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comparison chipseeker.xml @ 3:535321abf9a4 draft

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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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2:cb133602cd9b 3:535321abf9a4
1 <tool id="chipseeker" name="ChIPseeker" version="1.14.2.1"> 1 <tool id="chipseeker" name="ChIPseeker" version="1.14.2.2">
2 <description>for ChIP peak annotation and visualization</description> 2 <description>for ChIP peak annotation and visualization</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.14.2">bioconductor-chipseeker</requirement> 4 <requirement type="package" version="1.14.2">bioconductor-chipseeker</requirement>
5 <requirement type="package" version="1.4.4">r-optparse</requirement> 5 <requirement type="package" version="1.4.4">r-optparse</requirement>
6 </requirements> 6 </requirements>
29 -F $adv.flankgeneinfo 29 -F $adv.flankgeneinfo
30 -D $adv.flankgenedist 30 -D $adv.flankgenedist
31 #end if 31 #end if
32 -f $format 32 -f $format
33 -p $pdf 33 -p $pdf
34 -r $rdata
34 ]]> 35 ]]>
35 </command> 36 </command>
36 <inputs> 37 <inputs>
37 <param name="peaks" type="data" format="bed,interval,tabular" label="Peaks file" help="A peaks file in BED format." /> 38 <param name="peaks" type="data" format="bed,interval,tabular" label="Peaks file" help="A peaks file in BED format." />
38 <conditional name="gtf_source"> 39 <conditional name="gtf_source">
56 <option value="interval" selected="True">Interval</option> 57 <option value="interval" selected="True">Interval</option>
57 <option value="tabular">Tabular (tab-separated)</option> 58 <option value="tabular">Tabular (tab-separated)</option>
58 </param> 59 </param>
59 <param name="pdf" type="boolean" truevalue="True" falsevalue="" checked="True" label="Output PDF of plots?" help="Default: Yes" /> 60 <param name="pdf" type="boolean" truevalue="True" falsevalue="" checked="True" label="Output PDF of plots?" help="Default: Yes" />
60 <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" /> 61 <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" />
62 <param name="rdata" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output RData file?"
63 help="Output all the data used by R to construct the tables and plots, can be loaded into R. Default: No">
64 </param>
61 65
62 <section name="adv" expanded="false" title="Advanced Options"> 66 <section name="adv" expanded="false" title="Advanced Options">
63 <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." /> 67 <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." />
64 <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."/> 68 <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."/>
65 <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."/> 69 <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."/>
77 <filter>pdf</filter> 81 <filter>pdf</filter>
78 </data> 82 </data>
79 <data name="out_rscript" format="txt" from_work_dir="out_rscript.txt" label="${tool.name} on ${on_string}: Rscript"> 83 <data name="out_rscript" format="txt" from_work_dir="out_rscript.txt" label="${tool.name} on ${on_string}: Rscript">
80 <filter>rscript</filter> 84 <filter>rscript</filter>
81 </data> 85 </data>
86 <data name="out_rdata" format="rdata" from_work_dir="ChIPseeker_analysis.RData" label="${tool.name} on ${on_string}: RData file">
87 <filter>rdata</filter>
88 </data>
82 </outputs> 89 </outputs>
83 90
84 <tests> 91 <tests>
85 <!-- Ensure bed and GTF inputs and all outputs work --> 92 <!-- Ensure bed and GTF inputs and all outputs work -->
86 <test expect_num_outputs="3"> 93 <test expect_num_outputs="4">
87 <param name="peaks" value="in.bed" ftype="bed"/> 94 <param name="peaks" value="in.bed" ftype="bed"/>
88 <param name="gtf_source_select" value="history"/> 95 <param name="gtf_source_select" value="history"/>
89 <param name="gtf_hist" value="in.gtf"/> 96 <param name="gtf_hist" value="in.gtf"/>
90 <param name="rscript" value="True"/> 97 <param name="rscript" value="True"/>
98 <param name="rdata" value="True"/>
91 <output name="out_tab" ftype="interval" file="out.int" /> 99 <output name="out_tab" ftype="interval" file="out.int" />
92 <output name="out_plots" file="out.pdf" compare="sim_size"/> 100 <output name="out_plots" file="out.pdf" compare="sim_size"/>
93 <output name="out_rscript" > 101 <output name="out_rscript" >
94 <assert_contents> 102 <assert_contents>
95 <has_text_matching expression="peakAnno.*annotatePeak" /> 103 <has_text_matching expression="peakAnno.*annotatePeak" />
96 </assert_contents> 104 </assert_contents>
97 </output> 105 </output>
106 <output name="out_rdata" file="out.rdata" compare="sim_size" />
98 </test> 107 </test>
99 <!-- Ensure built-in GTF works --> 108 <!-- Ensure built-in GTF works -->
100 <test expect_num_outputs="2"> 109 <test expect_num_outputs="2">
101 <param name="peaks" value="in.interval" ftype="interval"/> 110 <param name="peaks" value="in.interval" ftype="interval"/>
102 <param name="gtf_source_select" value="cached"/> 111 <param name="gtf_source_select" value="cached"/>
168 18 346463 347342 DiffBind 0 . 177 18 346463 347342 DiffBind 0 .
169 18 399013 400382 DiffBind 0 . 178 18 399013 400382 DiffBind 0 .
170 18 371109 372102 DiffBind 0 . 179 18 371109 372102 DiffBind 0 .
171 ===== ====== ====== ======== ===== ====== 180 ===== ====== ====== ======== ===== ======
172 181
173 A GTF file for annotation. 182 A GTF file for annotation. The GTF file must have fields called "gene_id" and gene_name".
174 183
175 ----- 184 -----
176 185
177 **Outputs** 186 **Outputs**
178 187
179 This tool outputs 188 This tool outputs
180 189
181 * a file of annotated peaks in Interval or Tabular format 190 * a file of annotated peaks in Interval or Tabular format
182 * a PDF of plots (plotAnnoPie, vennpie, upsetplot) 191 * a PDF of plots (plotAnnoPie, vennpie, upsetplot)
192
193 Optionally, you can choose to output
194
183 * the R script used by this tool 195 * the R script used by this tool
196 * an RData file
184 197
185 **Annotated peaks** 198 **Annotated peaks**
186 199
187 Annotation similar to below will be added to the input file. 200 Annotation similar to below will be added to the input file.
188 201
189 Example - **Interval format**: 202 Example - **Interval format**:
190 203
191 ===== ====== ====== ===================================================================================================================================================== 204 ===== ====== ====== =====================================================================================================================================================
192 Chrom Start End Comment 205 Chrom Start End Comment
193 ===== ====== ====== ===================================================================================================================================================== 206 ===== ====== ====== =====================================================================================================================================================
194 18 394599 396513 DiffBind|0|.|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256| 3869 207 18 394599 396513 DiffBind|0|.|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENST00000400256| 3869|COLEC12|ENSG00000158270
195 18 111566 112005 DiffBind|0|.|Promoter (<=1kb)|1|111568|112005| 438|1|ENSG00000263006|ENST00000608049| 0 208 18 346463 347342 DiffBind|0|.|Exon (ENST00000400256/ENSG00000158270, exon 1 of 1)|1|346465|400382|53918|2|ENST00000400256|53040|COLEC12|ENSG00000158270
196 18 346463 347342 DiffBind|0|.|Exon (ENST00000400256/ENSG00000158270, exon 1 of 1)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256|53040 209 18 399013 400382 DiffBind|0|.|Promoter (<=1kb)|1|346465|400382|53918|2|ENST00000400256| 0|COLEC12|ENSG00000158270
197 18 399013 400382 DiffBind|0|.|Promoter (<=1kb)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256| 0 210 18 371109 372102 DiffBind|0|.|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENST00000400256|28280|COLEC12|ENSG00000158270
198 18 371109 372102 DiffBind|0|.|Intron (ENST00000400256/ENSG00000158270, intron 1 of 1)|1|346465|400382|53918|2|ENSG00000158270|ENST00000400256|28280 211 18 111566 112005 DiffBind|0|.|Promoter (<=1kb)|1|111568|112005| 438|1|ENST00000608049| 0|ROCK1P1|ENSG00000263006
199 ===== ====== ====== ===================================================================================================================================================== 212 ===== ====== ====== =====================================================================================================================================================
200 213
201 Columns contain the following data: 214 Columns contain the following data:
202 215
203 * **Chrom**: Chromosome name 216 * **Chrom**: Chromosome name
210 * *geneChr* 223 * *geneChr*
211 * *geneStart* 224 * *geneStart*
212 * *geneEnd* 225 * *geneEnd*
213 * *geneLength* 226 * *geneLength*
214 * *geneStrand* 227 * *geneStrand*
215 * *geneId*
216 * *transcriptId* 228 * *transcriptId*
217 * *distanceToTSS* 229 * *distanceToTSS*
230 * *geneName*
231 * *geneId*
218 232
219 Example - **Tabular format**: 233 Example - **Tabular format**:
220 234
221 ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== =============== ============= 235 ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== ============= ======== ===============
222 Chrom Start End Name Score Strand Comment annotation geneChr geneStart geneEnd geneLength geneStrand geneId transcriptId distanceToTSS 236 Chrom Start End Name Score Strand Comment annotation geneChr geneStart geneEnd geneLength geneStrand transcriptId distanceToTSS geneName geneId
223 ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== =============== ============= 237 ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== ============= ======== ===============
224 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 238 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
225 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 0 239 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
226 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 240 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
227 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 0 241 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
228 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 242 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
229 ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== =============== ============= 243 ===== ====== ====== ======== ====== ====== =========================================== ======================================================= ======= ========= ======= ========== ========== =============== ============= ======== ===============
230 244
231 .. _ChIPseeker: https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html 245 .. _ChIPseeker: https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html
232 .. _`ChIPseeker vignette`: http://bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html 246 .. _`ChIPseeker vignette`: http://bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html
233 247
234 ]]></help> 248 ]]></help>