| Previous changeset 12:903be3cf2a29 (2024-11-26) |
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Commit message:
planemo upload for repository https://github.com/jonasbucherETH/galaxy/blob/dev/tools/my_tools/rgreat/.shed.yml commit 3132b5f614fa6b70081233041c5f21348059f900 |
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modified:
rgreat.R rgreat.xml |
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added:
test-data/dmRegions.tsv test-data/output_hyper.rds test-data/output_hypo.rds test-data/significantRegions_hyper.tsv test-data/significantRegions_hypo.tsv |
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| diff -r 903be3cf2a29 -r 29cae736023c rgreat.R --- a/rgreat.R Tue Nov 26 08:53:58 2024 +0000 +++ b/rgreat.R Tue Nov 26 10:33:39 2024 +0000 |
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| @@ -89,8 +89,8 @@ opt <- parse_args(parser) # Set defaults for parameters if not provided -min_gene_set_size <- if (!is.null(opt$min_gene_set_size)) opt$min_gene_set_size else 10 -mode <- if (!is.null(opt$mode)) opt$mode else 'twoClosest' +min_gene_set_size <- if (!is.null(opt$min_gene_set_size)) opt$min_gene_set_size else 5 +mode <- if (!is.null(opt$mode)) opt$mode else 'basalPlusExt' extend_from <- if (!is.null(opt$extend_from)) opt$extend_from else 'TSS' extension <- if (!is.null(opt$extension)) opt$extension else 1000000 @@ -107,20 +107,20 @@ exclude <- if (!is.null(opt$exclude)) opt$exclude else NULL # Debugging: Print options to verify -cat("Input:", opt$input, "\n") -cat("Output:", opt$output, "\n") -cat("BioMart Dataset:", opt$biomart_dataset, "\n") -cat("Min Gene Set Size:", min_gene_set_size, "\n") -cat("Mode:", mode, "\n") -if (mode == 'basalPlusExt') { - cat("Basal Upstream:", basal_upstream, "\n") - cat("Basal Downstream:", basal_downstream, "\n") -} -cat("Extend From:", extend_from, "\n") -cat("Extension:", extension, "\n") -if (!is.null(exclude)) { - cat("Exclude Regions:", exclude, "\n") -} +#cat("Input:", opt$input, "\n") +#cat("Output:", opt$output, "\n") +#cat("BioMart Dataset:", opt$biomart_dataset, "\n") +#cat("Min Gene Set Size:", min_gene_set_size, "\n") +#cat("Mode:", mode, "\n") +#if (mode == 'basalPlusExt') { +# cat("Basal Upstream:", basal_upstream, "\n") +# cat("Basal Downstream:", basal_downstream, "\n") +#} +#cat("Extend From:", extend_from, "\n") +#cat("Extension:", extension, "\n") +#if (!is.null(exclude)) { +# cat("Exclude Regions:", exclude, "\n") +#} # Load input file (assuming RDS format) #dmrseq_output <- readRDS(opt$input) |
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| diff -r 903be3cf2a29 -r 29cae736023c rgreat.xml --- a/rgreat.xml Tue Nov 26 08:53:58 2024 +0000 +++ b/rgreat.xml Tue Nov 26 10:33:39 2024 +0000 |
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| @@ -83,7 +83,7 @@ <option value="true">Yes</option> </param> <when value="true"> - <param name="min_gene_set_size" type="integer" value="10" min="1" label="Minimal size of gene sets" help="Minimal size of gene sets to be considered in the analysis." /> + <param name="min_gene_set_size" type="integer" value="5" min="1" label="Minimal size of gene sets" help="Minimal size of gene sets to be considered in the analysis." /> <conditional name="gene_extension_mode"> <param name="mode" type="select" label="Mode to extend genes"> <option value="basalPlusExt">Basal Plus Extension</option> @@ -98,8 +98,8 @@ <when value="oneClosest" /> </conditional> <param name="extend_from" type="select" label="Extend gene from"> - <option value="tss">TSS only</option> - <option value="complete">Complete gene</option> + <option value="TSS">TSS only</option> + <option value="gene">Complete gene</option> </param> <param name="extension" type="integer" value="1000000" min="0" label="Extension from basal domains" help="Extensions from the basal domains." /> <param name="exclude" type="text" area="true" optional="true" label="Excluded regions" help="Regions that are excluded from analysis such as gap regions. The value can also be a vector of chromosome names. Use 'gap' to remove gap regions for the corresponding organism." > @@ -123,13 +123,13 @@ <param name="cytosine_context" value="CG"/> <param name="biomart_dataset" value="hsapiens_gene_ensembl"/> <param name="advanced_options" value="true"/> - <param name="min_gene_set_size" value="15"/> + <param name="min_gene_set_size" value="5"/> <param name="mode" value="basalPlusExt"/> <param name="basal_upstream" value="5000"/> <param name="basal_downstream" value="1000"/> - <param name="extend_from" value="tss"/> + <param name="extend_from" value="TSS"/> <param name="extension" value="1000000"/> - <param name="exclude" value="gap"/> + <param name="exclude" value=""/> <output name="output_hypo" file="output_hypo.rds"/> <output name="output_hyper" file="output_hyper.rds"/> </test> |
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| diff -r 903be3cf2a29 -r 29cae736023c test-data/dmRegions.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dmRegions.tsv Tue Nov 26 10:33:39 2024 +0000 |
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| b'@@ -0,0 +1,4777 @@\n+seqnames\tstart\tend\twidth\tstrand\tL\tarea\tbeta\tstat\tpval\tqval\tindex.start\tindex.end\tindex.width\n+chr21\t9795652\t9891778\t96127\t*\t1624\t674.164793127837\t-0.881030354498182\t-105.839134827103\t0.000803212851405623\t0.00248777210007345\t437\t2060\t1624\n+chr21\t9916614\t9967560\t50947\t*\t346\t123.452999506715\t-0.850918273966775\t-50.6124214971496\t0.000803212851405623\t0.00248777210007345\t2202\t2547\t346\n+chr21\t40151874\t40213291\t61418\t*\t575\t221.211867849455\t-0.909376644482898\t-49.1731744362661\t0.000803212851405623\t0.00248777210007345\t196669\t197243\t575\n+chr21\t40908798\t40961535\t52738\t*\t433\t163.436167752532\t-0.910826196882291\t-44.4157048917509\t0.000803212851405623\t0.00248777210007345\t202356\t202788\t433\n+chr21\t39986230\t40047077\t60848\t*\t540\t182.146657521484\t-0.80865526499766\t-42.8329771539184\t0.000803212851405623\t0.00248777210007345\t195407\t195946\t540\n+chr21\t10189039\t10206547\t17509\t*\t236\t75.5858421232305\t-0.774128887302767\t-40.8896764359017\t0.000803212851405623\t0.00248777210007345\t4413\t4648\t236\n+chr21\t9733894\t9788922\t55029\t*\t354\t83.4105377448774\t-0.549605329623464\t-40.8522128416669\t0.000803212851405623\t0.00248777210007345\t48\t401\t354\n+chr21\t40333724\t40378696\t44973\t*\t412\t150.728004630737\t-0.856456581172022\t-38.9751298385552\t0.000803212851405623\t0.00248777210007345\t198080\t198491\t412\n+chr21\t40463227\t40500196\t36970\t*\t331\t126.366105771484\t-0.906197569788817\t-37.2497143057657\t0.000803212851405623\t0.00248777210007345\t199134\t199464\t331\n+chr21\t22885652\t22932851\t47200\t*\t267\t103.40362765276\t-0.927459530262099\t-35.304074964089\t0.000803212851405623\t0.00248777210007345\t57222\t57488\t267\n+chr21\t41093809\t41135685\t41877\t*\t353\t130.373590932841\t-0.879560102617418\t-34.5233770671965\t0.000803212851405623\t0.00248777210007345\t203751\t204103\t353\n+chr21\t40125410\t40150716\t25307\t*\t205\t82.9726601272913\t-0.971165680076776\t-34.2177537769091\t0.000803212851405623\t0.00248777210007345\t196464\t196668\t205\n+chr21\t41006659\t41029135\t22477\t*\t151\t64.294053502814\t-1.01662859581982\t-34.1007430885297\t0.000803212851405623\t0.00248777210007345\t203131\t203281\t151\n+chr21\t40514089\t40540904\t26816\t*\t172\t69.3226546753877\t-0.925968288000678\t-33.0219104282469\t0.000803212851405623\t0.00248777210007345\t199537\t199708\t172\n+chr21\t40082944\t40106937\t23994\t*\t200\t82.8574696999542\t-0.977093882090216\t-32.4640486158801\t0.000803212851405623\t0.00248777210007345\t196201\t196400\t200\n+chr21\t31333789\t31373645\t39857\t*\t255\t97.0107238631928\t-0.866686205705504\t-32.3359831856872\t0.000803212851405623\t0.00248777210007345\t108693\t108947\t255\n+chr21\t31173561\t31191350\t17790\t*\t118\t47.7013083921242\t-0.985911290045436\t-32.0871655217625\t0.000803212851405623\t0.00248777210007345\t107777\t107894\t118\n+chr21\t22403530\t22442996\t39467\t*\t253\t94.7339501522988\t-0.879005912175637\t-31.8199852003307\t0.000803212851405623\t0.00248777210007345\t54747\t54999\t253\n+chr21\t41370705\t41405406\t34702\t*\t293\t98.3098998787271\t-0.817185743320058\t-31.4262528774106\t0.000803212851405623\t0.00248777210007345\t205714\t206006\t293\n+chr21\t44872165\t44905039\t32875\t*\t419\t124.593233577504\t-0.739176189177794\t-31.3347799061576\t0.000803212851405623\t0.00248777210007345\t265076\t265494\t419\n+chr21\t30552192\t30581228\t29037\t*\t188\t82.7744697209254\t-1.00882255179702\t-31.3317301901573\t0.000803212851405623\t0.00248777210007345\t104573\t104760\t188\n+chr21\t33159678\t33203779\t44102\t*\t299\t88.5964431835904\t-0.706984910672696\t-31.0850836301352\t0.000803212851405623\t0.00248777210007345\t128357\t128655\t299\n+chr21\t14746537\t14768351\t21815\t*\t110\t42.9280665695245\t-0.959768081567282\t-30.1813622122098\t0.000803212851405623\t0.00248777210007345\t12150\t12259\t110\n+chr21\t19882538\t19909370\t26833\t*\t138\t56.6809024720221\t-0.975398280842656\t-29.7417796302862\t0.000803212851405623\t0.00248777210007345\t41001\t41138\t138\n+chr21\t14967731\t14995042\t27312\t*\t153\t61.9229821605167\t-0.991990116429107\t-29.5476347455794\t0.000803212851405623\t0.00248777210007345\t13163\t13315\t153\n+chr21\t20673344\t20695129\t21786\t*\t116\t51.1205684371906\t-1.01575173276853\t-29.5425271934756\t0.000803212851405623\t0.00248777210007345\t44924\t45039\t116\n+chr21\t18729631\t18761558\t3192'..b'hr21\t39069762\t39070333\t572\t*\t5\t0.527638170942104\t0.102372265651883\t0.704509506710015\t0.743775100401606\t0.748161305711473\t186037\t186041\t5\n+chr21\t42517644\t42517867\t224\t*\t5\t0.52792737110498\t0.111565217115261\t0.69692929436147\t0.746184738955823\t0.750427103232894\t221875\t221879\t5\n+chr21\t34877312\t34877567\t256\t*\t5\t0.842577671088227\t0.107903137901285\t0.683654216023685\t0.755020080321285\t0.75915282181357\t145957\t145961\t5\n+chr21\t39400510\t39400629\t120\t*\t6\t1.11465960873754\t-0.1429054880641\t-0.677878234317068\t0.756626506024096\t0.760607912601786\t189605\t189610\t6\n+chr21\t42886981\t428872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| diff -r 903be3cf2a29 -r 29cae736023c test-data/output_hyper.rds |
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| Binary file test-data/output_hyper.rds has changed |
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| diff -r 903be3cf2a29 -r 29cae736023c test-data/output_hypo.rds |
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| Binary file test-data/output_hypo.rds has changed |
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| diff -r 903be3cf2a29 -r 29cae736023c test-data/significantRegions_hyper.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/significantRegions_hyper.tsv Tue Nov 26 10:33:39 2024 +0000 |
| b |
| b'@@ -0,0 +1,286 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|
| b |
| diff -r 903be3cf2a29 -r 29cae736023c test-data/significantRegions_hypo.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/significantRegions_hypo.tsv Tue Nov 26 10:33:39 2024 +0000 |
| b |
| b'@@ -0,0 +1,3607 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|