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comparison deseq2.xml @ 27:d027d1f4984e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
author iuc
date Mon, 28 Jun 2021 05:14:25 +0000
parents 6a3a025714d3
children 7ff33c2d525b
comparison
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26:6a3a025714d3 27:d027d1f4984e
1 <tool id="deseq2" name="DESeq2" version="2.11.40.6+galaxy1"> 1 <tool id="deseq2" name="DESeq2" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@">
2 <description>Determines differentially expressed features from count tables</description> 2 <description>Determines differentially expressed features from count tables</description>
3 <macros> 3 <macros>
4 <import>deseq2_macros.xml</import> 4 <import>deseq2_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <expand macro='requirements'/>
7 <requirement type="package" version="1.22.1">bioconductor-deseq2</requirement> 7 <expand macro='edam_ontology' />
8 <!-- Optional dependency of tximport, needed to import kallisto results https://github.com/galaxyproject/usegalaxy-playbook/issues/161 --> 8 <expand macro='xrefs'/>
9 <requirement type="package" version="2.26.2">bioconductor-rhdf5</requirement>
10 <requirement type="package" version="1.10.0">bioconductor-tximport</requirement>
11 <requirement type="package" version="1.34.1">bioconductor-genomicfeatures</requirement>
12 <requirement type="package" version="1.20.2">r-getopt</requirement>
13 <requirement type="package" version="0.8.0">r-ggrepel</requirement>
14 <requirement type="package" version="3.0.1">r-gplots</requirement>
15 <requirement type="package" version="1.0.10">r-pheatmap</requirement>
16 <requirement type="package" version="0.2.20">r-rjson</requirement>
17 </requirements>
18 <stdio> 9 <stdio>
19 <regex match="Execution halted" 10 <regex match="Execution halted"
20 source="both" 11 source="both"
21 level="fatal" 12 level="fatal"
22 description="Execution halted." /> 13 description="Execution halted." />
47 #import json 38 #import json
48 #import os 39 #import os
49 Rscript '${__tool_directory__}/deseq2.R' 40 Rscript '${__tool_directory__}/deseq2.R'
50 --cores \${GALAXY_SLOTS:-1} 41 --cores \${GALAXY_SLOTS:-1}
51 -o '$deseq_out' 42 -o '$deseq_out'
52 #if $pdf: 43 #if 'pdf' in $output_options.output_selector:
53 -p '$plots' 44 -p '$plots'
54 #end if 45 #end if
55 #if $normCounts: 46 -A $output_options.alpha_ma
47 #if 'normCounts' in $output_options.output_selector:
56 -n '$counts_out' 48 -n '$counts_out'
57 #end if 49 #end if
58 #if $normRLog: 50 #if 'normRLog' in $output_options.output_selector:
59 -r '$rlog_out' 51 -r '$rlog_out'
60 #end if 52 #end if
61 #if $normVST: 53 #if 'normVST' in $output_options.output_selector:
62 -v '$vst_out' 54 -v '$vst_out'
63 #end if 55 #end if
64 #set $filename_to_element_identifiers = {} 56 #set $filename_to_element_identifiers = {}
65 #set $temp_factor_names = list() 57 #set $temp_factor_names = list()
66 #for $factor in $select_data.rep_factorName: 58 #for $factor in $select_data.rep_factorName:
88 80
89 $header 81 $header
90 82
91 -f '#echo json.dumps(temp_factor_names)#' 83 -f '#echo json.dumps(temp_factor_names)#'
92 -l '#echo json.dumps(filename_to_element_identifiers)#' 84 -l '#echo json.dumps(filename_to_element_identifiers)#'
93 #if $esf: 85 #if $advanced_options.esf:
94 -e $esf 86 -e $advanced_options.esf
95 #end if 87 #end if
96 -t $fit_type 88 -t $advanced_options.fit_type
97 #if $batch_factors: 89 #if $batch_factors:
98 --batch_factors '$batch_factors' 90 --batch_factors '$batch_factors'
99 #end if 91 #end if
100 #if $outlier_replace_off: 92 #if $advanced_options.outlier_replace_off:
101 -a 93 -a
102 #end if 94 #end if
103 #if $outlier_filter_off: 95 #if $advanced_options.outlier_filter_off:
104 -b 96 -b
105 #end if 97 #end if
106 #if $auto_mean_filter_off: 98 #if $advanced_options.auto_mean_filter_off:
107 -c 99 -c
108 #end if 100 #end if
109 #if $many_contrasts: 101 #if 'many_contrasts' in $output_options.output_selector
110 -m 102 -m
111 #end if 103 #end if
112 #if $tximport.tximport_selector == 'tximport': 104 #if $tximport.tximport_selector == 'tximport':
113 -i 105 -i
114 -y $tximport.txtype 106 -y $tximport.txtype
166 </when> 158 </when>
167 </conditional> 159 </conditional>
168 </when> 160 </when>
169 <when value="count" /> 161 <when value="count" />
170 </conditional> 162 </conditional>
171 <param name="pdf" type="boolean" truevalue="1" falsevalue="0" checked="true" 163 <section name="advanced_options" title="Advanced options">
172 label="Visualising the analysis results" 164 <param name="esf" type="select" label="Method for estimateSizeFactors"
173 help="output an additional PDF files" /> 165 help="Method for estimation: either 'ratio', 'poscounts', or 'iterate'. 'ratio' uses the standard median ratio method introduced in DESeq.
174 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false" 166 The size factor is the median ratio of the sample over a 'pseudosample': for each gene, the geometric mean of all samples.
175 label="Output normalized counts table" /> 167 'poscounts' and 'iterate' offer alternative estimators, which can be used even when all genes contain a sample with a zero (a problem
176 <param name="normRLog" type="boolean" truevalue="1" falsevalue="0" checked="false" 168 for the default method, as the geometric mean becomes zero, and the ratio undefined). The 'poscounts' estimator deals with a gene with
177 label="Output rLog normalized table" /> 169 some zeros, by calculating a modified geometric mean by taking the n-th root of the product of the non-zero counts. This evolved out of
178 <param name="normVST" type="boolean" truevalue="1" falsevalue="0" checked="false" 170 use cases with Paul McMurdie's phyloseq package for metagenomic samples. The 'iterate' estimator iterates between estimating the dispersion
179 label="Output VST normalized table" /> 171 with a design of ~1, and finding a size factor vector by numerically optimizing the likelihood of the ~1 model.">
180 <param name="many_contrasts" type="boolean" truevalue="1" falsevalue="0" checked="false" 172 <option value="" selected="true">No Selection (use default)</option>
181 label="Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)" 173 <option value="ratio">ratio</option>
182 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" /> 174 <option value="poscounts">poscounts</option>
183 <param name="esf" type="select" label="(Optional) Method for estimateSizeFactors" 175 <option value="iterate">iterate</option>
184 help="Method for estimation: either 'ratio', 'poscounts', or 'iterate'. 'ratio' uses the standard median ratio method introduced in DESeq. 176 </param>
185 The size factor is the median ratio of the sample over a 'pseudosample': for each gene, the geometric mean of all samples. 177 <param name="fit_type" type="select" label="Fit type">
186 'poscounts' and 'iterate' offer alternative estimators, which can be used even when all genes contain a sample with a zero (a problem 178 <option value="1" selected="true">parametric</option>
187 for the default method, as the geometric mean becomes zero, and the ratio undefined). The 'poscounts' estimator deals with a gene with 179 <option value="2">local</option>
188 some zeros, by calculating a modified geometric mean by taking the n-th root of the product of the non-zero counts. This evolved out of 180 <option value="3">mean</option>
189 use cases with Paul McMurdie's phyloseq package for metagenomic samples. The 'iterate' estimator iterates between estimating the dispersion 181 </param>
190 with a design of ~1, and finding a size factor vector by numerically optimizing the likelihood of the ~1 model."> 182 <param name="outlier_replace_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
191 <option value="" selected="true">No Selection (use default)</option> 183 label="Turn off outliers replacement (only affects with >6 replicates)"
192 <option value="ratio">ratio</option> 184 help="When there are more than 6 replicates for a given sample, the DESeq2 will automatically replace
193 <option value="poscounts">poscounts</option> 185 counts with large Cook’s distance with the trimmed mean over all samples, scaled up by the size factor
194 <option value="iterate">iterate</option> 186 or normalization factor for that sample" />
195 </param> 187 <param name="outlier_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
196 <param name="fit_type" type="select" label="Fit type"> 188 label="Turn off outliers filtering (only affects with >2 replicates)"
197 <option value="1" selected="true">parametric</option> 189 help="When there are more than 2 replicates for a given sample, the DESeq2 will automatically
198 <option value="2">local</option> 190 filter genes which contain a Cook’s distance above a cutoff" />
199 <option value="3">mean</option> 191 <param name="auto_mean_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
200 </param> 192 label="Turn off independent filtering"
201 <param name="outlier_replace_off" type="boolean" truevalue="1" falsevalue="0" checked="false" 193 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
202 label="Turn off outliers replacement (only affects with >6 replicates)" 194 </section>
203 help="When there are more than 6 replicates for a given sample, the DESeq2 will automatically replace 195 <section name="output_options" title="Output options">
204 counts with large Cook’s distance with the trimmed mean over all samples, scaled up by the size factor 196 <param name="output_selector" type="select" multiple="True" display="checkboxes" label="Output selector">
205 or normalization factor for that sample" /> 197 <option value="pdf" selected="True">Generate plots for visualizing the analysis results</option>
206 <param name="outlier_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false" 198 <option value="normCounts">Output rLog normalized table</option>
207 label="Turn off outliers filtering (only affects with >2 replicates)" 199 <option value="normVST">Output VST normalized table</option>
208 help="When there are more than 2 replicates for a given sample, the DESeq2 will automatically 200 <option value="normRLog">Output rLog normalized table</option>
209 filter genes which contain a Cook’s distance above a cutoff" /> 201 <option value="many_contrasts">Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)</option>
210 <param name="auto_mean_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false" 202 </param>
211 label="Turn off independent filtering" 203 <param name="alpha_ma" type="float" min="0" max="0.5" value="0.1" label="Alpha value for MA-plot" help="Default value is 0.1. This option is only meaninful when plots are generated" />
212 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" /> 204 </section>
213 </inputs> 205 </inputs>
214 <outputs> 206 <outputs>
215 <data name="deseq_out" format="tabular" label="DESeq2 result file on ${on_string}"> 207 <data name="deseq_out" format="tabular" label="DESeq2 result file on ${on_string}">
216 <filter>many_contrasts is False</filter> 208 <filter>'many_contrasts' not in output_options['output_selector']</filter>
217 <actions> 209 <actions>
218 <action name="column_names" type="metadata" default="GeneID,Base mean,log2(FC),StdErr,Wald-Stats,P-value,P-adj" /> 210 <action name="column_names" type="metadata" default="GeneID,Base mean,log2(FC),StdErr,Wald-Stats,P-value,P-adj" />
219 </actions> 211 </actions>
220 </data> 212 </data>
221 <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}"> 213 <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}">
222 <filter>many_contrasts is True</filter> 214 <filter>output_options['output_selector'] and 'many_contrasts' in output_options['output_selector']</filter>
223 <discover_datasets pattern="(?P&lt;designation&gt;.+_vs_.+)" format="tabular" directory="." visible="false"/> 215 <discover_datasets pattern="(?P&lt;designation&gt;.+_vs_.+)" format="tabular" directory="." visible="false"/>
224 </collection> 216 </collection>
225 <data name="plots" format="pdf" label="DESeq2 plots on ${on_string}"> 217 <data name="plots" format="pdf" label="DESeq2 plots on ${on_string}">
226 <filter>pdf == True</filter> 218 <filter>output_options['output_selector'] and 'pdf' in output_options['output_selector']</filter>
227 </data> 219 </data>
228 <data name="counts_out" format="tabular" label="Normalized counts file on ${on_string}"> 220 <data name="counts_out" format="tabular" label="Normalized counts file on ${on_string}">
229 <filter>normCounts == True</filter> 221 <filter>output_options['output_selector'] and 'normCounts' in output_options['output_selector']</filter>
230 </data> 222 </data>
231 <data name="rlog_out" format="tabular" label="rLog-Normalized counts file on ${on_string}"> 223 <data name="rlog_out" format="tabular" label="rLog-Normalized counts file on ${on_string}">
232 <filter>normRLog == True</filter> 224 <filter>output_options['output_selector'] and 'normRLog' in output_options['output_selector']</filter>
233 </data> 225 </data>
234 <data name="vst_out" format="tabular" label="VST-Normalized counts file on ${on_string}"> 226 <data name="vst_out" format="tabular" label="VST-Normalized counts file on ${on_string}">
235 <filter>normVST == True</filter> 227 <filter>output_options['output_selector'] and 'normVST' in output_options['output_selector']</filter>
236 </data> 228 </data>
237 </outputs> 229 </outputs>
238 <tests> 230 <tests>
239 <!--Ensure counts files with header works --> 231 <!--Ensure counts files with header works -->
240 <test expect_num_outputs="4"> 232 <test expect_num_outputs="4">
247 <repeat name="rep_factorLevel"> 239 <repeat name="rep_factorLevel">
248 <param name="factorLevel" value="Untreated"/> 240 <param name="factorLevel" value="Untreated"/>
249 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/> 241 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
250 </repeat> 242 </repeat>
251 </repeat> 243 </repeat>
252 <param name="pdf" value="False"/> 244 <section name="output_options">
253 <param name="normCounts" value="True"/> 245 <param name="output_selector" value="normCounts,normRLog,normVST"/>
254 <param name="normRLog" value="True"/> 246 </section>
255 <param name="normVST" value="True"/>
256 <output name="counts_out"> 247 <output name="counts_out">
257 <assert_contents> 248 <assert_contents>
258 <has_text_matching expression="GSM461176_untreat_single.counts\tGSM461177_untreat_paired.counts\tGSM461178_untreat_paired.counts\tGSM461182_untreat_single.counts\tGSM461179_treat_single.counts\tGSM461180_treat_paired.counts\tGSM461181_treat_paired.counts" /> 249 <has_text_matching expression="GSM461176_untreat_single.counts\tGSM461177_untreat_paired.counts\tGSM461178_untreat_paired.counts\tGSM461182_untreat_single.counts\tGSM461179_treat_single.counts\tGSM461180_treat_paired.counts\tGSM461181_treat_paired.counts" />
259 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" /> 250 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
260 </assert_contents> 251 </assert_contents>
289 <param name="factorLevel" value="Untreated"/> 280 <param name="factorLevel" value="Untreated"/>
290 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/> 281 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
291 </repeat> 282 </repeat>
292 </repeat> 283 </repeat>
293 <param name="batch_factors" value="batch_factors.tab"/> 284 <param name="batch_factors" value="batch_factors.tab"/>
294 <param name="pdf" value="False"/> 285 <section name="output_options">
295 <param name="normCounts" value="True"/> 286 <param name="output_selector" value="normCounts"/>
287 </section>
296 <output name="deseq_out"> 288 <output name="deseq_out">
297 <assert_contents> 289 <assert_contents>
298 <has_text_matching expression="FBgn0003360\t1933.*\t-2.9.*\t0.1.*\t-26.*\t1.*-152\t4.*-149" /> 290 <has_text_matching expression="FBgn0003360\t1933.*\t-2.9.*\t0.1.*\t-26.*\t1.*-152\t4.*-149" />
299 </assert_contents> 291 </assert_contents>
300 </output> 292 </output>
311 <param name="factorLevel" value="Untreated"/> 303 <param name="factorLevel" value="Untreated"/>
312 <param name="countsFile" value="GSM461176_untreat_single.counts.noheader,GSM461177_untreat_paired.counts.noheader,GSM461178_untreat_paired.counts.noheader,GSM461182_untreat_single.counts.noheader"/> 304 <param name="countsFile" value="GSM461176_untreat_single.counts.noheader,GSM461177_untreat_paired.counts.noheader,GSM461178_untreat_paired.counts.noheader,GSM461182_untreat_single.counts.noheader"/>
313 </repeat> 305 </repeat>
314 </repeat> 306 </repeat>
315 <param name="header" value="False"/> 307 <param name="header" value="False"/>
316 <param name="pdf" value="False"/> 308 <section name="output_options">
317 <param name="normCounts" value="True"/> 309 <param name="output_selector" value="normCounts,normRLog,normVST"/>
318 <param name="normRLog" value="True"/> 310 </section>
319 <param name="normVST" value="True"/>
320 <output name="counts_out"> 311 <output name="counts_out">
321 <assert_contents> 312 <assert_contents>
322 <has_text_matching expression="GSM461176_untreat_single.counts.noheader\tGSM461177_untreat_paired.counts.noheader\tGSM461178_untreat_paired.counts.noheader\tGSM461182_untreat_single.counts.noheader\tGSM461179_treat_single.counts.noheader\tGSM461180_treat_paired.counts.noheader\tGSM461181_treat_paired.counts.noheader" /> 313 <has_text_matching expression="GSM461176_untreat_single.counts.noheader\tGSM461177_untreat_paired.counts.noheader\tGSM461178_untreat_paired.counts.noheader\tGSM461182_untreat_single.counts.noheader\tGSM461179_treat_single.counts.noheader\tGSM461180_treat_paired.counts.noheader\tGSM461181_treat_paired.counts.noheader" />
323 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" /> 314 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
324 </assert_contents> 315 </assert_contents>
352 <repeat name="rep_factorLevel"> 343 <repeat name="rep_factorLevel">
353 <param name="factorLevel" value="Untreated"/> 344 <param name="factorLevel" value="Untreated"/>
354 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/> 345 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/>
355 </repeat> 346 </repeat>
356 </repeat> 347 </repeat>
357 <param name="pdf" value="False"/> 348 <section name="output_options">
349 <param name="output_selector" value=""/>
350 </section>
358 <param name="tximport_selector" value="tximport"/> 351 <param name="tximport_selector" value="tximport"/>
359 <param name="txtype" value="sailfish"/> 352 <param name="txtype" value="sailfish"/>
360 <param name="mapping_format_selector" value="tabular"/> 353 <param name="mapping_format_selector" value="tabular"/>
361 <param name="tabular_file" value="tx2gene.tab"/> 354 <param name="tabular_file" value="tx2gene.tab"/>
362 <output name="deseq_out" > 355 <output name="deseq_out" >
376 <repeat name="rep_factorLevel"> 369 <repeat name="rep_factorLevel">
377 <param name="factorLevel" value="Untreated"/> 370 <param name="factorLevel" value="Untreated"/>
378 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/> 371 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/>
379 </repeat> 372 </repeat>
380 </repeat> 373 </repeat>
381 <param name="pdf" value="False"/> 374 <section name="output_options">
375 <param name="output_selector" value=""/>
376 </section>
382 <param name="tximport_selector" value="tximport"/> 377 <param name="tximport_selector" value="tximport"/>
383 <param name="txtype" value="sailfish"/> 378 <param name="txtype" value="sailfish"/>
384 <param name="mapping_format_selector" value="gtf"/> 379 <param name="mapping_format_selector" value="gtf"/>
385 <param name="gtf_file" value="GRCh38_latest_genomic.gff"/> 380 <param name="gtf_file" value="GRCh38_latest_genomic.gff"/>
386 <output name="deseq_out" > 381 <output name="deseq_out" >
400 <repeat name="rep_factorLevel"> 395 <repeat name="rep_factorLevel">
401 <param name="factorLevel" value="Untreated"/> 396 <param name="factorLevel" value="Untreated"/>
402 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/> 397 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/>
403 </repeat> 398 </repeat>
404 </repeat> 399 </repeat>
405 <param name="pdf" value="False"/> 400 <section name="output_options">
401 <param name="output_selector" value=""/>
402 </section>
406 <param name="tximport_selector" value="tximport"/> 403 <param name="tximport_selector" value="tximport"/>
407 <param name="txtype" value="sailfish"/> 404 <param name="txtype" value="sailfish"/>
408 <param name="mapping_format_selector" value="gtf"/> 405 <param name="mapping_format_selector" value="gtf"/>
409 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/> 406 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/>
410 <output name="deseq_out" > 407 <output name="deseq_out" >
435 <repeat name="rep_factorLevel"> 432 <repeat name="rep_factorLevel">
436 <param name="factorLevel" value="Untreated"/> 433 <param name="factorLevel" value="Untreated"/>
437 <param name="groups" value="primary:untreated"/> 434 <param name="groups" value="primary:untreated"/>
438 </repeat> 435 </repeat>
439 </repeat> 436 </repeat>
440 <param name="pdf" value="False"/> 437 <section name="output_options">
438 <param name="output_selector" value=""/>
439 </section>
441 <param name="tximport_selector" value="tximport"/> 440 <param name="tximport_selector" value="tximport"/>
442 <param name="txtype" value="sailfish"/> 441 <param name="txtype" value="sailfish"/>
443 <param name="mapping_format_selector" value="tabular"/> 442 <param name="mapping_format_selector" value="tabular"/>
444 <param name="tabular_file" value="tx2gene.tab"/> 443 <param name="tabular_file" value="tx2gene.tab"/>
445 <output name="deseq_out" > 444 <output name="deseq_out" >
470 <repeat name="rep_factorLevel"> 469 <repeat name="rep_factorLevel">
471 <param name="factorLevel" value="Untreated"/> 470 <param name="factorLevel" value="Untreated"/>
472 <param name="groups" value="primary:untreated"/> 471 <param name="groups" value="primary:untreated"/>
473 </repeat> 472 </repeat>
474 </repeat> 473 </repeat>
475 <param name="pdf" value="False"/> 474 <section name="output_options">
475 <param name="output_selector" value="many_contrasts"/>
476 </section>
476 <param name="tximport_selector" value="tximport"/> 477 <param name="tximport_selector" value="tximport"/>
477 <param name="txtype" value="sailfish"/> 478 <param name="txtype" value="sailfish"/>
478 <param name="mapping_format_selector" value="tabular"/> 479 <param name="mapping_format_selector" value="tabular"/>
479 <param name="tabular_file" value="tx2gene.tab"/> 480 <param name="tabular_file" value="tx2gene.tab"/>
480 <param name="many_contrasts" value="true"/>
481 <output_collection name="split_output" type="list" count="1"> 481 <output_collection name="split_output" type="list" count="1">
482 <element name="Treatment_Treated_vs_Untreated"> 482 <element name="Treatment_Treated_vs_Untreated">
483 <assert_contents> 483 <assert_contents>
484 <has_text_matching expression="HOXC11\t0.557.*\t0.324.*\t0.437.*\t0.741.*\t0.458.*\t0.999.*"/> 484 <has_text_matching expression="HOXC11\t0.557.*\t0.324.*\t0.437.*\t0.741.*\t0.458.*\t0.999.*"/>
485 </assert_contents> 485 </assert_contents>
486 </element> 486 </element>
487 </output_collection> 487 </output_collection>
488 </test>
489 <!--Test alpha_ma option-->
490 <test expect_num_outputs="1">
491 <repeat name="rep_factorName">
492 <param name="factorName" value="Treatment"/>
493 <repeat name="rep_factorLevel">
494 <param name="factorLevel" value="Treated"/>
495 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/>
496 </repeat>
497 <repeat name="rep_factorLevel">
498 <param name="factorLevel" value="Untreated"/>
499 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/>
500 </repeat>
501 </repeat>
502 <section name="output_options">
503 <param name="output_selector" value=""/>
504 <param name="alpha_ma" value="0.05"/>
505 </section>
506 <param name="tximport_selector" value="tximport"/>
507 <param name="txtype" value="sailfish"/>
508 <param name="mapping_format_selector" value="gtf"/>
509 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/>
510 <output name="deseq_out" >
511 <assert_contents>
512 <has_text_matching expression="ENSG00000168671\t1.8841.*\t-0.1180.*\t0.7429.*\t-0.1589.*\t0.8737.*\t0.9999.*" />
513 </assert_contents>
514 </output>
488 </test> 515 </test>
489 </tests> 516 </tests>
490 <help><![CDATA[ 517 <help><![CDATA[
491 .. class:: infomark 518 .. class:: infomark
492 519
582 ====== ========================================================== 609 ====== ==========================================================
583 610
584 .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html 611 .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html
585 .. _tximport: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html 612 .. _tximport: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html
586 ]]></help> 613 ]]></help>
587 <citations> 614 <expand macro="citations" />
588 <citation type="doi">10.1186/s13059-014-0550-8</citation>
589 </citations>
590 </tool> 615 </tool>