Mercurial > repos > bgruening > diffbind
changeset 10:d7725c5596ab draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit f970dcbe9d0e4c3714b1db74c404ea34223cf8ed
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 04:51:25 -0400 |
| parents | 6171163112de |
| children | 4c7ab9995f9e |
| files | diffbind.R diffbind.xml test-data/DiffBind_analysis.RData test-data/out_plots.pdf |
| diffstat | 4 files changed, 98 insertions(+), 84 deletions(-) [+] |
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--- a/diffbind.R Sun Jan 28 05:10:25 2018 -0500 +++ b/diffbind.R Tue Mar 20 04:51:25 2018 -0400 @@ -21,7 +21,8 @@ 'infile' , 'i', 1, "character", 'format', 'f', 1, "character", 'th', 't', 1, "double", - 'bmatrix', 'b', 0, "logical" + 'bmatrix', 'b', 0, "logical", + "rdaOpt", "r", 0, "logical" ), byrow=TRUE, ncol=4); opt = getopt(spec); @@ -43,6 +44,7 @@ sample_analyze = dba.analyze(sample_contrast) diff_bind = dba.report(sample_analyze) orvals = dba.plotHeatmap(sample_analyze, contrast=1, correlations=FALSE) +dev.off() 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, col.names = FALSE) @@ -53,5 +55,10 @@ write.table(as.data.frame(bmat), file="bmatrix.tab", sep="\t", quote=FALSE, row.names=FALSE, col.names=FALSE) } -dev.off() +## Output RData file + +if (!is.null(opt$rdaOpt)) { + save.image(file = "DiffBind_analysis.RData") +} + sessionInfo()
--- a/diffbind.xml Sun Jan 28 05:10:25 2018 -0500 +++ b/diffbind.xml Tue Mar 20 04:51:25 2018 -0400 @@ -1,10 +1,8 @@ -<tool id="diffbind" name="DiffBind" version="2.6.5.0"> +<tool id="diffbind" name="DiffBind" version="2.6.6.0"> <description> differential binding analysis of ChIP-Seq peak data</description> <requirements> - <requirement type="package" version="2.6.5">bioconductor-diffbind</requirement> + <requirement type="package" version="2.6.6">bioconductor-diffbind</requirement> <requirement type="package" version="1.20.0">r-getopt</requirement> - <!--added rmysql requirement to remove: "Warning: namespace ‘RMySQL’ is not available"--> - <requirement type="package" version="0.10.11">r-rmysql</requirement> </requirements> <stdio> <regex match="Execution halted" @@ -21,7 +19,7 @@ description="An undefined error occured, please check your intput carefully and contact your administrator." /> </stdio> <version_command><![CDATA[ -echo $(R --version | grep version | grep -v GNU)", DiffBind version" $(R --vanilla --slave -e "library(DiffBind); cat(sessionInfo()\$otherPkgs\$DiffBind\$Version)" 2> /dev/null | grep -v -i "WARNING: ")," getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rmysql version" $(R --vanilla --slave -e "library(rmysql); cat(sessionInfo()\$otherPkgs\$rmysql\$Version)" 2> /dev/null | grep -v -i "WARNING: ") +echo $(R --version | grep version | grep -v GNU)", DiffBind version" $(R --vanilla --slave -e "library(DiffBind); cat(sessionInfo()\$otherPkgs\$DiffBind\$Version)" 2> /dev/null | grep -v -i "WARNING: ") ]]></version_command> <command><![CDATA[ ## seems that diffbind also needs file extensions to work properly @@ -39,13 +37,17 @@ Rscript '$__tool_directory__/diffbind.R' -i $infile -o '$outfile' + -t $th + -f $out.format -p '$plots' - -f $format - -t $th - #if $binding_affinity_matrix: + #if $out.binding_matrix: -b #end if + + #if $out.rdata: + -r + #end if ]]> </command> <configfiles> @@ -66,7 +68,7 @@ #end for]]></configfile> </configfiles> <inputs> - <repeat name="samples" title="Samples" min="2"> + <repeat name="samples" title="Samples" min="4"> <param name="sample_id" type="text" value="Sample ID" label="Specify a sample id" help="e.g. BT474.1-" /> <param name="tissue" type="text" value="Tissue" label="Specify the tissue" help="e.g. BT474" /> <param name="factor" type="text" value="Factor Name" label="Specify a factor name" help="e.g. ER" /> @@ -79,32 +81,41 @@ <param name="th" type="float" value="1" min="0" max="1" label="FDR Threshold" help="Significance threshold; all sites with FDR less than or equal to this value will be included in the report. A value of 1 will include all binding sites in the report. Default: 1"/> - <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true" - label="Visualising the analysis results" - help="output an additional PDF file" /> - <param name="format" type="select" label="Output Format"> - <option value="bed">BED</option> - <option value="gff">GFF</option> - <option value="wig">WIG</option> - </param> - <param name="binding_affinity_matrix" type="boolean" truevalue="True" falsevalue="" checked="False" label="Output binding affinity matrix?" help="Output a table of the binding scores" /> + + <!-- Output Options --> + <section name="out" expanded="false" title="Output Options"> + <param name="format" type="select" label="Output Format"> + <option value="bed">BED</option> + <option value="gff">GFF</option> + <option value="wig">WIG</option> + </param> + <param name="pdf" type="boolean" truevalue="True" falsevalue="" checked="False" label="Visualising the analysis results" help="output an additional PDF file" /> + <param name="binding_matrix" type="boolean" truevalue="True" falsevalue="" checked="False" label="Output binding affinity matrix?" help="Output a table of the binding scores" /> + <param name="rdata" type="boolean" truevalue="True" falsevalue="" checked="False" label="Output RData file?" help="Output all the data used by R to construct the plots and tables, can be loaded into R. Default: No"> + </param> + </section> </inputs> + <outputs> - <data name="outfile" format="bed" label="Differential binding sites on ${on_string}"> + <data name="outfile" format="bed" label="${tool.name} on ${on_string}: Differentially bound sites"> <change_format> <when input="format" value="wig" format="wig" /> <when input="format" value="gff" format="gff" /> </change_format> </data> - <data name="plots" format="pdf" label="Differential binding sites on ${on_string}"> - <filter>pdf == True</filter> + <data name="plots" format="pdf" label="${tool.name} on ${on_string}: Plots"> + <filter>out['pdf']</filter> </data> - <data name="binding_matrix" format="tabular" from_work_dir="bmatrix.tab" label="Differential binding sites on ${on_string}"> - <filter>binding_affinity_matrix == True</filter> + <data name="binding_matrix" format="tabular" from_work_dir="bmatrix.tab" label="${tool.name} on ${on_string}: Binding matrix"> + <filter>out['binding_matrix']</filter> + </data> + <data name="rdata" format="rdata" from_work_dir="DiffBind_analysis.RData" label="${tool.name} on ${on_string}: RData file"> + <filter>out['rdata']</filter> </data> </outputs> + <tests> - <test> + <test expect_num_outputs="4"> <repeat name="samples"> <param name="sample_id" value="BT4741" /> <param name="tissue" value="BT474" /> @@ -142,9 +153,12 @@ <param name="peaks" ftype="bed" value="MCF7_ER_2.bed.gz" /> </repeat> <param name="pdf" value="True" /> - <param name="binding_affinity_matrix" value="True" /> + <param name="binding_matrix" value="True" /> + <param name="rdata" value="True" /> <output name="outfile" value="out_diffbind.bed" /> + <output name="plots" value="out_plots.pdf" compare="sim_size" /> <output name="binding_matrix" value="out_binding.matrix" /> + <output name="rdata" value="DiffBind_analysis.RData" compare="sim_size"/> </test> </tests> <help><![CDATA[ @@ -166,7 +180,7 @@ in peak sets, and identifying statistically significantly differentially bound sites based on evidence of binding affinity (measured by differences in read densities). To this end it uses statistical routines developed in an RNA-Seq context (primarily the Bioconductor packages -edgeR and DESeq2 ). Additionally, the package builds on Rgraphics routines to provide a +edgeR and DESeq2). Additionally, the package builds on Rgraphics routines to provide a set of standardized plots to aid in binding analysis. The `DiffBind User Guide`_ includes a brief overview of the processing flow, followed by four sections of @@ -182,6 +196,8 @@ .. _`Bioconductor package`: https://bioconductor.org/packages/release/bioc/html/DiffBind.html .. _`DiffBind User Guide`: https://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf +----- + **Inputs** DiffBind works primarily with peaksets, which are sets of genomic intervals representing @@ -194,7 +210,7 @@ **Sample Information** -You have to specify your sample information in the tool form above. +You have to specify your sample information in the tool form above, where Condition contains the groups you want to compare. Example: @@ -214,26 +230,6 @@ ZR752 ZR75 ER Responsive 2 ============= ========== ========== ============= ============= -Or provide a sample sheet tabular file such as below. - -Example: - - ======== ====== ====== ========== ========== ========= ==================== ========= ===================== ================= ========== - SampleID Tissue Factor Condition Treatment Replicate bamReads ControlID bamControl Peaks PeakCaller - ======== ====== ====== ========== ========== ========= ==================== ========= ===================== ================= ========== - BT4741 BT474 ER Resistant Full-Media 1 Chr18_BT474_ER_1.bam BT474c Chr18_BT474_input.bam BT474_ER_1.bed.gz bed - BT4742 BT474 ER Resistant Full-Media 2 Chr18_BT474_ER_2.bam BT474c Chr18_BT474_input.bam BT474_ER_2.bed.gz bed - MCF71 MCF7 ER Responsive Full-Media 1 Chr18_MCF7_ER_1.bam MCF7c Chr18_MCF7_input.bam MCF7_ER_1.bed.gz bed - MCF72 MCF7 ER Responsive Full-Media 2 Chr18_MCF7_ER_2.bam MCF7c Chr18_MCF7_input.bam MCF7_ER_2.bed.gz bed - MCF73 MCF7 ER Responsive Full-Media 3 Chr18_MCF7_ER_3.bam MCF7c Chr18_MCF7_input.bam MCF7_ER_3.bed.gz bed - T47D1 T47D ER Responsive Full-Media 1 Chr18_T47D_ER_1.bam T47Dc Chr18_T47D_input.bam T47D_ER_1.bed.gz bed - T47D2 T47D ER Responsive Full-Media 2 Chr18_T47D_ER_2.bam T47Dc Chr18_T47D_input.bam T47D_ER_2.bed.gz bed - MCF7r1 MCF7 ER Resistant Full-Media 1 Chr18_TAMR_ER_1.bam TAMRc Chr18_TAMR_input.bam TAMR_ER_1.bed.gz bed - MCF7r2 MCF7 ER Resistant Full-Media 2 Chr18_TAMR_ER_2.bam TAMRc Chr18_TAMR_input.bam TAMR_ER_2.bed.gz bed - ZR751 ZR75 ER Responsive Full-Media 1 Chr18_ZR75_ER_1.bam ZR75c Chr18_ZR75_input.bam ZR75_ER_1.bed.gz bed - ZR752 ZR75 ER Responsive Full-Media 2 Chr18_ZR75_ER_2.bam ZR75c Chr18_ZR75_input.bam ZR75_ER_2.bed.gz bed - ======== ====== ====== ========== ========== ========= ==================== ========= ===================== ================= ========== - **Peak files** @@ -259,37 +255,49 @@ * BAM file which contains the mapped sequencing reads can be associated with each peakset * Control BAM file represents a control dataset and are optional, but have to specified for all when used. +----- **Outputs** +This tool outputs + + * differentially bound sites in BED, WIG or GFF format + +Optionally, under **Output Options** you can choose to output + + * a correlation heatmap plot + * a binding affinity matrix + * an RData file + +**Differentially Bound Sites** + As output format you can choose BED, GFF, WIG. -Example: - -======== ====== =======+ -seqnames ranges strand Conc Conc_Resistant +Example - BED format: -2452 chr18 [64490686, 64491186] * | 6.36 1.39 -1291 chr18 [34597713, 34598213] * | 5.33 0.22 -976 chr18 [26860997, 26861497] * | 7.3 3.13 -2338 chr18 [60892900, 60893400] * | 7.13 1.84 -2077 chr18 [55569087, 55569587] * | 5.52 1.89 + ===== ====== ====== ===== ==== ==== ==== ==== ===== ======== ======== + 1 2 3 4 5 6 7 8 9 10 **11** + ===== ====== ====== ===== ==== ==== ==== ==== ===== ======== ======== + chr18 394600 396513 1914 * 7.15 7.89 5.55 2.35 7.06e-24 9.84e-21 + chr18 111567 112005 439 * 5.71 3.63 6.53 -2.89 1.27e-08 8.88e-06 + chr18 346464 347342 879 * 5 3.24 5.77 -2.52 6.51e-06 0.00303 + chr18 399014 400382 1369 * 7.62 8.05 7 1.04 1.04e-05 0.00364 + chr18 371110 372102 993 * 4.63 5.36 3.07 2.3 8.1e-05 0.0226 + ===== ====== ====== ===== ==== ==== ==== ==== ===== ======== ======== -Conc_Responsive Fold p-value FDR -<numeric> <numeric> <numeric> <numeric> -2452 7 -5.61 3.57e-10 1.02e-06 -1291 5.97 -5.75 1.1e-09 1.57e-06 -976 7.92 -4.79 1.1e-08 1.05e-05 -2338 7.77 -5.93 1.68e-08 1.17e-05 -2077 6.13 -4.23 2.36e-08 1.17e-05 + Columns contain the following data: -The value columns show the -Conc mean read concentration over all the samples (the default calculation uses log2 normalized ChIP read counts with control read counts subtracted) -Conc_Resistant mean concentration over the first (Resistant) group -Conc_Responsive mean concentration over second (Responsive) group -Fold column shows the difference in mean concentrations between the two groups (Conc_Resistant - Conc_Responsive), with a positive value indicating increased binding affinity in the Resistant group and a negative value indicating increased binding affinity in the Responsive group. -p-value confidence measure for identifying these sites as differentially bound -FDR a multiple testing corrected FDR p-value +* **1st**: Chromosome name +* **2nd**: Start position of site +* **3rd**: End position of site +* **4th**: Length of site +* **5th**: Strand +* **6th**: Mean read concentration over all the samples (the default calculation uses log2 normalized ChIP read counts with control read counts subtracted) +* **7th**: Mean concentration over the first (e.g. Resistant) group +* **8th**: Mean concentration over second (e.g. Responsive) group +* **9th**: Fold shows the difference in mean concentrations between the two groups (e.g. Resistant - Responsive), with a positive value indicating increased binding affinity in the first group and a negative value indicating increased binding affinity in the second group. +* **10th**: P-value confidence measure for identifying these sites as differentially bound +* **11th**: a multiple testing corrected FDR p-value **Binding Affinity Matrix** @@ -315,7 +323,7 @@ ZR752 ZR75 ER Responsive Full-Media 2 counts 2845 0.22 ====== ====== ====== ========== ========== ========= ====== ========= ==== - +----- **More Information** @@ -328,21 +336,18 @@ #. Plotting and reporting - * **Reading in peaksets**: +**Reading in peaksets**: The first step is to read in a set of peaksets and associated -metadata. Peaksets are derived either from ChIP-Seq peak callers, such as MACS -([1]), or using some other criterion (e.g. genomic windows, or all the promoter regions -in a genome). The easiest way to read in peaksets is using a comma-separated value -(csv) sample sheet with one line for each peakset. (Spreadsheets in Excel® format, with -a .xls or .xlsx suffix, are also accepted.) A single experiment can have more than +metadata. Peaksets are derived either from ChIP-Seq peak callers, such as **MACS2**, or using some other criterion (e.g. genomic windows, or all the promoter regions +in a genome). A single experiment can have more than one associated peakset; e.g. if multiple peak callers are used for comparison purposes each sample would have more than one line in the sample sheet. Once the peaksets are read in, a merging function finds all overlapping peaks and derives a single set of unique genomic intervals covering all the supplied peaks (a consensus peakset for the experiment). - * **Occupancy analysis**: +**Occupancy analysis**: Peaksets, especially those generated by peak callers, provide an insight into the potential occupancy of the protein being ChIPed for at specific @@ -356,7 +361,7 @@ a consensus peakset, representing an overall set of candidate binding sites to be used in further analysis. - * **Counting reads**: +**Counting reads**: Once a consensus peakset has been derived, DiffBind can use the supplied sequence read files to count how many reads overlap each interval for each @@ -368,7 +373,7 @@ data. The binding affinity matrix is used for QC plotting as well as for subsequent differential analysis. - * **Differential binding affinity analysis**: +**Differential binding affinity analysis**: The core functionality of DiffBind is the differential binding affinity analysis, which enables binding sites to be identified that @@ -378,7 +383,7 @@ This will assign a p-value and FDR to each candidate binding site indicating confidence that they are differentially bound. - * **Plotting and reporting**: +**Plotting and reporting**: Once one or more contrasts have been run, DiffBind provides a number of functions for reporting and plotting the results. MA plots give an @@ -387,7 +392,9 @@ of reads within differentially bound sites corresponding to whether they gain or lose affinity between the two sample groups. A reporting mechanism enables differentially bound sites to be extracted for further processing, such as annotation, motif, and -pathway analyses. +pathway analyses. *Note that currently only the correlation plot is implemented in this Galaxy tool.* + +----- **References**