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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
author iuc
date Mon, 08 Jul 2024 18:31:51 +0000
parents 2605cbdaa7d8
children
comparison
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17:2605cbdaa7d8 18:f907216064f6
1 <tool id="diffbind" name="DiffBind" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="diffbind" name="DiffBind" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description> differential binding analysis of ChIP-Seq peak data</description> 2 <description> differential binding analysis of ChIP-Seq peak data</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">2.10.0</token> 4 <token name="@TOOL_VERSION@">3.12.0</token>
5 <token name="@VERSION_SUFFIX@">1</token> 5 <token name="@VERSION_SUFFIX@">0</token>
6 <token name="@PROFILE@">22.05</token> 6 <token name="@PROFILE@">22.05</token>
7 </macros> 7 </macros>
8 <xrefs> 8 <xrefs>
9 <xref type="bio.tools">diffbind</xref> 9 <xref type="bio.tools">diffbind</xref>
10 <xref type="bioconductor">diffbind</xref> 10 <xref type="bioconductor">diffbind</xref>
11 </xrefs> 11 </xrefs>
12 <requirements> 12 <requirements>
13 <requirement type="package" version="@TOOL_VERSION@">bioconductor-diffbind</requirement> 13 <requirement type="package" version="@TOOL_VERSION@">bioconductor-diffbind</requirement>
14 <requirement type="package" version="3.5.1">r-base</requirement> 14 <requirement type="package" version="1.20.4">r-getopt</requirement>
15 <requirement type="package" version="1.20.3">r-getopt</requirement> 15 <requirement type="package" version="4.0.16">bioconductor-edger</requirement>
16 <requirement type="package" version="0.2.20">r-rjson</requirement>
17 </requirements> 16 </requirements>
18 <stdio> 17 <stdio>
19 <regex match="Execution halted" 18 <regex match="Execution halted"
20 source="both" 19 source="both"
21 level="fatal" 20 level="fatal"
69 68
70 #if str( $g.bamcontrol ) != 'None': 69 #if str( $g.bamcontrol ) != 'None':
71 #for $ctrl in $g.bamcontrol: 70 #for $ctrl in $g.bamcontrol:
72 #set $ctrl_name = re.sub('[^\w\-]', '_', str($ctrl.element_identifier)) 71 #set $ctrl_name = re.sub('[^\w\-]', '_', str($ctrl.element_identifier))
73 #set $ctrl_file = $ctrl_name + "-bamcontrol.bam" 72 #set $ctrl_file = $ctrl_name + "-bamcontrol.bam"
74 #set ctrl_index = $ctrl_name + "-bamcontrol.bai" 73 #set $ctrl_index = $ctrl_name + "-bamcontrol.bai"
75 #if $ctrl_file not in json.dumps($temp_factor): 74 #if $ctrl_file not in json.dumps($temp_factor):
76 ln -s '${ctrl}' '${ctrl_file}' && 75 ln -s '${ctrl}' '${ctrl_file}' &&
77 ln -s '${ctrl.metadata.bam_index}' '${ctrl_index}' && 76 ln -s '${ctrl.metadata.bam_index}' '${ctrl_index}' &&
78 #end if 77 #end if
79 #set $bam_controls[str($ctrl.element_identifier)] = str($ctrl_file) 78 #set $bam_controls[str($ctrl.element_identifier)] = str($ctrl_file)
92 91
93 Rscript '$__tool_directory__/diffbind.R' 92 Rscript '$__tool_directory__/diffbind.R'
94 93
95 -i '#echo json.dumps(temp_factor_names)#' 94 -i '#echo json.dumps(temp_factor_names)#'
96 -o '$outfile' 95 -o '$outfile'
96 -m '$method'
97 -t $th 97 -t $th
98 -f $out.format 98 -f $out.format
99 -p '$plots' 99 -p '$plots'
100 100 -O $minoverlap
101 #if $scorecol: 101 #if $use_blacklist:
102 -n "$scorecol" 102 -B
103 #end if 103 #end if
104 -n $scorecol
104 #if $lowerbetter: 105 #if $lowerbetter:
105 -l "$lowerbetter" 106 -l "$lowerbetter"
106 #end if 107 #end if
107 #if $summits: 108 #if $summits:
108 -s "$summits" 109 -s "$summits"
136 </param> 137 </param>
137 <param name="peaks" type="data" format="bed" multiple="true" label="Peak files" help="Result of your Peak calling experiment"/> 138 <param name="peaks" type="data" format="bed" multiple="true" label="Peak files" help="Result of your Peak calling experiment"/>
138 <param name="bamreads" type="data" format="bam" multiple="true" label="Read BAM files" help="Specify the Read BAM files used in the Peak calling. The input order of the BAM files for the samples MUST match the input order of the peaks files."/> 139 <param name="bamreads" type="data" format="bam" multiple="true" label="Read BAM files" help="Specify the Read BAM files used in the Peak calling. The input order of the BAM files for the samples MUST match the input order of the peaks files."/>
139 <param name="bamcontrol" type="data" format="bam" multiple="true" optional="True" label="Control BAM files" help="If specifying a control BAM file, all samples are required to specify one, see Help section below. The input order of the BAM files for the samples MUST match the input order of the peaks files."/> 140 <param name="bamcontrol" type="data" format="bam" multiple="true" optional="True" label="Control BAM files" help="If specifying a control BAM file, all samples are required to specify one, see Help section below. The input order of the BAM files for the samples MUST match the input order of the peaks files."/>
140 </repeat> 141 </repeat>
141 142 <param name="method" type="select" label="Underlying method by which to analyze differential binding affinity">
142 <param name="scorecol" type="integer" min="0" value="8" label="Score Column" help="Column in peak files that contains peak scores. Default: 8 (narrowPeak)"> 143 <option value="DBA_DESEQ2" selected="True">DESeq2</option>
144 <option value="DBA_EDGER">edgeR</option>
145 </param>
146 <param name="use_blacklist" type="boolean" truevalue="True" falsevalue="" checked="False" label="Filters peak intervals that overlap a blacklist from ENCODE" help="Works with human, mouse, worm and fly. Assembly version is determined from the BAM files." />
147 <param name="minoverlap" type="integer" min="1" value="2" label="Only include peaks in at least this many peaksets in the main binding matrix">
148 <sanitizer>
149 <valid initial="string.digits"/>
150 </sanitizer>
151 </param>
152 <param name="scorecol" type="integer" min="0" value="5" label="Score Column" help="Column in peak files that contains peak scores. Default: 5 (narrowPeak)">
143 <sanitizer> 153 <sanitizer>
144 <valid initial="string.digits"/> 154 <valid initial="string.digits"/>
145 </sanitizer> 155 </sanitizer>
146 </param> 156 </param>
147 <param name="lowerbetter" type="boolean" truevalue="True" falsevalue="" checked="False" label="Lower score is better?" help="DiffBind by default assumes that a higher score indicates a better peak, for example narrowPeaks -log10pvalue. If this is not the case, for example if the score is a p-value or FDR, set this option to Yes. Default: No" /> 157 <param name="lowerbetter" type="boolean" truevalue="True" falsevalue="" checked="False" label="Lower score is better?" help="DiffBind by default assumes that a higher score indicates a better peak, for example narrowPeaks -log10pvalue. If this is not the case, for example if the score is a p-value or FDR, set this option to Yes. Default: No" />
224 <assert_contents> 234 <assert_contents>
225 <has_text text="SessionInfo"/> 235 <has_text text="SessionInfo"/>
226 </assert_contents> 236 </assert_contents>
227 </output> 237 </output>
228 </test> 238 </test>
239 <!-- Ensure EDGER works -->
240 <test expect_num_outputs="3">
241 <repeat name="rep_group">
242 <param name="groupName" value="Resistant"/>
243 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
244 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" />
245 </repeat>
246 <repeat name="rep_group">
247 <param name="groupName" value="Responsive"/>
248 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/>
249 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" />
250 </repeat>
251 <param name="scorecol" value="5" />
252 <param name="method" value="DBA_EDGER" />
253 <param name="format" value="interval"/>
254 <param name="pdf" value="True" />
255 <param name="binding_matrix" value="True" />
256 <param name="rscript" value="False"/>
257 <output name="outfile" ftype="interval" value="out_diffbind_edger.interval" />
258 <output name="plots" value="out_plots_edger.pdf" compare="sim_size" />
259 <output name="binding_matrix" value="out_binding_matrix_edger.tab" />
260 </test>
229 <!-- Ensure control BAMs input works --> 261 <!-- Ensure control BAMs input works -->
230 <test expect_num_outputs="1"> 262 <test expect_num_outputs="1">
231 <repeat name="rep_group"> 263 <repeat name="rep_group">
232 <param name="groupName" value="Resistant"/> 264 <param name="groupName" value="Resistant"/>
233 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/> 265 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
273 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" /> 305 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" />
274 </repeat> 306 </repeat>
275 <param name="scorecol" value="5" /> 307 <param name="scorecol" value="5" />
276 <param name="format" value="tabular"/> 308 <param name="format" value="tabular"/>
277 <output name="outfile" ftype="tabular" file="out_diffbind.tab" /> 309 <output name="outfile" ftype="tabular" file="out_diffbind.tab" />
310 </test>
311 <!-- Ensure minoverlap works -->
312 <test expect_num_outputs="1">
313 <repeat name="rep_group">
314 <param name="groupName" value="Resistant"/>
315 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
316 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" />
317 </repeat>
318 <repeat name="rep_group">
319 <param name="groupName" value="Responsive"/>
320 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/>
321 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" />
322 </repeat>
323 <param name="minoverlap" value="1" />
324 <param name="scorecol" value="5" />
325 <param name="format" value="tabular"/>
326 <output name="outfile" ftype="tabular" file="out_diffbind_minoverlap1.tab" />
327 </test>
328 <!-- Ensure blacklist filtering works -->
329 <test expect_num_outputs="1">
330 <repeat name="rep_group">
331 <param name="groupName" value="Resistant"/>
332 <param name="peaks" ftype="bed" value="BT474_ER_1.bed.gz,BT474_ER_2.bed.gz"/>
333 <param name="bamreads" ftype="bam" value="BT474_ER_1.bam,BT474_ER_2.bam" />
334 </repeat>
335 <repeat name="rep_group">
336 <param name="groupName" value="Responsive"/>
337 <param name="peaks" ftype="bed" value="MCF7_ER_1.bed.gz,MCF7_ER_2.bed.gz"/>
338 <param name="bamreads" ftype="bam" value="MCF7_ER_1.bam,MCF7_ER_2.bam" />
339 </repeat>
340 <param name="use_blacklist" value="True"/>
341 <param name="scorecol" value="5" />
342 <param name="format" value="tabular"/>
343 <output name="outfile" ftype="tabular" file="out_diffbind_blacklist.tab" />
278 </test> 344 </test>
279 </tests> 345 </tests>
280 <help><![CDATA[ 346 <help><![CDATA[
281 347
282 .. class:: infomark 348 .. class:: infomark
418 Example - **BED format**: 484 Example - **BED format**:
419 485
420 ===== ====== ====== ======== ===== ====== 486 ===== ====== ====== ======== ===== ======
421 Chrom Start End Name Score Strand 487 Chrom Start End Name Score Strand
422 ===== ====== ====== ======== ===== ====== 488 ===== ====== ====== ======== ===== ======
423 chr18 394599 396513 DiffBind 0 \. 489 chr18 394599 396513 DiffBind 0 \.
424 chr18 111566 112005 DiffBind 0 \. 490 chr18 111566 112005 DiffBind 0 \.
425 chr18 346463 347342 DiffBind 0 \. 491 chr18 346463 347342 DiffBind 0 \.
426 chr18 399013 400382 DiffBind 0 \. 492 chr18 399013 400382 DiffBind 0 \.
427 chr18 371109 372102 DiffBind 0 \. 493 chr18 371109 372102 DiffBind 0 \.
428 ===== ====== ====== ======== ===== ====== 494 ===== ====== ====== ======== ===== ======
429 495
430 Example - **Tabular format**: 496 Example - **Tabular format**:
431 497
432 ===== ====== ====== ======== ===== ====== ==== =============== ============== ===== ======== ======== 498 ===== ====== ====== ======== ===== ====== ==== =============== ============== ===== ======== ========