Mercurial > repos > rnateam > chipseeker
diff chipseeker.xml @ 2:195cba35110e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
| author | rnateam |
|---|---|
| date | Fri, 01 Jun 2018 02:14:08 -0400 |
| parents | 2019b4dd86a8 |
| children | a6d072a82158 |
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--- a/chipseeker.xml Tue May 29 15:07:04 2018 -0400 +++ b/chipseeker.xml Fri Jun 01 02:14:08 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="chipseeker" name="ChIPseeker" version="1.14.2.1"> +<tool id="chipseeker" name="ChIPseeker" version="1.14.2.2"> <description>for ChIP peak annotation and visualization</description> <requirements> <requirement type="package" version="1.14.2">bioconductor-chipseeker</requirement> @@ -23,18 +23,19 @@ -i '$peaks' -G '$gtf' - -u $upstream - -d $downstream - #if $flankgeneinfo: - -F $flankgeneinfo - -D $flankgenedist + -u $adv.upstream + -d $adv.downstream + #if $adv.flankgeneinfo: + -F $adv.flankgeneinfo + -D $adv.flankgenedist #end if -f $format -p $pdf + -r $rdata ]]> </command> <inputs> - <param name="peaks" type="data" format="bed,interval" label="Peaks file" help="A peaks file in BED format." /> + <param name="peaks" type="data" format="bed,interval,tabular" label="Peaks file" help="A peaks file in BED format." /> <conditional name="gtf_source"> <param name="gtf_source_select" type="select" label="Annotation source" help="Select a GTF to use for annotation source."> <option value="cached" selected="true">Use a built-in GTF</option> @@ -52,16 +53,22 @@ <param name="gtf_hist" type="data" format="gtf" label="Select a history GTF" /> </when> </conditional> - <param name="upstream" type="integer" min="0" value="3000" label="TSS upstream region" help="User can define TSS (transcription start site) region, by default TSS is defined from -3kb to +3kb." /> - <param name="downstream" type="integer" min="0" value="3000" label="TSS downstream region" help="User can define TSS (transcription start site) region, by default TSS is defined from -3kb to +3kb."/> - <param name="flankgeneinfo" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Add flanking gene information?" help="If specified all genes within the flanking gene distance are reported for each peak. Default: No."/> - <param name="flankgenedist" type="integer" min="0" value="5000" label="Flanking gene distance" help="If flanking gene info is turned on the flanking distance can be specified. Default: 5000."/> <param name="format" type="select" label="Output Format"> <option value="interval" selected="True">Interval</option> <option value="tabular">Tabular (tab-separated)</option> </param> <param name="pdf" type="boolean" truevalue="True" falsevalue="" checked="True" label="Output PDF 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" /> + <param name="rdata" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output RData file?" + help="Output all the data used by R to construct the tables and plots, can be loaded into R. Default: No"> + </param> + + <section name="adv" expanded="false" title="Advanced Options"> + <param name="upstream" type="integer" min="0" value="3000" label="TSS upstream region" help="User can define TSS (transcription start site) region, by default TSS is defined from -3kb to +3kb." /> + <param name="downstream" type="integer" min="0" value="3000" label="TSS downstream region" help="User can define TSS (transcription start site) region, by default TSS is defined from -3kb to +3kb."/> + <param name="flankgeneinfo" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Add flanking gene information?" help="If specified all genes within the flanking gene distance are reported for each peak. Default: No."/> + <param name="flankgenedist" type="integer" min="0" value="5000" label="Flanking gene distance" help="If flanking gene info is turned on the flanking distance can be specified. Default: 5000."/> + </section> </inputs> <outputs> @@ -76,15 +83,19 @@ <data name="out_rscript" format="txt" from_work_dir="out_rscript.txt" label="${tool.name} on ${on_string}: Rscript"> <filter>rscript</filter> </data> + <data name="out_rdata" format="rdata" from_work_dir="ChIPseeker_analysis.RData" label="${tool.name} on ${on_string}: RData file"> + <filter>rdata</filter> + </data> </outputs> <tests> <!-- Ensure bed and GTF inputs and all outputs work --> - <test expect_num_outputs="3"> + <test expect_num_outputs="4"> <param name="peaks" value="in.bed" ftype="bed"/> <param name="gtf_source_select" value="history"/> <param name="gtf_hist" value="in.gtf"/> <param name="rscript" value="True"/> + <param name="rdata" value="True"/> <output name="out_tab" ftype="interval" file="out.int" /> <output name="out_plots" file="out.pdf" compare="sim_size"/> <output name="out_rscript" > @@ -92,6 +103,7 @@ <has_text_matching expression="peakAnno.*annotatePeak" /> </assert_contents> </output> + <output name="out_rdata" file="out.rdata" compare="sim_size" /> </test> <!-- Ensure built-in GTF works --> <test expect_num_outputs="2"> @@ -137,14 +149,23 @@ **What it does** -ChIPseeker_ is a Bioconductor package for annotating ChIP-seq data analysis. See -the `ChIPseeker vignette`_ for more information. +ChIPseeker_ is a Bioconductor package for annotating ChIP-seq data analysis. Peak Annotation is performed by the annotatePeak function. The position and strand information of nearest genes are reported, in addition to the distance from the peak to the TSS of its nearest gene. Users can define the TSS (transcription start site) region under **Advanced Options**, by default the TSS region is defined from -3kb to +3kb. The genomic region of the peak is reported in the annotation column. Since some annotations may overlap for a peak, ChIPseeker adopts the following priority in genomic annotation: + +* Promoter +* 5’ UTR +* 3’ UTR +* Exon +* Intron +* Downstream +* Intergenic + +ChIPseeker also produces plots to help users visualise the overlaps in annotation for peaks, for example, the vennpie and upsetplot. See the `ChIPseeker vignette`_ for more information. ----- **Inputs** -A peaks file in BED or Interval format e.g from MACS2 or DiffBind. +A peaks file in BED, Interval or Tabular format e.g from MACS2 or DiffBind. Example: @@ -158,7 +179,7 @@ 18 371109 372102 DiffBind 0 . ===== ====== ====== ======== ===== ====== -A GTF file for annotation. +A GTF file for annotation. The GTF file must have fields called "gene_id" and gene_name". ----- @@ -167,8 +188,12 @@ This tool outputs * a file of annotated peaks in Interval or Tabular format - * a PDF of plots + * a PDF of plots (plotAnnoPie, vennpie, upsetplot) + +Optionally, you can choose to output + * the R script used by this tool + * an RData file **Annotated peaks** @@ -179,11 +204,11 @@ ===== ====== ====== ===================================================================================================================================================== Chrom Start End Comment ===== ====== ====== ===================================================================================================================================================== - 18 394599 396513 DiffBind|0|.|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256| 3869 - 18 111566 112005 DiffBind|0|.|Promoter (<=1kb)|1|111568|112005| 438|1|ENSG00000263006|ENST00000608049| 0 - 18 346463 347342 DiffBind|0|.|Exon (ENST00000400256/ENSG00000158270, exon 1 of 1)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256|53040 - 18 399013 400382 DiffBind|0|.|Promoter (<=1kb)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256| 0 - 18 371109 372102 DiffBind|0|.|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256|28280 + 18 394599 396513 DiffBind|0|.|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENST00000400256| 3869|COLEC12|ENSG00000158270 + 18 346463 347342 DiffBind|0|.|Exon (ENST00000400256/ENSG00000158270, exon 1 of 1)|1|346465|400382|53918|2|ENST00000400256|53040|COLEC12|ENSG00000158270 + 18 399013 400382 DiffBind|0|.|Promoter (<=1kb)|1|346465|400382|53918|2|ENST00000400256| 0|COLEC12|ENSG00000158270 + 18 371109 372102 DiffBind|0|.|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENST00000400256|28280|COLEC12|ENSG00000158270 + 18 111566 112005 DiffBind|0|.|Promoter (<=1kb)|1|111568|112005| 438|1|ENST00000608049| 0|ROCK1P1|ENSG00000263006 ===== ====== ====== ===================================================================================================================================================== Columns contain the following data: @@ -200,21 +225,22 @@ * *geneEnd* * *geneLength* * *geneStrand* - * *geneId* * *transcriptId* * *distanceToTSS* + * *geneName* + * *geneId* Example - **Tabular format**: - ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== =============== ============= - Chrom Start End Name Score Strand Comment annotation geneChr geneStart geneEnd geneLength geneStrand geneId transcriptId distanceToTSS - ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== =============== ============= - 18 394599 396513 DiffBind 0 . 1914|7.15|5.55|7.89|-2.35|7.06e-24|9.84e-21 Intron (ENST00000400256/ENSG00000158270, intron 1 of 1) 1 346465 400382 53918 2 ENSG00000158270 ENST00000400256 3869 - 18 111566 112005 DiffBind 0 . 439|5.71|6.53|3.63|2.89|1.27e-08|8.88e-06 Promoter (<=1kb) 1 111568 112005 438 1 ENSG00000263006 ENST00000608049 0 - 18 346463 347342 DiffBind 0 . 879|5|5.77|3.24|2.52|6.51e-06|0.00303 Exon (ENST00000400256/ENSG00000158270, exon 1 of 1) 1 346465 400382 53918 2 ENSG00000158270 ENST00000400256 53040 - 18 399013 400382 DiffBind 0 . 1369|7.62|7|8.05|-1.04|1.04e-05|0.00364 Promoter (<=1kb) 1 346465 400382 53918 2 ENSG00000158270 ENST00000400256 0 - 18 371109 372102 DiffBind 0 . 993|4.63|3.07|5.36|-2.3|8.1e-05|0.0226 Intron (ENST00000400256/ENSG00000158270, intron 1 of 1) 1 346465 400382 53918 2 ENSG00000158270 ENST00000400256 28280 - ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== =============== ============= + ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== ============= ======== =============== + Chrom Start End Name Score Strand Comment annotation geneChr geneStart geneEnd geneLength geneStrand transcriptId distanceToTSS geneName geneId + ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== ============= ======== =============== + 18 394599 396513 DiffBind 0 . 1914|7.15|5.55|7.89|-2.35|7.06e-24|9.84e-21 Intron (ENST00000400256/ENSG00000158270, intron 1 of 1) 1 346465 400382 53918 2 ENST00000400256 3869 COLEC12 ENSG00000158270 + 18 346463 347342 DiffBind 0 . 879|5|5.77|3.24|2.52|6.51e-06|0.00303 Exon (ENST00000400256/ENSG00000158270, exon 1 of 1) 1 346465 400382 53918 2 ENST00000400256 53040 COLEC12 ENSG00000158270 + 18 399013 400382 DiffBind 0 . 1369|7.62|7|8.05|-1.04|1.04e-05|0.00364 Promoter (<=1kb) 1 346465 400382 53918 2 ENST00000400256 0 COLEC12 ENSG00000158270 + 18 371109 372102 DiffBind 0 . 993|4.63|3.07|5.36|-2.3|8.1e-05|0.0226 Intron (ENST00000400256/ENSG00000158270, intron 1 of 1) 1 346465 400382 53918 2 ENST00000400256 28280 COLEC12 ENSG00000158270 + 18 111566 112005 DiffBind 0 . 439|5.71|6.53|3.63|2.89|1.27e-08|8.88e-06 Promoter (<=1kb) 1 111568 112005 438 1 ENST00000608049 0 ROCK1P1 ENSG00000263006 + ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== ============= ======== =============== .. _ChIPseeker: https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html .. _`ChIPseeker vignette`: http://bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html