| Next changeset 1:95f779f4adb7 (2018-05-29) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 9324a8e21c41d62b461dce9c3c17df544e5cd0ce |
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added:
chipseeker.xml test-data/in.diffbind test-data/out.pdf test-data/out.tab |
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| diff -r 000000000000 -r 58ef4507ce5a chipseeker.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chipseeker.xml Thu May 24 18:25:40 2018 -0400 |
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| @@ -0,0 +1,142 @@ +<tool id="chipseeker" name="ChIPseeker" version="1.14.2"> + <description>for ChIP peak annotation and visualization</description> + <requirements> + <requirement type="package" version="1.14.2">bioconductor-chipseeker</requirement> + <requirement type="package" version="3.4.0">bioconductor-txdb.hsapiens.ucsc.hg38.knowngene</requirement> + <requirement type="package" version="3.2.2">bioconductor-txdb.hsapiens.ucsc.hg19.knowngene</requirement> + <requirement type="package" version="3.4.0">bioconductor-txdb.Mmusculus.UCSC.mm10.knownGene</requirement> + <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement> + <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement> + </requirements> + <version_command><![CDATA[ +echo $(R --version | grep version | grep -v GNU)", ChIPseeker version" $(R --vanilla --slave -e "library(ChIPseeker); cat(sessionInfo()\$otherPkgs\$ChIPseeker\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", TxDb.Hsapiens.UCSC.hg38.knownGene version" $(R --vanilla --slave -e "library(TxDb.Hsapiens.UCSC.hg38.knownGene); cat(sessionInfo()\$otherPkgs\$TxDb.Hsapiens.UCSC.hg38.knownGene\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", TxDb.Hsapiens.UCSC.hg19.knownGene version" $(R --vanilla --slave -e "library(TxDb.Hsapiens.UCSC.hg19.knownGene); cat(sessionInfo()\$otherPkgs\$TxDb.Hsapiens.UCSC.hg19.knownGene\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", TxDb.Mmusculus.UCSC.mm10.knownGene version" $(R --vanilla --slave -e "library(TxDb.Mmusculus.UCSC.mm10.knownGene); cat(sessionInfo()\$otherPkgs\$TxDb.Mmusculus.UCSC.mm10.knownGene\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Hs.eg.db version" $(R --vanilla --slave -e "library(org.Hs.eg.db); cat(sessionInfo()\$otherPkgs\$org.Hs.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", org.Mm.eg.db version" $(R --vanilla --slave -e "library(org.Mm.eg.db); cat(sessionInfo()\$otherPkgs\$org.Mm.eg.db\$Version)" 2> /dev/null | grep -v -i "WARNING: ") + ]]></version_command> + <command detect_errors="exit_code"><![CDATA[ + #if $rscript: + cp '${chipseeker_script}' '${out_rscript}' && + #end if + Rscript '${chipseeker_script}' + ]]> + </command> + <configfiles> + <configfile name="chipseeker_script"><![CDATA[ +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. +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +suppressPackageStartupMessages(library(ChIPseeker)) + +genome <- "${genome}" + +if (genome == "hg38") { + suppressPackageStartupMessages({ + library(TxDb.Hsapiens.UCSC.hg38.knownGene) + library(org.Hs.eg.db) + }) + txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene + annodb <- "org.Hs.eg.db" +} else if (genome == "hg19") { + suppressPackageStartupMessages({ + library(TxDb.Hsapiens.UCSC.hg19.knownGene) + library(org.Hs.eg.db) + }) + txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene + annodb <- "org.Hs.eg.db" +} else if (genome == "mm10") { + suppressPackageStartupMessages({ + library(TxDb.Mmusculus.UCSC.mm10.knownGene) + library(org.Mm.eg.db) + }) + txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene + annodb <- "org.Mm.eg.db" +} else { + cat(paste("Genome not supported", genome)) +} + +peaks <- readPeakFile('$peaks_file') +peakAnno <- annotatePeak(peaks, TxDb=txdb, annoDb=annodb) +write.table(peakAnno, file='$out_tab', sep="\t", row.names=FALSE, quote=FALSE) + +if (!is.null("${pdf}")) { + pdf("out.pdf", width=14) + plotAnnoPie(peakAnno) + plotAnnoBar(peakAnno) + vennpie(peakAnno) + upsetplot(peakAnno) + plotDistToTSS(peakAnno, title="Distribution of transcription factor-binding loci\nrelative to TSS") + dev.off() +} + ]]></configfile> + </configfiles> + + <inputs> + <param name="peaks_file" type="data" format="bed" label="Peaks file" help="A peaks file in BED format." /> + <param name="genome" type="select" label="Genome" help="Select the genome. Options are hg38, hg19 or mm10."> + <option value="hg38">hg38</option> + <option value="hg19">hg19</option> + <option value="mm10">mm10</option> + </param> + + <param name="pdf" type="boolean" truevalue="True" falsevalue="" checked="True" label="Output a PDF file of plots?" help="Default: Yes" /> + <param name="rscript" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used to annotate the IDs will be provided as a text file in the output. Default: No" /> + </inputs> + + <outputs> + <data name="out_tab" format="tabular" from_work_dir="out.tab" label="${tool.name} on ${on_string}: Annotated Peaks" /> + <data name="out_plots" format="pdf" from_work_dir="out.pdf" label="${tool.name} on ${on_string}: Plots"> + <filter>pdf</filter> + </data> + <data name="out_rscript" format="txt" from_work_dir="out_rscript.txt" label="${tool.name} on ${on_string}: Rscript"> + <filter>rscript</filter> + </data> + </outputs> + + <tests> + <!-- Ensure outputs work --> + <test expect_num_outputs="3"> + <param name="peaks_file" value="in.diffbind" ftype="bed"/> + <param name="genome" value="hg19"/> + <param name="rscript" value="True"/> + <output name="out_tab" file="out.tab" /> + <output name="out_plots" file="out.pdf" compare="sim_size"/> + <output name="out_rscript" > + <assert_contents> + <has_text_matching expression="peakAnno.*annotatePeak" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**What it does** + +ChIPseeker_ is a Bioconductor package for annotating ChIP-seq data analysis. See +the `ChIPseeker vignette`_ for more information. + +----- + +**Inputs** + +A peaks file in BED format e.g from MACS2 or DiffBind. + +----- + +**Outputs** + +This tool outputs + + * a table of annotated peaks + * a PDF of plots + * the R script used by this tool + +.. _ChIPseeker: https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html +.. _`ChIPseeker vignette`: http://bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html + +]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btv145</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 58ef4507ce5a test-data/in.diffbind --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in.diffbind Thu May 24 18:25:40 2018 -0400 |
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| @@ -0,0 +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 |
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| diff -r 000000000000 -r 58ef4507ce5a test-data/out.pdf |
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| Binary file test-data/out.pdf has changed |
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| diff -r 000000000000 -r 58ef4507ce5a test-data/out.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.tab Thu May 24 18:25:40 2018 -0400 |
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| @@ -0,0 +1,6 @@ +seqnames start end width strand width.1 strand.1 Conc Conc_Responsive Conc_Resistant Fold p.value FDR annotation geneChr geneStart geneEnd geneLength geneStrand geneId transcriptId distanceToTSS ENSEMBL SYMBOL GENENAME +chr18 394601 396513 1913 * 1914 * 7.15 5.55 7.89 -2.35 7.06e-24 9.84e-21 Intron (uc002kkm.3/81035, intron 2 of 9) 18 319355 500729 181375 2 81035 uc002kkm.3 104216 ENSG00000158270 COLEC12 collectin subfamily member 12 +chr18 111568 112005 438 * 439 * 5.71 6.53 3.63 2.89 1.27e-08 8.88e-06 Promoter (2-3kb) 18 109065 122222 13158 1 727758 uc002kke.3 2503 ENSG00000263006 ROCK1P1 Rho associated coiled-coil containing protein kinase 1 pseudogene 1 +chr18 346465 347342 878 * 879 * 5 5.77 3.24 2.52 6.51e-06 0.00303 Exon (uc002kkm.3/81035, exon 5 of 10) 18 225089 268059 42971 2 9984 uc002kkl.2 -78406 ENSG00000079134 THOC1 THO complex 1 +chr18 399015 400382 1368 * 1369 * 7.62 7 8.05 -1.04 1.04e-05 0.00364 Intron (uc002kkm.3/81035, intron 2 of 9) 18 319355 500729 181375 2 81035 uc002kkm.3 100347 ENSG00000158270 COLEC12 collectin subfamily member 12 +chr18 371111 372102 992 * 993 * 4.63 3.07 5.36 -2.3 8.1e-05 0.0226 Intron (uc002kkm.3/81035, intron 2 of 9) 18 225089 268059 42971 2 9984 uc002kkl.2 -103052 ENSG00000079134 THOC1 THO complex 1 |