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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
| author | rnateam |
|---|---|
| date | Tue, 29 May 2018 15:08:04 -0400 |
| parents | 58ef4507ce5a |
| children | cb133602cd9b |
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<tool id="chipseeker" name="ChIPseeker" version="1.14.2.1"> <description>for ChIP peak annotation and visualization</description> <requirements> <requirement type="package" version="1.14.2">bioconductor-chipseeker</requirement> <requirement type="package" version="1.4.4">r-optparse</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: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ") ]]></version_command> <command detect_errors="exit_code"><![CDATA[ #set gtf = "refgtf" #if $gtf_source.gtf_source_select == "history": ln -s '${gtf_source.gtf_hist}' $gtf && #else if $gtf_source.gtf_source_select == "cached": ln -s '${gtf_source.gtf_builtin.fields.path}' $gtf && #end if #if $rscript: cp '$__tool_directory__/chipseeker.R' '$out_rscript' && #end if Rscript '$__tool_directory__/chipseeker.R' -i '$peaks' -G '$gtf' -u $upstream -d $downstream #if $flankgeneinfo: -F $flankgeneinfo -D $flankgenedist #end if -f $format -p $pdf ]]> </command> <inputs> <param name="peaks" type="data" format="bed,interval" 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> <option value="history">Use a GTF from history</option> </param> <when value="cached"> <param name="gtf_builtin" type="select" label="Select a built-in GTF" help="If the GTF file for your transcriptome of interest is not listed, contact your Galaxy administrator"> <options from_data_table="gene_sets"> <filter type="sort_by" column="2" /> <validator type="no_options" message="No GTF file is available." /> </options> </param> </when> <when value="history"> <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" /> </inputs> <outputs> <data name="out_tab" format="interval" from_work_dir="out.tab" label="${tool.name} on ${on_string}: Annotated Peaks" > <change_format> <when input="format" value="tabular" format="tabular" /> </change_format> </data> <data name="out_plots" format="pdf" from_work_dir="out.pdf" label="${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 bed and GTF inputs and all outputs work --> <test expect_num_outputs="3"> <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"/> <output name="out_tab" ftype="interval" file="out.int" /> <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> <!-- Ensure built-in GTF works --> <test expect_num_outputs="2"> <param name="peaks" value="in.interval" ftype="interval"/> <param name="gtf_source_select" value="cached"/> <output name="out_tab" ftype="interval" file="outint.int" /> <output name="out_plots" file="out.pdf" compare="sim_size"/> </test> <!-- Ensure tabular output works --> <test expect_num_outputs="2"> <param name="peaks" value="in.interval" ftype="interval"/> <param name="gtf_source_select" value="history"/> <param name="gtf_hist" value="in.gtf"/> <param name="format" value="tabular"/> <output name="out_tab" ftype="tabular" file="outint.tab" /> <output name="out_plots" file="out.pdf" compare="sim_size"/> </test> <!-- Ensure TSS region specification works --> <test expect_num_outputs="2"> <param name="peaks" value="in.interval" ftype="interval"/> <param name="gtf_source_select" value="history"/> <param name="gtf_hist" value="in.gtf"/> <param name="upstream" value="1000" /> <param name="downstream" value="1000" /> <param name="format" value="tabular"/> <output name="out_tab" ftype="tabular" file="outtss.tab" /> <output name="out_plots" file="out.pdf" compare="sim_size"/> </test> <!-- Ensure flanking genes works --> <test expect_num_outputs="2"> <param name="peaks" value="in.interval" ftype="interval"/> <param name="gtf_source_select" value="history"/> <param name="gtf_hist" value="in.gtf"/> <param name="flankgeneinfo" value="True" /> <param name="format" value="tabular"/> <output name="out_tab" ftype="tabular" file="outflank.tab" /> <output name="out_plots" file="out.pdf" compare="sim_size"/> </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 or Interval format e.g from MACS2 or DiffBind. Example: ===== ====== ====== ======== ===== ====== Chrom Start End Name Score Strand ===== ====== ====== ======== ===== ====== 18 394599 396513 DiffBind 0 . 18 111566 112005 DiffBind 0 . 18 346463 347342 DiffBind 0 . 18 399013 400382 DiffBind 0 . 18 371109 372102 DiffBind 0 . ===== ====== ====== ======== ===== ====== A GTF file for annotation. ----- **Outputs** This tool outputs * a file of annotated peaks in Interval or Tabular format * a PDF of plots * the R script used by this tool **Annotated peaks** Annotation similar to below will be added to the input file. Example - **Interval format**: ===== ====== ====== ===================================================================================================================================================== 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 ===== ====== ====== ===================================================================================================================================================== Columns contain the following data: * **Chrom**: Chromosome name * **Start**: Start position of site * **End**: End position of site * **Comment**: The pipe ("|") separated values in this column correspond to: * *<Any additional input columns>* * *annotation* (Promoter, 5’ UTR, 3’ UTR, Exon, Intron, Downstream, Intergenic) * *geneChr* * *geneStart* * *geneEnd* * *geneLength* * *geneStrand* * *geneId* * *transcriptId* * *distanceToTSS* 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 ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== =============== ============= .. _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>