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comparison deseq2.xml @ 18:3bf1b3ec1ddf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
author iuc
date Fri, 16 Nov 2018 14:47:19 -0500
parents d9e5cadc7f0b
children c56e0689e46e
comparison
equal deleted inserted replaced
17:d9e5cadc7f0b 18:3bf1b3ec1ddf
1 <tool id="deseq2" name="DESeq2" version="2.11.40.2"> 1 <tool id="deseq2" name="DESeq2" version="2.11.40.3">
2 <description>Determines differentially expressed features from count tables</description> 2 <description>Determines differentially expressed features from count tables</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement> 4 <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement>
5 <requirement type="package" version="1.6.0">bioconductor-tximport</requirement> 5 <requirement type="package" version="1.6.0">bioconductor-tximport</requirement>
6 <requirement type="package" version="1.30.0">bioconductor-genomicfeatures</requirement> 6 <requirement type="package" version="1.30.0">bioconductor-genomicfeatures</requirement>
41 -p '$plots' 41 -p '$plots'
42 #end if 42 #end if
43 #if $normCounts: 43 #if $normCounts:
44 -n '$counts_out' 44 -n '$counts_out'
45 #end if 45 #end if
46 #if $normRLog:
47 -r '$rlog_out'
48 #end if
49 #if $normVST:
50 -v '$vst_out'
51 #end if
46 #set $filename_to_element_identifiers = {} 52 #set $filename_to_element_identifiers = {}
47 #set $temp_factor_names = list() 53 #set $temp_factor_names = list()
48 #for $factor in $rep_factorName: 54 #for $factor in $rep_factorName:
49 #set $temp_factor = list() 55 #set $temp_factor = list()
50 #for $level in $factor.rep_factorLevel: 56 #for $level in $factor.rep_factorLevel:
61 67
62 $header 68 $header
63 69
64 -f '#echo json.dumps(temp_factor_names)#' 70 -f '#echo json.dumps(temp_factor_names)#'
65 -l '#echo json.dumps(filename_to_element_identifiers)#' 71 -l '#echo json.dumps(filename_to_element_identifiers)#'
72 #if $esf:
73 -e $esf
74 #end if
66 -t $fit_type 75 -t $fit_type
67 #if $batch_factors 76 #if $batch_factors:
68 --batch_factors '$batch_factors' 77 --batch_factors '$batch_factors'
69 #end if 78 #end if
70 #if $outlier_replace_off: 79 #if $outlier_replace_off:
71 -a 80 -a
72 #end if 81 #end if
140 <param name="pdf" type="boolean" truevalue="1" falsevalue="0" checked="true" 149 <param name="pdf" type="boolean" truevalue="1" falsevalue="0" checked="true"
141 label="Visualising the analysis results" 150 label="Visualising the analysis results"
142 help="output an additional PDF files" /> 151 help="output an additional PDF files" />
143 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false" 152 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
144 label="Output normalized counts table" /> 153 label="Output normalized counts table" />
154 <param name="normRLog" type="boolean" truevalue="1" falsevalue="0" checked="false"
155 label="Output rLog normalized table" />
156 <param name="normVST" type="boolean" truevalue="1" falsevalue="0" checked="false"
157 label="Output VST normalized table" />
145 <param name="many_contrasts" type="boolean" truevalue="1" falsevalue="0" checked="false" 158 <param name="many_contrasts" type="boolean" truevalue="1" falsevalue="0" checked="false"
146 label="Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)" 159 label="Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)"
147 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" /> 160 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
161 <param name="esf" type="select" label="(Optional) Method for estimateSizeFactors"
162 help="Method for estimation: either 'ratio', 'poscounts', or 'iterate'. 'ratio' uses the standard median ratio method introduced in DESeq.
163 The size factor is the median ratio of the sample over a 'pseudosample': for each gene, the geometric mean of all samples.
164 'poscounts' and 'iterate' offer alternative estimators, which can be used even when all genes contain a sample with a zero (a problem
165 for the default method, as the geometric mean becomes zero, and the ratio undefined). The 'poscounts' estimator deals with a gene with
166 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
167 use cases with Paul McMurdie's phyloseq package for metagenomic samples. The 'iterate' estimator iterates between estimating the dispersion
168 with a design of ~1, and finding a size factor vector by numerically optimizing the likelihood of the ~1 model.">
169 <option value="" selected="true">No Selection (use default)</option>
170 <option value="ratio">ratio</option>
171 <option value="poscounts">poscounts</option>
172 <option value="iterate">iterate</option>
173 </param>
148 <param name="fit_type" type="select" label="Fit type"> 174 <param name="fit_type" type="select" label="Fit type">
149 <option value="1" selected="true">parametric</option> 175 <option value="1" selected="true">parametric</option>
150 <option value="2">local</option> 176 <option value="2">local</option>
151 <option value="3">mean</option> 177 <option value="3">mean</option>
152 </param> 178 </param>
178 <filter>pdf == True</filter> 204 <filter>pdf == True</filter>
179 </data> 205 </data>
180 <data format="tabular" name="counts_out" label="Normalized counts file on ${on_string}"> 206 <data format="tabular" name="counts_out" label="Normalized counts file on ${on_string}">
181 <filter>normCounts == True</filter> 207 <filter>normCounts == True</filter>
182 </data> 208 </data>
209 <data format="tabular" name="rlog_out" label="rLog-Normalized counts file on ${on_string}">
210 <filter>normRLog == True</filter>
211 </data>
212 <data format="tabular" name="vst_out" label="VST-Normalized counts file on ${on_string}">
213 <filter>normVST == True</filter>
214 </data>
183 </outputs> 215 </outputs>
184 <tests> 216 <tests>
185 <!--Ensure counts files with header works --> 217 <!--Ensure counts files with header works -->
186 <test expect_num_outputs="2"> 218 <test expect_num_outputs="4">
187 <repeat name="rep_factorName"> 219 <repeat name="rep_factorName">
188 <param name="factorName" value="Treatment"/> 220 <param name="factorName" value="Treatment"/>
189 <repeat name="rep_factorLevel"> 221 <repeat name="rep_factorLevel">
190 <param name="factorLevel" value="Treated"/> 222 <param name="factorLevel" value="Treated"/>
191 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/> 223 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
195 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/> 227 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
196 </repeat> 228 </repeat>
197 </repeat> 229 </repeat>
198 <param name="pdf" value="False"/> 230 <param name="pdf" value="False"/>
199 <param name="normCounts" value="True"/> 231 <param name="normCounts" value="True"/>
232 <param name="normRLog" value="True"/>
233 <param name="normVST" value="True"/>
200 <output name="counts_out"> 234 <output name="counts_out">
201 <assert_contents> 235 <assert_contents>
202 <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" /> 236 <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" />
203 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" /> 237 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
238 </assert_contents>
239 </output>
240 <output name="rlog_out">
241 <assert_contents>
242 <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" />
243 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
244 </assert_contents>
245 </output>
246 <output name="vst_out">
247 <assert_contents>
248 <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="FBgn0000003\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*" />
204 </assert_contents> 250 </assert_contents>
205 </output> 251 </output>
206 <output name="deseq_out" > 252 <output name="deseq_out" >
207 <assert_contents> 253 <assert_contents>
208 <has_text_matching expression="FBgn0003360\t1933.9504.*\t-2.8399.*\t0.1309.*-21.6851.*2.831.*8.024" /> 254 <has_text_matching expression="FBgn0003360\t1933.9504.*\t-2.8399.*\t0.1309.*-21.6851.*2.831.*8.024" />
230 <has_text_matching expression="FBgn0003360\t1933.*\t-2.9.*\t0.1.*\t-26.*\t1.*-152\t4.*-149" /> 276 <has_text_matching expression="FBgn0003360\t1933.*\t-2.9.*\t0.1.*\t-26.*\t1.*-152\t4.*-149" />
231 </assert_contents> 277 </assert_contents>
232 </output> 278 </output>
233 </test> 279 </test>
234 <!--Ensure counts files without header works --> 280 <!--Ensure counts files without header works -->
235 <test expect_num_outputs="2"> 281 <test expect_num_outputs="4">
236 <repeat name="rep_factorName"> 282 <repeat name="rep_factorName">
237 <param name="factorName" value="Treatment"/> 283 <param name="factorName" value="Treatment"/>
238 <repeat name="rep_factorLevel"> 284 <repeat name="rep_factorLevel">
239 <param name="factorLevel" value="Treated"/> 285 <param name="factorLevel" value="Treated"/>
240 <param name="countsFile" value="GSM461179_treat_single.counts.noheader,GSM461180_treat_paired.counts.noheader,GSM461181_treat_paired.counts.noheader"/> 286 <param name="countsFile" value="GSM461179_treat_single.counts.noheader,GSM461180_treat_paired.counts.noheader,GSM461181_treat_paired.counts.noheader"/>
245 </repeat> 291 </repeat>
246 </repeat> 292 </repeat>
247 <param name="header" value="False"/> 293 <param name="header" value="False"/>
248 <param name="pdf" value="False"/> 294 <param name="pdf" value="False"/>
249 <param name="normCounts" value="True"/> 295 <param name="normCounts" value="True"/>
296 <param name="normRLog" value="True"/>
297 <param name="normVST" value="True"/>
250 <output name="counts_out"> 298 <output name="counts_out">
251 <assert_contents> 299 <assert_contents>
252 <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" /> 300 <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" />
253 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" /> 301 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
302 </assert_contents>
303 </output>
304 <output name="rlog_out">
305 <assert_contents>
306 <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" />
307 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
308 </assert_contents>
309 </output>
310 <output name="vst_out">
311 <assert_contents>
312 <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="FBgn0000003\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*" />
254 </assert_contents> 314 </assert_contents>
255 </output> 315 </output>
256 <output name="deseq_out" > 316 <output name="deseq_out" >
257 <assert_contents> 317 <assert_contents>
258 <has_text_matching expression="FBgn0003360\t1933.9504.*\t-2.8399.*\t0.1309.*-21.6851.*2.831.*8.024" /> 318 <has_text_matching expression="FBgn0003360\t1933.9504.*\t-2.8399.*\t0.1309.*-21.6851.*2.831.*8.024" />