t2796\t3084\t3461\t3725\t1584\n+tRNA:Arg-CCT-1-1\t320\t375\t240\t169\t255\t85\n+tRNA:Gln-CTG-2-5\t2657\t6892\t1990\t2146\t2741\t809\n+tRNA:Thr-AGT-1-1\t2577\t4321\t4456\t839\t15667\t255\n+tRNA:Asp-GTC-1-9\t2020\t2941\t3302\t3513\t3744\t1609\n+tRNA:Asp-GTC-1-7\t2074\t2841\t3430\t3515\t4363\t1789\n+tRNA:Asp-GTC-1-8\t2076\t2790\t3206\t3517\t3747\t1645\n+tRNA:Asp-GTC-1-3\t2046\t2803\t3220\t3420\t3742\t1692\n+tRNA:Phe-GAA-1-3\t707\t2965\t681\t790\t588\t190\n+tRNA:Asp-GTC-1-2\t2168\t2962\t7408\t4900\t8905\t2609\n+tRNA:Asp-GTC-1-1\t2071\t2765\t3190\t3404\t3788\t1627\n+tRNA:Gln-CTG-2-4\t2749\t7126\t1942\t2108\t2647\t744\n+tRNA:Gln-CTG-3-1\t2308\t4895\t1690\t1941\t2456\t701\n+tRNA:Arg-TCT-2-1\t7\t50\t15\t10\t19\t6\n+tRNA:Gln-CTG-2-2\t2879\t7184\t5438\t3746\t8954\t1430\n+tRNA:Gln-CTG-2-3\t2765\t7244\t2042\t2194\t2745\t812\n+tRNA:Arg-TCT-3-1\t0\t6\t0\t1\t5\t0\n+tRNA:Trp-CCA-2-1\t285\t823\t223\t208\t225\t101\n+tRNA:Asp-GTC-2-1\t1944\t2314\t2815\t3085\t3464\t1463\n+tRNA:Thr-AGT-3-1Psi\t9\t0\t6\t3\t13\t3\n+tRNA:Gln-TTG-1-1\t1588\t3272\t988\t1138\t1521\t498\n+tRNA:Pro-AGG-1-7\t5616\t11013\t10703\t9079\t15579\t4001\n+tRNA:Leu-CAA-2-2\t2310\t3313\t1056\t875\t1231\t559\n+tRNA:Pro-AGG-1-6\t5533\t11036\t10934\t9192\t16057\t4018\n+tRNA:Pro-AGG-1-5\t5623\t11024\t10826\t9211\t16144\t4181\n+tRNA:Met-CAT-1-3\t43\t183\t103\t93\t233\t100\n+tRNA:Pro-CGG-2-2\t1213\t3314\t1241\t1051\t1386\t551\n+tRNA:Pro-CGG-2-3\t1443\t3151\t3325\t2037\t2776\t1302\n+tRNA:Lys-CTT-1-13\t5229\t10076\t4339\t3923\t4447\t1523\n+tRNA:Met-CAT-2-1\t119\t1035\t240\t259\t329\t148\n+tRNA:Lys-CTT-1-12\t5401\t10443\t4432\t4034\t4502\t1582\n+tRNA:Cys-GCA-1-4\t4642\t4530\t7287\t6574\t8176\t2506\n+tRNA:Cys-GCA-1-3\t4680\t4592\t7300\t6354\t8143\t2403\n+tRNA:Cys-GCA-1-1\t4630\t4506\t7450\t6412\t8090\t2437\n+tRNA:Cys-GCA-1-2\t4621\t4622\t7192\t6411\t8028\t2506\n+tRNA:Cys-GCA-3-1\t2435\t2157\t1447\t1339\t1585\t600\n+tRNA:Cys-GCA-2-1\t57\t79\t31\t48\t44\t26\n+tRNA:Glu-CTC-3-7\t3727\t3426\t8119\t9074\t9798\t5113\n+tRNA:Glu-CTC-3-2\t3699\t3455\t7866\t9028\t9818\t5056\n+tRNA:Glu-CTC-3-3\t3720\t3434\t7945\t8859\t9800\t5103\n+tRNA:Glu-CTC-3-1\t3769\t3391\t8047\t8798\t9699\t5085\n+tRNA:Met-CAT-1-4\t38\t194\t131\t99\t236\t88\n+tRNA:Leu-CAG-1-2\t2515\t3408\t910\t885\t1233\t561\n+tRNA:Leu-CAG-1-3\t2547\t3261\t941\t810\t1131\t551\n+tRNA:Leu-CAG-1-4\t2567\t3434\t901\t809\t1139\t575\n+tRNA:Leu-CAG-1-5\t2620\t3269\t907\t870\t1171\t562\n+tRNA:Leu-CAG-1-6\t2561\t3226\t901\t837\t1132\t574\n+tRNA:Leu-CAG-1-7\t2583\t3310\t924\t838\t1125\t558\n+tRNA:Ala-AGC-2-1\t4318\t4409\t2184\t2403\t2616\t1024\n+tRNA:Val-TAC-1-1\t9250\t23338\t12449\t7476\t16453\t4168\n+tRNA:Val-TAC-1-2\t5846\t20236\t4515\t3102\t6231\t1078\n+tRNA:Cys-GCA-4-1\t87\t112\t70\t99\t105\t75\n+tRNA:Glu-CTC-4-1\t5291\t5143\t11877\t12928\t16410\t6067\n+tRNA:Ile-TAT-1-1\t240\t698\t484\t468\t532\t275\n+tRNA:Ile-TAT-1-2\t157\t618\t239\t232\t217\t110\n+tRNA:iMet-CAT-1-3\t1511\t17719\t1965\t2637\t1334\t993\n+tRNA:Gln-TTG-2-1\t1205\t2654\t726\t912\t1041\t366\n+tRNA:Tyr-GTA-1-1\t153\t224\t227\t166\t196\t89\n+tRNA:Tyr-GTA-2-1\t216\t1179\t75\t59\t119\t45\n+tRNA:Pro-CGG-2-1\t1412\t3039\t10900\t6275\t10443\t4808\n+tRNA:Phe-GAA-1-2\t606\t2908\t677\t735\t581\t189\n+tRNA:Phe-GAA-1-1\t665\t2956\t632\t755\t581\t163\n+tRNA:Gln-CTG-2-1\t2696\t7117\t1967\t2139\t2498\t736\n+tRNA:Pro-CGG-1-1\t1828\t7683\t1301\t1345\t1645\t377\n+tRNA:Ala-AGC-2-4\t4386\t4574\t2227\t2386\t2634\t1091\n+tRNA:Glu-TTC-1-3\t1047\t1386\t1111\t1127\t1113\t588\n+tRNA:Leu-TAA-2-1\t408\t1007\t259\t237\t247\t106\n+tRNA:Asn-GTT-1-9\t111\t320\t58\t80\t76\t19\n+tRNA:Arg-CCT-1-3\t369\t400\t220\t161\t255\t78\n+tRNA:Trp-CCA-2-5\t271\t825\t378\t350\t320\t179\n+tRNA:Arg-TCG-2-4\t80\t125\t74\t58\t102\t34\n+tRNA:Thr-TGT-2-3\t32\t431\t105\t133\t78\t23\n+tRNA:Thr-TGT-2-4\t48\t432\t128\t159\t94\t33\n+tRNA:Leu-CAG-1-8\t2608\t3387\t959\t813\t1208\t552\n' 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