| Previous changeset 12:fa56d93f7980 (2018-04-19) Next changeset 14:c97a786e8fb5 (2018-06-07) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610 |
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modified:
diffbind.R diffbind.xml test-data/DiffBind_analysis.RData test-data/out_diffbind.tab |
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added:
test-data/out_binding_matrix.tab test-data/out_diffbind.bed test-data/out_diffbind.interval |
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removed:
test-data/out_analysis_info.txt test-data/out_binding.matrix test-data/out_rscript.txt |
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| diff -r fa56d93f7980 -r 1de83981d43c diffbind.R --- a/diffbind.R Thu Apr 19 17:15:53 2018 -0400 +++ b/diffbind.R Wed May 30 12:25:42 2018 -0400 |
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| @@ -94,12 +94,49 @@ # Output differential binding sites resSorted <- diff_bind[order(diff_bind$FDR),] -write.table(as.data.frame(resSorted), file = opt$outfile, sep="\t", quote = FALSE, append=TRUE, row.names = FALSE) +# Convert from GRanges (1-based) to 0-based format (adapted from https://www.biostars.org/p/89341/) +if (opt$format == "bed") { + resSorted <- data.frame(Chrom=seqnames(resSorted), + Start=start(resSorted) - 1, + End=end(resSorted), + Name=rep("DiffBind", length(resSorted)), + Score=rep("0", length(resSorted)), + Strand=gsub("\\*", ".", strand(resSorted))) +} else if (opt$format == "interval") { + # Output as interval + df <- as.data.frame(resSorted) + extrainfo <- NULL + for (i in 1:nrow(df)) { + extrainfo[i] <- paste0(c(df$width[i], df[i, 6:ncol(df)]), collapse="|") + } + resSorted <- data.frame(Chrom=seqnames(resSorted), + Start=start(resSorted) - 1, + End=end(resSorted), + Name=rep("DiffBind", length(resSorted)), + Score=rep("0", length(resSorted)), + Strand=gsub("\\*", ".", strand(resSorted)), + Comment=extrainfo) +} else { + # Output as 0-based tabular + resSorted <- data.frame(Chrom=seqnames(resSorted), + Start=start(resSorted) - 1, + End=end(resSorted), + Name=rep("DiffBind", length(resSorted)), + Score=rep("0", length(resSorted)), + Strand=gsub("\\*", ".", strand(resSorted)), + mcols(resSorted)) +} +write.table(resSorted, file = opt$outfile, sep="\t", quote = FALSE, append=TRUE, row.names = FALSE) # Output binding affinity scores if (!is.null(opt$bmatrix)) { bmat <- dba.peakset(sample_count, bRetrieve=TRUE, DataType=DBA_DATA_FRAME) - write.table(as.data.frame(bmat), file="bmatrix.tab", sep="\t", quote=FALSE, row.names=FALSE) + # Output as 0-based tabular + bmat <- data.frame(Chrom=bmat[, 1], + Start=bmat[, 2] - 1, + End=bmat[, 3], + bmat[, 4:ncol(bmat)]) + write.table(bmat, file="bmatrix.tab", sep="\t", quote=FALSE, row.names=FALSE) } # Output RData file |
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| diff -r fa56d93f7980 -r 1de83981d43c diffbind.xml --- a/diffbind.xml Thu Apr 19 17:15:53 2018 -0400 +++ b/diffbind.xml Wed May 30 12:25:42 2018 -0400 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="diffbind" name="DiffBind" version="2.6.6.2">\n+<tool id="diffbind" name="DiffBind" version="2.6.6.3">\n <description> differential binding analysis of ChIP-Seq peak data</description>\n <requirements>\n <requirement type="package" version="2.6.6">bioconductor-diffbind</requirement>\n@@ -106,7 +106,7 @@\n <inputs>\n <repeat name="rep_group" title="Group" min="2" max="2" default="2">\n <param name="groupName" type="text" label="Name"\n- help="Name for the Group that the peak and BAM files belong to e.g. Resistant/Responsive (two Groups in total must be specified for DiffBind). NOTE: Please only use letters, numbers or underscores.">\n+ help="Name for the Group that the peak and BAM files belong to e.g. Resistant/Responsive (two Groups must be specified for DiffBind). NOTE: Please only use letters, numbers or underscores.">\n <sanitizer>\n <valid initial="string.letters,string.digits"><add value="_" /></valid>\n </sanitizer>\n@@ -133,9 +133,9 @@\n <!-- Output Options -->\n <section name="out" expanded="false" title="Output Options">\n <param name="format" type="select" label="Output Format">\n+ <option value="interval" selected="True">Interval</option>\n <option value="bed">BED</option>\n- <option value="gff">GFF</option>\n- <option value="wig">WIG</option>\n+ <option value="tabular">Tabular (tab-separated)</option>\n </param>\n <param name="pdf" type="boolean" truevalue="True" falsevalue="" checked="False" label="Visualising the analysis results" help="output an additional PDF file" />\n <param name="binding_matrix" type="boolean" truevalue="True" falsevalue="" checked="False" label="Output binding affinity matrix?" help="Output a table of the binding scores" />\n@@ -146,7 +146,12 @@\n </inputs>\n \n <outputs>\n- <data name="outfile" format="tabular" label="${tool.name} on ${on_string}: Differentially bound sites" />\n+ <data name="outfile" format="interval" label="${tool.name} on ${on_string}: Differentially bound sites">\n+ <change_format>\n+ <when input="out.format" value="bed" format="bed" />\n+ <when input="out.format" value="tabular" format="tabular" />\n+ </change_format>\n+ </data>\n <data name="plots" format="pdf" label="${tool.name} on ${on_string}: Plots">\n <filter>out[\'pdf\']</filter>\n </data>\n@@ -165,34 +170,72 @@\n </outputs>\n \n <tests>\n+ <!-- Ensure outputs work -->\n <test expect_num_outputs="6">\n <repeat name="rep_group">\n <param name="groupName" value="Resistant"/>\n- <param name="peaks" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>\n+ <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>\n <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" />\n </repeat>\n <repeat name="rep_group">\n <param name="groupName" value="Responsive"/>\n- <param name="peaks" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/>\n+ <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/>\n <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" />\n </repeat>\n <param name="scorecol" value="5" />\n+ <param name="format" value="interval"/>\n <param name="pdf" value="True" />\n <param name="binding_matrix" value="True" />\n <param name="rdata" value="True" />\n <param name="rscript" value="True"/>\n <param name="analysis_info" value="True"/>\n- <output name="outfile" value="out_diffbind.tab" />\n+ <output name="outfile" ftype="interval" value="out_d'..b'\n-* **FDR**: a multiple testing corrected FDR p-value\n+* **Chrom**: Chromosome name\n+* **Start**: Start position of site\n+* **End**: End position of site\n+* **Score**: 0\n+* **Name**: DiffBind\n+* **Strand**: Strand\n+* **Comment**: The pipe ("|") separated values in this column correspond to:\n+\n+ * *width*: Length of site\n+ * *Conc*: Mean read concentration over all the samples (the default calculation uses log2 normalized ChIP read counts with control read counts subtracted)\n+ * *Conc_Group1*: Mean concentration over the first group (e.g. Responsive)\n+ * *Conc_Group2*: Mean concentration over second group (e.g. Resistant)\n+ * *Fold*: Fold shows the difference in mean concentrations between the two groups (e.g. Responsive - Resistant), with a positive value indicating increased binding affinity in the first group and a negative value indicating increased binding affinity in the second group.\n+ * *p.value*: P-value confidence measure for identifying these sites as differentially bound\n+ * *FDR*: a multiple testing corrected FDR p-value\n+\n+Example - **BED format**:\n+\n+ ===== ====== ====== ======== ===== ======\n+ Chrom Start End Name Score Strand\n+ ===== ====== ====== ======== ===== ======\n+ chr18 394599 396513 DiffBind 0 \\. \n+ chr18 111566 112005 DiffBind 0 \\. \n+ chr18 346463 347342 DiffBind 0 \\. \n+ chr18 399013 400382 DiffBind 0 \\. \n+ chr18 371109 372102 DiffBind 0 \\. \n+ ===== ====== ====== ======== ===== ======\n+\n+Example - **Tabular format**:\n+\n+ ===== ====== ====== ======== ===== ====== ==== =============== ============== ===== ======== ========\n+ Chrom Start End Name Score Strand Conc Conc_Responsive Conc_Resistant Fold p.value FDR\n+ ===== ====== ====== ======== ===== ====== ==== =============== ============== ===== ======== ========\n+ chr18 394599 396513 DiffBind 0 \\. 7.15 5.55 7.89 -2.35 7.06E-24 9.84E-21\n+ chr18 111566 112005 DiffBind 0 \\. 5.71 6.53 3.63 2.89 1.27E-08 8.88E-06\n+ chr18 346463 347342 DiffBind 0 \\. 5 5.77 3.24 2.52 6.51E-06 0.00303\n+ chr18 399013 400382 DiffBind 0 \\. 7.62 7 8.05 -1.04 1.04E-05 0.00364\n+ chr18 371109 372102 DiffBind 0 \\. 4.63 3.07 5.36 -2.3 8.10E-05 0.0226\n+ ===== ====== ====== ======== ===== ====== ==== =============== ============== ===== ======== ========\n \n \n **Binding Affinity Matrix**\n \n The final result of counting is a binding affinity matrix containing a (normalized) read count for each sample at every potential binding site. With this matrix, the samples can be re-clustered using affinity, rather than occupancy, data. The binding affinity matrix can be used for QC plotting as well as for subsequent\n-differential analysis.\n+differential analysis. Note that this output is a tabular 0-based format.\n \n Example:\n \n ===== ====== ====== ========= ========= ========== ==========\n- CHR START END MCF7_ER_1 MCF7_ER_2 BT474_ER_1 BT474_ER_2\n+ Chrom Start End MCF7_ER_1 MCF7_ER_2 BT474_ER_1 BT474_ER_2\n ===== ====== ====== ========= ========= ========== ==========\n chr18 111567 112005 137.6152 59.87837 29.41393 19.95945\n chr18 189223 189652 19.95945 12.60597 11.55547 23.11095\n@@ -426,6 +499,8 @@\n .. _`Bioconductor package`: https://bioconductor.org/packages/release/bioc/html/DiffBind.html\n .. _`DiffBind User Guide`: https://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf\n .. _`Bioconductor post`: https://support.bioconductor.org/p/69924/\n+.. _here: https://galaxyproject.org/learn/datatypes/#interval\n+.. _`Biostars post`: https://www.biostars.org/p/84686/\n \n ]]>\n </help>\n' |
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| diff -r fa56d93f7980 -r 1de83981d43c test-data/DiffBind_analysis.RData |
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| Binary file test-data/DiffBind_analysis.RData has changed |
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| diff -r fa56d93f7980 -r 1de83981d43c test-data/out_analysis_info.txt --- a/test-data/out_analysis_info.txt Thu Apr 19 17:15:53 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,83 +0,0 @@ -dba.count Info - -4 Samples, 1394 sites in matrix (2141 total): - ID Tissue Condition Caller Intervals -1 MCF7_ER_1_bed MCF7_ER_1_bed Responsive macs 1556 -2 MCF7_ER_2_bed MCF7_ER_2_bed Responsive macs 1046 -3 BT474_ER_1_bed BT474_ER_1_bed Resistant macs 1080 -4 BT474_ER_2_bed BT474_ER_2_bed Resistant macs 1122 - -dba.analyze Info - -4 Samples, 1394 sites in matrix: - ID Tissue Condition Caller Intervals FRiP -1 MCF7_ER_1_bed MCF7_ER_1_bed Responsive counts 1394 0.38 -2 MCF7_ER_2_bed MCF7_ER_2_bed Responsive counts 1394 0.22 -3 BT474_ER_1_bed BT474_ER_1_bed Resistant counts 1394 0.27 -4 BT474_ER_2_bed BT474_ER_2_bed Resistant counts 1394 0.25 - -1 Contrast: - Group1 Members1 Group2 Members2 DB.DESeq2 -1 Responsive 2 Resistant 2 5 - -SessionInfo - -R version 3.4.1 (2017-06-30) -Platform: x86_64-apple-darwin14.5.0 (64-bit) -Running under: OS X El Capitan 10.11.6 - -Matrix products: default -BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib -LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib - -locale: -[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_US.UTF-8 - -attached base packages: -[1] parallel stats4 methods stats graphics grDevices utils -[8] datasets base - -other attached packages: - [1] bindrcpp_0.2 rjson_0.2.15 - [3] DiffBind_2.6.6 SummarizedExperiment_1.8.0 - [5] DelayedArray_0.4.1 matrixStats_0.52.2 - [7] Biobase_2.38.0 GenomicRanges_1.30.3 - [9] GenomeInfoDb_1.14.0 IRanges_2.12.0 -[11] S4Vectors_0.16.0 BiocGenerics_0.24.0 -[13] getopt_1.20.0 - -loaded via a namespace (and not attached): - [1] Category_2.44.0 bitops_1.0-6 bit64_0.9-5 - [4] RColorBrewer_1.1-2 progress_1.1.2 httr_1.3.1 - [7] Rgraphviz_2.22.0 tools_3.4.1 backports_1.0.5 - [10] R6_2.2.2 rpart_4.1-13 KernSmooth_2.23-15 - [13] Hmisc_4.0-3 DBI_0.8 lazyeval_0.2.1 - [16] colorspace_1.3-2 nnet_7.3-12 gridExtra_2.3 - [19] DESeq2_1.18.1 prettyunits_1.0.2 bit_1.1-12 - [22] compiler_3.4.1 sendmailR_1.2-1 graph_1.56.0 - [25] htmlTable_1.9 labeling_0.3 rtracklayer_1.38.0 - [28] caTools_1.17.1 scales_0.5.0 checkmate_1.8.2 - [31] BatchJobs_1.6 genefilter_1.60.0 RBGL_1.54.0 - [34] stringr_1.3.0 digest_0.6.12 Rsamtools_1.30.0 - [37] foreign_0.8-67 AnnotationForge_1.20.0 XVector_0.18.0 - [40] htmltools_0.3.6 base64enc_0.1-3 pkgconfig_2.0.1 - [43] limma_3.34.6 htmlwidgets_1.0 rlang_0.2.0 - [46] RSQLite_2.0 BBmisc_1.11 bindr_0.1.1 - [49] GOstats_2.44.0 hwriter_1.3.2 BiocParallel_1.12.0 - [52] gtools_3.5.0 acepack_1.4.1 dplyr_0.7.4 - [55] RCurl_1.95-4.8 magrittr_1.5 Formula_1.2-1 - [58] GO.db_3.5.0 GenomeInfoDbData_0.99.1 Matrix_1.2-12 - [61] Rcpp_0.12.15 munsell_0.4.3 stringi_1.1.6 - [64] edgeR_3.20.7 zlibbioc_1.24.0 gplots_3.0.1 - [67] fail_1.3 plyr_1.8.4 grid_3.4.1 - [70] blob_1.1.1 ggrepel_0.7.0 gdata_2.18.0 - [73] lattice_0.20-34 Biostrings_2.46.0 splines_3.4.1 - [76] GenomicFeatures_1.28.5 annotate_1.56.0 locfit_1.5-9.1 - [79] knitr_1.20 pillar_1.2.1 systemPipeR_1.12.0 - [82] geneplotter_1.56.0 biomaRt_2.34.2 glue_1.2.0 - [85] XML_3.98-1.6 ShortRead_1.36.0 latticeExtra_0.6-28 - [88] data.table_1.10.4 gtable_0.2.0 amap_0.8-14 - [91] assertthat_0.2.0 ggplot2_2.2.1 xtable_1.8-2 - [94] survival_2.40-1 tibble_1.4.2 pheatmap_1.0.8 - [97] GenomicAlignments_1.14.1 AnnotationDbi_1.40.0 memoise_1.1.0 -[100] cluster_2.0.6 brew_1.0-6 GSEABase_1.40.0 |
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| diff -r fa56d93f7980 -r 1de83981d43c test-data/out_binding.matrix --- a/test-data/out_binding.matrix Thu Apr 19 17:15:53 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,1395 +0,0 @@\n-CHR\tSTART\tEND\tMCF7_ER_1_bed\tMCF7_ER_2_bed\tBT474_ER_1_bed\tBT474_ER_2_bed\n-chr18\t111567\t112005\t137.615208000375\t59.878372946728\t29.4139375878664\t19.9594576489093\n-chr18\t189223\t189652\t19.9594576489093\t12.6059732519427\t11.5554754809475\t23.110950961895\n-chr18\t215232\t216063\t11.5554754809475\t15.7574665649284\t31.5149331298568\t72.4843461986707\n-chr18\t311530\t312172\t17.8584621069189\t11.5554754809475\t54.6258840917518\t43.0704086108043\n-chr18\t346464\t347342\t75.6358395116564\t40.9694130688139\t21.0099554199046\t16.8079643359236\n-chr18\t356560\t357362\t11.5554754809475\t14.7069687939332\t57.7773774047375\t53.5753863207566\n-chr18\t371110\t372102\t8.40398216796182\t9.45447993895705\t81.9388261376278\t82.989323908623\n-chr18\t394600\t396513\t56.7268796337423\t43.0704086108043\t510.541916703681\t438.05757050501\n-chr18\t399014\t400382\t156.524167878289\t117.655750351465\t558.864814169461\t496.885445680743\n-chr18\t498906\t500200\t767.913870597511\t278.381909313735\t196.443083176108\t181.736114382174\n-chr18\t503518\t504552\t99.7972882445466\t61.9793684887184\t194.342087634117\t231.10950961895\n-chr18\t531672\t532439\t44.1209063817996\t23.110950961895\t57.7773774047375\t73.5348439696659\n-chr18\t568036\t569332\t165.978647817246\t157.574665649284\t207.998558657055\t221.655029679993\n-chr18\t589046\t589875\t50.4238930077709\t72.4843461986707\t117.655750351466\t149.170683481322\n-chr18\t651923\t652540\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t657092\t657876\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t770235\t770992\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t832068\t832623\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t845064\t845849\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t922955\t924107\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t995240\t996193\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t1075317\t1075949\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t1147156\t1148528\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t1150202\t1150753\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t1220993\t1221400\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t1221403\t1222223\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t1241658\t1242294\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t1269916\t1270558\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t1302131\t1303494\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t1359568\t1360093\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t1392692\t1393631\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t1394274\t1394992\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t1460102\t1460758\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t1618037\t1618797\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t1903962\t1904450\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t1905463\t1907085\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t1995317\t1995795\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t2070406\t2071263\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t2084320\t2084599\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t2096239\t2097152\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t2156043\t2156770\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t2171820\t2172243\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t2185313\t2185959\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t2189792\t2190434\t1.05049777099523\t1.'..b'-chr18\t74662083\t74662612\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t74664965\t74666178\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t74755273\t74755853\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t74766525\t74767180\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t74800752\t74801820\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t74805140\t74805915\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t74813207\t74813783\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t74826803\t74827698\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t74850113\t74850847\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t74967232\t74968167\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t74974177\t74975856\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t75162079\t75162656\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t75306150\t75306689\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t75404862\t75405830\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t75463876\t75464359\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76166820\t76167943\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76212084\t76212732\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76244283\t76244913\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76247276\t76247878\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76355382\t76355883\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76382039\t76382699\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76398929\t76399745\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76431621\t76432094\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76528540\t76529917\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76533867\t76534686\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76566546\t76567310\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76574330\t76575226\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76652675\t76653264\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76653336\t76654222\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76734601\t76735073\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76749882\t76750469\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76759894\t76760344\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t76822532\t76823743\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t77062037\t77062828\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t77173663\t77174478\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t77300430\t77301170\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t77424530\t77425198\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t77438941\t77440103\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t77541065\t77541645\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t77694136\t77695082\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t77725047\t77725936\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t77968049\t77968792\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n-chr18\t77987486\t77988208\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n' |
| b |
| diff -r fa56d93f7980 -r 1de83981d43c test-data/out_binding_matrix.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_binding_matrix.tab Wed May 30 12:25:42 2018 -0400 |
| b |
| b'@@ -0,0 +1,1395 @@\n+Chrom\tStart\tEnd\tMCF7_ER_1_bed_gz\tMCF7_ER_2_bed_gz\tBT474_ER_1_bed_gz\tBT474_ER_2_bed_gz\n+chr18\t111566\t112005\t137.615208000375\t59.878372946728\t29.4139375878664\t19.9594576489093\n+chr18\t189222\t189652\t19.9594576489093\t12.6059732519427\t11.5554754809475\t23.110950961895\n+chr18\t215231\t216063\t11.5554754809475\t15.7574665649284\t31.5149331298568\t72.4843461986707\n+chr18\t311529\t312172\t17.8584621069189\t11.5554754809475\t54.6258840917518\t43.0704086108043\n+chr18\t346463\t347342\t75.6358395116564\t40.9694130688139\t21.0099554199046\t16.8079643359236\n+chr18\t356559\t357362\t11.5554754809475\t14.7069687939332\t57.7773774047375\t53.5753863207566\n+chr18\t371109\t372102\t8.40398216796182\t9.45447993895705\t81.9388261376278\t82.989323908623\n+chr18\t394599\t396513\t56.7268796337423\t43.0704086108043\t510.541916703681\t438.05757050501\n+chr18\t399013\t400382\t156.524167878289\t117.655750351465\t558.864814169461\t496.885445680743\n+chr18\t498905\t500200\t767.913870597511\t278.381909313735\t196.443083176108\t181.736114382174\n+chr18\t503517\t504552\t99.7972882445466\t61.9793684887184\t194.342087634117\t231.10950961895\n+chr18\t531671\t532439\t44.1209063817996\t23.110950961895\t57.7773774047375\t73.5348439696659\n+chr18\t568035\t569332\t165.978647817246\t157.574665649284\t207.998558657055\t221.655029679993\n+chr18\t589045\t589875\t50.4238930077709\t72.4843461986707\t117.655750351466\t149.170683481322\n+chr18\t651922\t652540\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t657091\t657876\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t770234\t770992\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t832067\t832623\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t845063\t845849\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t922954\t924107\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t995239\t996193\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t1075316\t1075949\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t1147155\t1148528\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t1150201\t1150753\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t1220992\t1221400\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t1221402\t1222223\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t1241657\t1242294\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t1269915\t1270558\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t1302130\t1303494\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t1359567\t1360093\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t1392691\t1393631\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t1394273\t1394992\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t1460101\t1460758\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t1618036\t1618797\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t1903961\t1904450\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t1905462\t1907085\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t1995316\t1995795\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t2070405\t2071263\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t2084319\t2084599\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t2096238\t2097152\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t2156042\t2156770\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t2171819\t2172243\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t2185312\t2185959\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t2189791\t2190434\t1.050'..b'+chr18\t74662082\t74662612\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t74664964\t74666178\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t74755272\t74755853\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t74766524\t74767180\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t74800751\t74801820\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t74805139\t74805915\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t74813206\t74813783\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t74826802\t74827698\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t74850112\t74850847\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t74967231\t74968167\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t74974176\t74975856\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t75162078\t75162656\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t75306149\t75306689\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t75404861\t75405830\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t75463875\t75464359\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t76166819\t76167943\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t76212083\t76212732\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t76244282\t76244913\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t76247275\t76247878\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t76355381\t76355883\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t76382038\t76382699\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t76398928\t76399745\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t76431620\t76432094\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t76528539\t76529917\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t76533866\t76534686\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t76566545\t76567310\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t76574329\t76575226\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t76652674\t76653264\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t76653335\t76654222\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t76734600\t76735073\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t76749881\t76750469\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t76759893\t76760344\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t76822531\t76823743\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t77062036\t77062828\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t77173662\t77174478\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t77300429\t77301170\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t77424529\t77425198\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t77438940\t77440103\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t77541064\t77541645\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t77694135\t77695082\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t77725046\t77725936\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t77968048\t77968792\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n+chr18\t77987485\t77988208\t1.05049777099523\t1.05049777099523\t1.05049777099523\t1.05049777099523\n' |
| b |
| diff -r fa56d93f7980 -r 1de83981d43c test-data/out_diffbind.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_diffbind.bed Wed May 30 12:25:42 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +Chrom Start End Name Score Strand +chr18 394599 396513 DiffBind 0 . +chr18 111566 112005 DiffBind 0 . +chr18 346463 347342 DiffBind 0 . +chr18 399013 400382 DiffBind 0 . +chr18 371109 372102 DiffBind 0 . |
| b |
| diff -r fa56d93f7980 -r 1de83981d43c test-data/out_diffbind.interval --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_diffbind.interval Wed May 30 12:25:42 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +Chrom Start End Name Score Strand Comment +chr18 394599 396513 DiffBind 0 . 1914|7.15|5.55|7.89|-2.35|7.06e-24|9.84e-21 +chr18 111566 112005 DiffBind 0 . 439|5.71|6.53|3.63|2.89|1.27e-08|8.88e-06 +chr18 346463 347342 DiffBind 0 . 879|5|5.77|3.24|2.52|6.51e-06|0.00303 +chr18 399013 400382 DiffBind 0 . 1369|7.62|7|8.05|-1.04|1.04e-05|0.00364 +chr18 371109 372102 DiffBind 0 . 993|4.63|3.07|5.36|-2.3|8.1e-05|0.0226 |
| b |
| diff -r fa56d93f7980 -r 1de83981d43c test-data/out_diffbind.tab --- a/test-data/out_diffbind.tab Thu Apr 19 17:15:53 2018 -0400 +++ b/test-data/out_diffbind.tab Wed May 30 12:25:42 2018 -0400 |
| b |
| @@ -1,6 +1,6 @@ -seqnames start end width strand Conc Conc_Responsive Conc_Resistant Fold p.value FDR -chr18 394600 396513 1914 * 7.15 5.55 7.89 -2.35 7.06e-24 9.84e-21 -chr18 111567 112005 439 * 5.71 6.53 3.63 2.89 1.27e-08 8.88e-06 -chr18 346464 347342 879 * 5 5.77 3.24 2.52 6.51e-06 0.00303 -chr18 399014 400382 1369 * 7.62 7 8.05 -1.04 1.04e-05 0.00364 -chr18 371110 372102 993 * 4.63 3.07 5.36 -2.3 8.1e-05 0.0226 +Chrom Start End Name Score Strand Conc Conc_Responsive Conc_Resistant Fold p.value FDR +chr18 394599 396513 DiffBind 0 . 7.15 5.55 7.89 -2.35 7.06e-24 9.84e-21 +chr18 111566 112005 DiffBind 0 . 5.71 6.53 3.63 2.89 1.27e-08 8.88e-06 +chr18 346463 347342 DiffBind 0 . 5 5.77 3.24 2.52 6.51e-06 0.00303 +chr18 399013 400382 DiffBind 0 . 7.62 7 8.05 -1.04 1.04e-05 0.00364 +chr18 371109 372102 DiffBind 0 . 4.63 3.07 5.36 -2.3 8.1e-05 0.0226 |
| b |
| diff -r fa56d93f7980 -r 1de83981d43c test-data/out_rscript.txt --- a/test-data/out_rscript.txt Thu Apr 19 17:15:53 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,119 +0,0 @@ -## Setup R error handling to go to stderr -options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) -# we need that to not crash galaxy with an UTF8 error on German LC settings. -Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") - -suppressPackageStartupMessages({ - library('getopt') - library('DiffBind') - library('rjson') -}) - -options(stringAsfactors = FALSE, useFancyQuotes = FALSE) -args <- commandArgs(trailingOnly = TRUE) - -#get options, using the spec as defined by the enclosed list. -#we read the options from the default: commandArgs(TRUE). -spec = matrix(c( - 'infile' , 'i', 1, "character", - 'outfile' , 'o', 1, "character", - 'scorecol', 'n', 1, "integer", - 'lowerbetter', 'l', 1, "logical", - 'summits', 's', 1, "integer", - 'th', 't', 1, "double", - 'format', 'f', 1, "character", - 'plots' , 'p', 2, "character", - 'bmatrix', 'b', 0, "logical", - "rdaOpt", "r", 0, "logical", - 'infoOpt' , 'a', 0, "logical", - 'verbose', 'v', 2, "integer", - 'help' , 'h', 0, "logical" -), byrow=TRUE, ncol=4); - -opt = getopt(spec); - -# if help was asked for print a friendly message -# and exit with a non-zero error code -if ( !is.null(opt$help) ) { - cat(getopt(spec, usage=TRUE)); - q(status=1); -} - -parser <- newJSONParser() -parser$addData(opt$infile) -factorList <- parser$getObject() -filenamesIn <- unname(unlist(factorList[[1]][[2]])) -peaks <- filenamesIn[grepl("peaks.bed", filenamesIn)] -bams <- filenamesIn[grepl("bamreads.bam", filenamesIn)] -ctrls <- filenamesIn[grepl("bamcontrol.bam", filenamesIn)] - -# get the group and sample id from the peaks filenames -groups <- sapply(strsplit(peaks,"-"), `[`, 1) -samples <- sapply(strsplit(peaks,"-"), `[`, 2) - -if ( length(ctrls) != 0 ) { - sampleTable <- data.frame(SampleID=samples, - Condition=groups, - bamReads=bams, - bamControl=ctrls, - Peaks=peaks, - Tissue=samples, # using "Tissue" column to display ids as labels in PCA plot - stringsAsFactors=FALSE) -} else { - sampleTable <- data.frame(SampleID=samples, - Replicate=samples, - Condition=groups, - bamReads=bams, - Peaks=peaks, - Tissue=samples, - stringsAsFactors=FALSE) -} - -sample = dba(sampleSheet=sampleTable, peakFormat='bed', scoreCol=opt$scorecol, bLowerScoreBetter=opt$lowerbetter) - -if ( !is.null(opt$summits) ) { - sample_count = dba.count(sample, summits=opt$summits) -} else { - sample_count = dba.count(sample) -} - -sample_contrast = dba.contrast(sample_count, categories=DBA_CONDITION, minMembers=2) -sample_analyze = dba.analyze(sample_contrast) -diff_bind = dba.report(sample_analyze, th=opt$th) - -# Generate plots -if ( !is.null(opt$plots) ) { - pdf(opt$plots) - orvals = dba.plotHeatmap(sample_analyze, contrast=1, correlations=FALSE, cexCol=0.8, th=opt$th) - dba.plotPCA(sample_analyze, contrast=1, th=opt$th, label=DBA_TISSUE, labelSize=0.3) - dba.plotMA(sample_analyze, th=opt$th) - dba.plotVolcano(sample_analyze, th=opt$th) - dba.plotBox(sample_analyze, th=opt$th) - dev.off() -} - -# Output differential binding sites -resSorted <- diff_bind[order(diff_bind$FDR),] -write.table(as.data.frame(resSorted), file = opt$outfile, sep="\t", quote = FALSE, append=TRUE, row.names = FALSE) - -# Output binding affinity scores -if (!is.null(opt$bmatrix)) { - bmat <- dba.peakset(sample_count, bRetrieve=TRUE, DataType=DBA_DATA_FRAME) - write.table(as.data.frame(bmat), file="bmatrix.tab", sep="\t", quote=FALSE, row.names=FALSE) -} - -# Output RData file -if (!is.null(opt$rdaOpt)) { - save.image(file = "DiffBind_analysis.RData") -} - -# Output analysis info -if (!is.null(opt$infoOpt)) { - info <- "DiffBind_analysis_info.txt" - cat("dba.count Info\n\n", file=info, append = TRUE) - capture.output(sample, file=info, append=TRUE) - cat("\ndba.analyze Info\n\n", file=info, append = TRUE) - capture.output(sample_analyze, file=info, append=TRUE) - cat("\nSessionInfo\n\n", file=info, append = TRUE) - capture.output(sessionInfo(), file=info, append=TRUE) -} \ No newline at end of file |