Mercurial > repos > bgruening > diffbind
comparison diffbind.xml @ 13:1de83981d43c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 13485bed6a57ec4a34cab4ec6bb8b36d219e3610
author | iuc |
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date | Wed, 30 May 2018 12:25:42 -0400 |
parents | fa56d93f7980 |
children | c97a786e8fb5 |
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12:fa56d93f7980 | 13:1de83981d43c |
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1 <tool id="diffbind" name="DiffBind" version="2.6.6.2"> | 1 <tool id="diffbind" name="DiffBind" version="2.6.6.3"> |
2 <description> differential binding analysis of ChIP-Seq peak data</description> | 2 <description> differential binding analysis of ChIP-Seq peak data</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="2.6.6">bioconductor-diffbind</requirement> | 4 <requirement type="package" version="2.6.6">bioconductor-diffbind</requirement> |
5 <requirement type="package" version="1.20.0">r-getopt</requirement> | 5 <requirement type="package" version="1.20.0">r-getopt</requirement> |
6 <requirement type="package" version="0.2.15">r-rjson</requirement> | 6 <requirement type="package" version="0.2.15">r-rjson</requirement> |
104 ]]> | 104 ]]> |
105 </command> | 105 </command> |
106 <inputs> | 106 <inputs> |
107 <repeat name="rep_group" title="Group" min="2" max="2" default="2"> | 107 <repeat name="rep_group" title="Group" min="2" max="2" default="2"> |
108 <param name="groupName" type="text" label="Name" | 108 <param name="groupName" type="text" label="Name" |
109 help="Name for the Group that the peak and BAM files belong to e.g. Resistant/Responsive (two Groups in total must be specified for DiffBind). NOTE: Please only use letters, numbers or underscores."> | 109 help="Name for the Group that the peak and BAM files belong to e.g. Resistant/Responsive (two Groups must be specified for DiffBind). NOTE: Please only use letters, numbers or underscores."> |
110 <sanitizer> | 110 <sanitizer> |
111 <valid initial="string.letters,string.digits"><add value="_" /></valid> | 111 <valid initial="string.letters,string.digits"><add value="_" /></valid> |
112 </sanitizer> | 112 </sanitizer> |
113 <validator type="empty_field" /> | 113 <validator type="empty_field" /> |
114 </param> | 114 </param> |
131 <param name="th" type="float" value="0.05" min="0" max="1" label="FDR Threshold" help="Significance threshold; all sites with FDR less than or equal to this value will be included in the output. A value of 1 will output all binding sites. Default: 0.05"/> | 131 <param name="th" type="float" value="0.05" min="0" max="1" label="FDR Threshold" help="Significance threshold; all sites with FDR less than or equal to this value will be included in the output. A value of 1 will output all binding sites. Default: 0.05"/> |
132 | 132 |
133 <!-- Output Options --> | 133 <!-- Output Options --> |
134 <section name="out" expanded="false" title="Output Options"> | 134 <section name="out" expanded="false" title="Output Options"> |
135 <param name="format" type="select" label="Output Format"> | 135 <param name="format" type="select" label="Output Format"> |
136 <option value="interval" selected="True">Interval</option> | |
136 <option value="bed">BED</option> | 137 <option value="bed">BED</option> |
137 <option value="gff">GFF</option> | 138 <option value="tabular">Tabular (tab-separated)</option> |
138 <option value="wig">WIG</option> | |
139 </param> | 139 </param> |
140 <param name="pdf" type="boolean" truevalue="True" falsevalue="" checked="False" label="Visualising the analysis results" help="output an additional PDF file" /> | 140 <param name="pdf" type="boolean" truevalue="True" falsevalue="" checked="False" label="Visualising the analysis results" help="output an additional PDF file" /> |
141 <param name="binding_matrix" type="boolean" truevalue="True" falsevalue="" checked="False" label="Output binding affinity matrix?" help="Output a table of the binding scores" /> | 141 <param name="binding_matrix" type="boolean" truevalue="True" falsevalue="" checked="False" label="Output binding affinity matrix?" help="Output a table of the binding scores" /> |
142 <param name="rdata" type="boolean" truevalue="True" falsevalue="" checked="False" label="Output RData file?" help="Output all the data used by R to construct the plots and tables, can be loaded into R. Default: No"/> | 142 <param name="rdata" type="boolean" truevalue="True" falsevalue="" checked="False" label="Output RData file?" help="Output all the data used by R to construct the plots and tables, can be loaded into R. Default: No"/> |
143 <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 will be provided as a text file in the output. Default: No"/> | 143 <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 will be provided as a text file in the output. Default: No"/> |
144 <param name="analysis_info" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output analysis info?" help="If this option is set to Yes, information from the dba.count and dba.analyze commmands will be output in a text file. Default: No"/> | 144 <param name="analysis_info" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output analysis info?" help="If this option is set to Yes, information from the dba.count and dba.analyze commmands will be output in a text file. Default: No"/> |
145 </section> | 145 </section> |
146 </inputs> | 146 </inputs> |
147 | 147 |
148 <outputs> | 148 <outputs> |
149 <data name="outfile" format="tabular" label="${tool.name} on ${on_string}: Differentially bound sites" /> | 149 <data name="outfile" format="interval" label="${tool.name} on ${on_string}: Differentially bound sites"> |
150 <change_format> | |
151 <when input="out.format" value="bed" format="bed" /> | |
152 <when input="out.format" value="tabular" format="tabular" /> | |
153 </change_format> | |
154 </data> | |
150 <data name="plots" format="pdf" label="${tool.name} on ${on_string}: Plots"> | 155 <data name="plots" format="pdf" label="${tool.name} on ${on_string}: Plots"> |
151 <filter>out['pdf']</filter> | 156 <filter>out['pdf']</filter> |
152 </data> | 157 </data> |
153 <data name="binding_matrix" format="tabular" from_work_dir="bmatrix.tab" label="${tool.name} on ${on_string}: Binding matrix"> | 158 <data name="binding_matrix" format="tabular" from_work_dir="bmatrix.tab" label="${tool.name} on ${on_string}: Binding matrix"> |
154 <filter>out['binding_matrix']</filter> | 159 <filter>out['binding_matrix']</filter> |
163 <filter>out['analysis_info']</filter> | 168 <filter>out['analysis_info']</filter> |
164 </data> | 169 </data> |
165 </outputs> | 170 </outputs> |
166 | 171 |
167 <tests> | 172 <tests> |
173 <!-- Ensure outputs work --> | |
168 <test expect_num_outputs="6"> | 174 <test expect_num_outputs="6"> |
169 <repeat name="rep_group"> | 175 <repeat name="rep_group"> |
170 <param name="groupName" value="Resistant"/> | 176 <param name="groupName" value="Resistant"/> |
171 <param name="peaks" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/> | 177 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/> |
172 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" /> | 178 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" /> |
173 </repeat> | 179 </repeat> |
174 <repeat name="rep_group"> | 180 <repeat name="rep_group"> |
175 <param name="groupName" value="Responsive"/> | 181 <param name="groupName" value="Responsive"/> |
176 <param name="peaks" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/> | 182 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/> |
177 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" /> | 183 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" /> |
178 </repeat> | 184 </repeat> |
179 <param name="scorecol" value="5" /> | 185 <param name="scorecol" value="5" /> |
186 <param name="format" value="interval"/> | |
180 <param name="pdf" value="True" /> | 187 <param name="pdf" value="True" /> |
181 <param name="binding_matrix" value="True" /> | 188 <param name="binding_matrix" value="True" /> |
182 <param name="rdata" value="True" /> | 189 <param name="rdata" value="True" /> |
183 <param name="rscript" value="True"/> | 190 <param name="rscript" value="True"/> |
184 <param name="analysis_info" value="True"/> | 191 <param name="analysis_info" value="True"/> |
185 <output name="outfile" value="out_diffbind.tab" /> | 192 <output name="outfile" ftype="interval" value="out_diffbind.interval" /> |
186 <output name="plots" value="out_plots.pdf" compare="sim_size" /> | 193 <output name="plots" value="out_plots.pdf" compare="sim_size" /> |
187 <output name="binding_matrix" value="out_binding.matrix" /> | 194 <output name="binding_matrix" value="out_binding_matrix.tab" /> |
188 <output name="rdata" value="DiffBind_analysis.RData" compare="sim_size"/> | 195 <output name="rdata" value="DiffBind_analysis.RData" compare="sim_size"/> |
189 <output name="rscript" value="out_rscript.txt"/> | 196 <output name="rscript"> |
190 <output name="analysis_info" value="out_analysis_info.txt" compare="sim_size" > | 197 <assert_contents> |
198 <has_text text="write.table"/> | |
199 </assert_contents> | |
200 </output> | |
201 <output name="analysis_info" compare="sim_size" > | |
191 <assert_contents> | 202 <assert_contents> |
192 <has_text text="SessionInfo"/> | 203 <has_text text="SessionInfo"/> |
193 </assert_contents> | 204 </assert_contents> |
194 </output> | 205 </output> |
206 </test> | |
207 <!-- Ensure BED output works --> | |
208 <test expect_num_outputs="1"> | |
209 <repeat name="rep_group"> | |
210 <param name="groupName" value="Resistant"/> | |
211 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/> | |
212 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" /> | |
213 </repeat> | |
214 <repeat name="rep_group"> | |
215 <param name="groupName" value="Responsive"/> | |
216 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/> | |
217 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" /> | |
218 </repeat> | |
219 <param name="scorecol" value="5" /> | |
220 <param name="format" value="bed"/> | |
221 <output name="outfile" ftype="bed" value="out_diffbind.bed" /> | |
222 </test> | |
223 <!-- Ensure tabular output works --> | |
224 <test expect_num_outputs="1"> | |
225 <repeat name="rep_group"> | |
226 <param name="groupName" value="Resistant"/> | |
227 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/> | |
228 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" /> | |
229 </repeat> | |
230 <repeat name="rep_group"> | |
231 <param name="groupName" value="Responsive"/> | |
232 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/> | |
233 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" /> | |
234 </repeat> | |
235 <param name="scorecol" value="5" /> | |
236 <param name="format" value="tabular"/> | |
237 <output name="outfile" ftype="tabular" file="out_diffbind.tab" /> | |
195 </test> | 238 </test> |
196 </tests> | 239 </tests> |
197 <help><![CDATA[ | 240 <help><![CDATA[ |
198 | 241 |
199 .. class:: infomark | 242 .. class:: infomark |
281 | 324 |
282 **Outputs** | 325 **Outputs** |
283 | 326 |
284 This tool outputs | 327 This tool outputs |
285 | 328 |
286 * a table of differentially bound sites | 329 * a table of differentially bound sites in Interval, BED or Tabular 0-based format |
287 | 330 |
288 Optionally, under **Output Options** you can choose to output | 331 Optionally, under **Output Options** you can choose to output |
289 | 332 |
290 * a PDF of plots (Heatmap, PCA, MA, Volcano, Boxplots) | 333 * a PDF of plots (Heatmap, PCA, MA, Volcano, Boxplots) |
291 * a binding affinity matrix | 334 * a binding affinity matrix |
293 * an RData file of the R objects generated | 336 * an RData file of the R objects generated |
294 * a text file with information on the analysis (number of Intervals, FriP scores, method used) | 337 * a text file with information on the analysis (number of Intervals, FriP scores, method used) |
295 | 338 |
296 **Differentially Bound Sites** | 339 **Differentially Bound Sites** |
297 | 340 |
341 The default output is Interval format, for information on Interval format see here_. Alternatively, you can choose to output BED or Tabular 0-based format as below. For an explanation of the 0-based and 1-based coordinate systems see this `Biostars post`_. | |
342 | |
343 Example - **Interval format**: | |
344 | |
345 ====== ====== ====== ======== ===== ====== =========================================== | |
346 Chrom Start End Name Score Strand **Comment** | |
347 ====== ====== ====== ======== ===== ====== =========================================== | |
348 chr18 394599 396513 DiffBind 0 \. 1914|7.15|5.55|7.89|-2.35|7.06e-24|9.84e-21 | |
349 chr18 111566 112005 DiffBind 0 \. 439|5.71|6.53|3.63|2.89|1.27e-08|8.88e-06 | |
350 chr18 346463 347342 DiffBind 0 \. 879|5|5.77|3.24|2.52|6.51e-06|0.00303 | |
351 chr18 399013 400382 DiffBind 0 \. 1369|7.62|7|8.05|-1.04|1.04e-05|0.00364 | |
352 chr18 371109 372102 DiffBind 0 \. 993|4.63|3.07|5.36|-2.3|8.1e-05|0.0226 | |
353 ====== ====== ====== ======== ===== ====== =========================================== | |
354 | |
355 Columns contain the following data: | |
356 | |
357 * **Chrom**: Chromosome name | |
358 * **Start**: Start position of site | |
359 * **End**: End position of site | |
360 * **Score**: 0 | |
361 * **Name**: DiffBind | |
362 * **Strand**: Strand | |
363 * **Comment**: The pipe ("|") separated values in this column correspond to: | |
364 | |
365 * *width*: Length of site | |
366 * *Conc*: Mean read concentration over all the samples (the default calculation uses log2 normalized ChIP read counts with control read counts subtracted) | |
367 * *Conc_Group1*: Mean concentration over the first group (e.g. Responsive) | |
368 * *Conc_Group2*: Mean concentration over second group (e.g. Resistant) | |
369 * *Fold*: Fold shows the difference in mean concentrations between the two groups (e.g. Responsive - Resistant), with a positive value indicating increased binding affinity in the first group and a negative value indicating increased binding affinity in the second group. | |
370 * *p.value*: P-value confidence measure for identifying these sites as differentially bound | |
371 * *FDR*: a multiple testing corrected FDR p-value | |
372 | |
373 Example - **BED format**: | |
374 | |
375 ===== ====== ====== ======== ===== ====== | |
376 Chrom Start End Name Score Strand | |
377 ===== ====== ====== ======== ===== ====== | |
378 chr18 394599 396513 DiffBind 0 \. | |
379 chr18 111566 112005 DiffBind 0 \. | |
380 chr18 346463 347342 DiffBind 0 \. | |
381 chr18 399013 400382 DiffBind 0 \. | |
382 chr18 371109 372102 DiffBind 0 \. | |
383 ===== ====== ====== ======== ===== ====== | |
384 | |
385 Example - **Tabular format**: | |
386 | |
387 ===== ====== ====== ======== ===== ====== ==== =============== ============== ===== ======== ======== | |
388 Chrom Start End Name Score Strand Conc Conc_Responsive Conc_Resistant Fold p.value FDR | |
389 ===== ====== ====== ======== ===== ====== ==== =============== ============== ===== ======== ======== | |
390 chr18 394599 396513 DiffBind 0 \. 7.15 5.55 7.89 -2.35 7.06E-24 9.84E-21 | |
391 chr18 111566 112005 DiffBind 0 \. 5.71 6.53 3.63 2.89 1.27E-08 8.88E-06 | |
392 chr18 346463 347342 DiffBind 0 \. 5 5.77 3.24 2.52 6.51E-06 0.00303 | |
393 chr18 399013 400382 DiffBind 0 \. 7.62 7 8.05 -1.04 1.04E-05 0.00364 | |
394 chr18 371109 372102 DiffBind 0 \. 4.63 3.07 5.36 -2.3 8.10E-05 0.0226 | |
395 ===== ====== ====== ======== ===== ====== ==== =============== ============== ===== ======== ======== | |
396 | |
397 | |
398 **Binding Affinity Matrix** | |
399 | |
400 The final result of counting is a binding affinity matrix containing a (normalized) read count for each sample at every potential binding site. With this matrix, the samples can be re-clustered using affinity, rather than occupancy, data. The binding affinity matrix can be used for QC plotting as well as for subsequent | |
401 differential analysis. Note that this output is a tabular 0-based format. | |
402 | |
298 Example: | 403 Example: |
299 | 404 |
300 ======== ====== ====== ===== ====== ===== =============== ============== ====== ======== ======== | |
301 seqnames start end width strand Conc Conc_Responsive Conc_Resistant Fold p.value **FDR** | |
302 ======== ====== ====== ===== ====== ===== =============== ============== ====== ======== ======== | |
303 chr18 394600 396513 1914 \* 7.15 5.55 7.89 -2.35 7.06e-24 9.84e-21 | |
304 chr18 111567 112005 439 \* 5.71 6.53 3.63 2.89 1.27e-08 8.88e-06 | |
305 chr18 346464 347342 879 \* 5 5.77 3.24 2.52 6.51e-06 0.00303 | |
306 chr18 399014 400382 1369 \* 7.62 7 8.05 -1.04 1.04e-05 0.00364 | |
307 chr18 371110 372102 993 \* 4.63 3.07 5.36 -2.3 8.1e-05 0.0226 | |
308 ======== ====== ====== ===== ====== ===== =============== ============== ====== ======== ======== | |
309 | |
310 Columns contain the following data: | |
311 | |
312 * **seqnames**: Chromosome name | |
313 * **start**: Start position of site | |
314 * **end**: End position of site | |
315 * **width**: Length of site | |
316 * **strand**: Strand | |
317 * **Conc**: Mean read concentration over all the samples (the default calculation uses log2 normalized ChIP read counts with control read counts subtracted) | |
318 * **Responsive**: Mean concentration over the first (e.g. Responsive) group | |
319 * **Resistant**: Mean concentration over second (e.g. Resistant) group | |
320 * **Fold**: Fold shows the difference in mean concentrations between the two groups (e.g. Responsive - Resistant), with a positive value indicating increased binding affinity in the first group and a negative value indicating increased binding affinity in the second group. | |
321 * **p.value**: P-value confidence measure for identifying these sites as differentially bound | |
322 * **FDR**: a multiple testing corrected FDR p-value | |
323 | |
324 | |
325 **Binding Affinity Matrix** | |
326 | |
327 The final result of counting is a binding affinity matrix containing a (normalized) read count for each sample at every potential binding site. With this matrix, the samples can be re-clustered using affinity, rather than occupancy, data. The binding affinity matrix can be used for QC plotting as well as for subsequent | |
328 differential analysis. | |
329 | |
330 Example: | |
331 | |
332 ===== ====== ====== ========= ========= ========== ========== | 405 ===== ====== ====== ========= ========= ========== ========== |
333 CHR START END MCF7_ER_1 MCF7_ER_2 BT474_ER_1 BT474_ER_2 | 406 Chrom Start End MCF7_ER_1 MCF7_ER_2 BT474_ER_1 BT474_ER_2 |
334 ===== ====== ====== ========= ========= ========== ========== | 407 ===== ====== ====== ========= ========= ========== ========== |
335 chr18 111567 112005 137.6152 59.87837 29.41393 19.95945 | 408 chr18 111567 112005 137.6152 59.87837 29.41393 19.95945 |
336 chr18 189223 189652 19.95945 12.60597 11.55547 23.11095 | 409 chr18 189223 189652 19.95945 12.60597 11.55547 23.11095 |
337 chr18 215232 216063 11.55547 15.75746 31.51493 72.48434 | 410 chr18 215232 216063 11.55547 15.75746 31.51493 72.48434 |
338 chr18 311530 312172 17.85846 11.55547 54.62588 43.07040 | 411 chr18 311530 312172 17.85846 11.55547 54.62588 43.07040 |
424 | 497 |
425 .. _DiffBind: https://bioconductor.org/packages/release/bioc/html/DiffBind.html | 498 .. _DiffBind: https://bioconductor.org/packages/release/bioc/html/DiffBind.html |
426 .. _`Bioconductor package`: https://bioconductor.org/packages/release/bioc/html/DiffBind.html | 499 .. _`Bioconductor package`: https://bioconductor.org/packages/release/bioc/html/DiffBind.html |
427 .. _`DiffBind User Guide`: https://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf | 500 .. _`DiffBind User Guide`: https://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf |
428 .. _`Bioconductor post`: https://support.bioconductor.org/p/69924/ | 501 .. _`Bioconductor post`: https://support.bioconductor.org/p/69924/ |
502 .. _here: https://galaxyproject.org/learn/datatypes/#interval | |
503 .. _`Biostars post`: https://www.biostars.org/p/84686/ | |
429 | 504 |
430 ]]> | 505 ]]> |
431 </help> | 506 </help> |
432 <citations> | 507 <citations> |
433 <citation type="doi">doi:10.1038/nature10730</citation> | 508 <citation type="doi">doi:10.1038/nature10730</citation> |