Mercurial > repos > rnateam > chipseeker
diff chipseeker.xml @ 3:535321abf9a4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
| author | rnateam |
|---|---|
| date | Fri, 01 Jun 2018 02:13:33 -0400 |
| parents | cb133602cd9b |
| children | 90fe78a19b55 |
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--- a/chipseeker.xml Wed May 30 06:12:27 2018 -0400 +++ b/chipseeker.xml Fri Jun 01 02:13:33 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> @@ -31,6 +31,7 @@ #end if -f $format -p $pdf + -r $rdata ]]> </command> <inputs> @@ -58,6 +59,9 @@ </param> <param name="pdf" type="boolean" truevalue="True" falsevalue="" checked="True" label="Output PDF of plots?" help="Default: Yes" /> <param name="rscript" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used to annotate the IDs will be provided as a text file in the output. Default: No" /> + <param name="rdata" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output RData file?" + help="Output all the data used by R to construct the tables and plots, can be loaded into R. Default: No"> + </param> <section name="adv" expanded="false" title="Advanced Options"> <param name="upstream" type="integer" min="0" value="3000" label="TSS upstream region" help="User can define TSS (transcription start site) region, by default TSS is defined from -3kb to +3kb." /> @@ -79,15 +83,19 @@ <data name="out_rscript" format="txt" from_work_dir="out_rscript.txt" label="${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" > @@ -95,6 +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"> @@ -170,7 +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". ----- @@ -180,7 +189,11 @@ * a file of annotated peaks in Interval or Tabular format * 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** @@ -191,11 +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: @@ -212,21 +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