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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
author iuc
date Sat, 19 May 2018 03:55:48 -0400
parents d0c39b5e78cf
children a416957ee305
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14:d0c39b5e78cf 15:9a616afdbda5
1 <tool id="deseq2" name="DESeq2" version="2.11.40.1"> 1 <tool id="deseq2" name="DESeq2" version="2.11.40.2">
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>
56 $temp_factor.append( {str($level.factorLevel): $count_files} ) 56 $temp_factor.append( {str($level.factorLevel): $count_files} )
57 #end for 57 #end for
58 $temp_factor.reverse() 58 $temp_factor.reverse()
59 $temp_factor_names.append([str($factor.factorName), $temp_factor]) 59 $temp_factor_names.append([str($factor.factorName), $temp_factor])
60 #end for 60 #end for
61
62 $header
63
61 -f '#echo json.dumps(temp_factor_names)#' 64 -f '#echo json.dumps(temp_factor_names)#'
62 -l '#echo json.dumps(filename_to_element_identifiers)#' 65 -l '#echo json.dumps(filename_to_element_identifiers)#'
63 -t $fit_type 66 -t $fit_type
64 #if $outlier_replace_off: 67 #if $outlier_replace_off:
65 -a 68 -a
100 </sanitizer> 103 </sanitizer>
101 </param> 104 </param>
102 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/> 105 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
103 </repeat> 106 </repeat>
104 </repeat> 107 </repeat>
108
109 <param name="header" type="boolean" truevalue="-H" falsevalue="" checked="true" label="Files have header?" help="If this option is set to Yes, the tool will assume that the count files have column headers in the first row. Default: Yes" />
105 110
106 <conditional name="tximport"> 111 <conditional name="tximport">
107 <param name="tximport_selector" type="select" label="Choice of Input data"> 112 <param name="tximport_selector" type="select" label="Choice of Input data">
108 <option value="count" selected="True">Count data (e.g. from HTSeq-count, featureCounts or StringTie)</option> 113 <option value="count" selected="True">Count data (e.g. from HTSeq-count, featureCounts or StringTie)</option>
109 <option value="tximport">TPM values (e.g. from kallisto, sailfish or salmon)</option> 114 <option value="tximport">TPM values (e.g. from kallisto, sailfish or salmon)</option>
172 <data format="tabular" name="counts_out" label="Normalized counts file on ${on_string}"> 177 <data format="tabular" name="counts_out" label="Normalized counts file on ${on_string}">
173 <filter>normCounts == True</filter> 178 <filter>normCounts == True</filter>
174 </data> 179 </data>
175 </outputs> 180 </outputs>
176 <tests> 181 <tests>
177 <!--Ensure tables output works--> 182 <!--Ensure counts files with header works -->
178 <test expect_num_outputs="2"> 183 <test expect_num_outputs="2">
179 <repeat name="rep_factorName"> 184 <repeat name="rep_factorName">
180 <param name="factorName" value="Treatment"/> 185 <param name="factorName" value="Treatment"/>
181 <repeat name="rep_factorLevel"> 186 <repeat name="rep_factorLevel">
182 <param name="factorLevel" value="Treated"/> 187 <param name="factorLevel" value="Treated"/>
187 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/> 192 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
188 </repeat> 193 </repeat>
189 </repeat> 194 </repeat>
190 <param name="pdf" value="False"/> 195 <param name="pdf" value="False"/>
191 <param name="normCounts" value="True"/> 196 <param name="normCounts" value="True"/>
192 <output name="counts_out" file="normalized_readcounts.tab"/> 197 <output name="counts_out">
193 <output name="deseq_out" file="deseq2_out.tab"/> 198 <assert_contents>
199 <has_text_matching expression="untreat1\tuntreat2\tuntreat3\tuntreat4\ttreat1\ttreat2\ttreat3" />
200 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
201 </assert_contents>
202 </output>
203 <output name="deseq_out" >
204 <assert_contents>
205 <has_text_matching expression="FBgn0003360\t1933.9504.*\t-2.8399.*\t0.1309.*-21.6851.*2.831.*8.024" />
206 </assert_contents>
207 </output>
208 </test>
209 <!--Ensure counts files without header works -->
210 <test expect_num_outputs="2">
211 <repeat name="rep_factorName">
212 <param name="factorName" value="Treatment"/>
213 <repeat name="rep_factorLevel">
214 <param name="factorLevel" value="Treated"/>
215 <param name="countsFile" value="GSM461179_treat_single.counts.noheader,GSM461180_treat_paired.counts.noheader,GSM461181_treat_paired.counts.noheader"/>
216 </repeat>
217 <repeat name="rep_factorLevel">
218 <param name="factorLevel" value="Untreated"/>
219 <param name="countsFile" value="GSM461176_untreat_single.counts.noheader,GSM461177_untreat_paired.counts.noheader,GSM461178_untreat_paired.counts.noheader,GSM461182_untreat_single.counts.noheader"/>
220 </repeat>
221 </repeat>
222 <param name="header" value="False"/>
223 <param name="pdf" value="False"/>
224 <param name="normCounts" value="True"/>
225 <output name="counts_out">
226 <assert_contents>
227 <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" />
228 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
229 </assert_contents>
230 </output>
231 <output name="deseq_out" >
232 <assert_contents>
233 <has_text_matching expression="FBgn0003360\t1933.9504.*\t-2.8399.*\t0.1309.*-21.6851.*2.831.*8.024" />
234 </assert_contents>
235 </output>
194 </test> 236 </test>
195 <!--Ensure Sailfish/Salmon input with tx2gene table works--> 237 <!--Ensure Sailfish/Salmon input with tx2gene table works-->
196 <test expect_num_outputs="1"> 238 <test expect_num_outputs="1">
197 <repeat name="rep_factorName"> 239 <repeat name="rep_factorName">
198 <param name="factorName" value="Treatment"/> 240 <param name="factorName" value="Treatment"/>
208 <param name="pdf" value="False"/> 250 <param name="pdf" value="False"/>
209 <param name="tximport_selector" value="tximport"/> 251 <param name="tximport_selector" value="tximport"/>
210 <param name="txtype" value="sailfish"/> 252 <param name="txtype" value="sailfish"/>
211 <param name="mapping_format_selector" value="tabular"/> 253 <param name="mapping_format_selector" value="tabular"/>
212 <param name="tabular_file" value="tx2gene.tab"/> 254 <param name="tabular_file" value="tx2gene.tab"/>
213 <output name="deseq_out" file="sailfish/out_deseq2_sailfish.tab"/> 255 <output name="deseq_out" >
214 </test> 256 <assert_contents>
257 <has_text_matching expression="MIR6859-2\t1.1858.*\t-1.5832.*\t1.2956.*\t-1.2219.*\t0.2217.*\t0.8868.*" />
258 </assert_contents>
259 </output>
260 </test>
215 </tests> 261 </tests>
216 <help><![CDATA[ 262 <help><![CDATA[
217 .. class:: infomark 263 .. class:: infomark
218 264
219 **What it does** 265 **What it does**
224 270
225 **Inputs** 271 **Inputs**
226 272
227 **Count Files** 273 **Count Files**
228 274
229 DESeq2_ takes count tables generated from **featureCounts**, **HTSeq-count** or **StringTie** as input. Count tables must be generated for each sample individually, should have no header rows, and rows should be in the same order. DESeq2 is capable of handling multiple factors that affect your experiment. The first factor you input is considered as the primary factor that affects gene expressions. Optionally, you can input one or more secondary factors that might influence your experiment. But the final output will be changes in genes due to primary factor in presence of secondary factors. Each factor has two levels/states. You need to select appropriate count table from your history for each factor level. 275 DESeq2_ takes count tables generated from **featureCounts**, **HTSeq-count** or **StringTie** as input. Count tables must be generated for each sample individually. One header row is assumed, but files with no header (e.g from HTSeq) can be input with the *Files have header?* option set to No. DESeq2 is capable of handling multiple factors that affect your experiment. The first factor you input is considered as the primary factor that affects gene expressions. Optionally, you can input one or more secondary factors that might influence your experiment. But the final output will be changes in genes due to primary factor in presence of secondary factors. Each factor has two levels/states. You need to select appropriate count table from your history for each factor level.
230 276
231 The following table gives some examples of factors and their levels: 277 The following table gives some examples of factors and their levels:
232 278
233 ========= ============== =============== 279 ========= ============== ===============
234 Factor Factor level 1 Factor level 2 280 Factor Factor level 1 Factor level 2
244 Gender Female Male 290 Gender Female Male
245 ========= ============== =============== 291 ========= ============== ===============
246 292
247 *Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level2. Here the order of factor levels is important. For example, for the factor 'Treatment' given in above table, DESeq2 computes fold changes of 'Treated' samples against 'Untreated', i.e. the values correspond to up or down regulations of genes in Treated samples. 293 *Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level2. Here the order of factor levels is important. For example, for the factor 'Treatment' given in above table, DESeq2 computes fold changes of 'Treated' samples against 'Untreated', i.e. the values correspond to up or down regulations of genes in Treated samples.
248 294
249 DESeq2_ can also take transcript-level counts from quantification tools such as, **kallisto**, **Salmon** and **Sailfish**, and this Galaxy wrapper incorporates the Bioconductor tximport_ package to process the transcript counts for DESeq2. 295 DESeq2_ can also take transcript-level counts from quantification tools such as, **kallisto**, **Salmon** and **Sailfish**, and this Galaxy wrapper incorporates the Bioconductor tximport_ package to process the transcript counts for DESeq2.
250 296
251 **Salmon or Sailfish Files** 297 **Salmon or Sailfish Files**
252 298
253 Salmon or Sailfish ``quant.sf`` files can be imported by setting type to *Salmon* or *Sailfish* respectively above. Note: for previous version of Salmon or Sailfish, in which the quant.sf files start with comment lines you will need to remove the comment lines before inputting here. An example of the format is shown below. 299 Salmon or Sailfish ``quant.sf`` files can be imported by setting type to *Salmon* or *Sailfish* respectively above. Note: for previous version of Salmon or Sailfish, in which the quant.sf files start with comment lines you will need to remove the comment lines before inputting here. An example of the format is shown below.
254 300
273 kallisto ``abundance.tsv`` files can be imported by setting type to *kallisto* above. An example of the format is shown below. 319 kallisto ``abundance.tsv`` files can be imported by setting type to *kallisto* above. An example of the format is shown below.
274 320
275 Example: 321 Example:
276 322
277 ============ ========== =============== =========== =========== 323 ============ ========== =============== =========== ===========
278 target_id length eff_length est_counts tpm 324 target_id length eff_length est_counts tpm
279 ------------ ---------- --------------- ----------- ----------- 325 ------------ ---------- --------------- ----------- -----------
280 NR_001526 164 20.4518 0 0 326 NR_001526 164 20.4518 0 0
281 NR_001526_1 164 20.4518 0 0 327 NR_001526_1 164 20.4518 0 0
282 NR_001526_2 164 20.4518 0 0 328 NR_001526_2 164 20.4518 0 0
283 NM_130786 1764 1956.04 109.165 2.47415 329 NM_130786 1764 1956.04 109.165 2.47415
284 NR_015380 2129 2139.53 85.5821 1.77331 330 NR_015380 2129 2139.53 85.5821 1.77331
285 NM_001198818 9360 7796.58 4.19648e-05 2.38616e-07 331 NM_001198818 9360 7796.58 4.19648e-05 2.38616e-07
286 NM_001198819 9527 7964.62 0 0 332 NM_001198819 9527 7964.62 0 0
287 NM_001198820 9410 7855.78 0 0 333 NM_001198820 9410 7855.78 0 0
288 NM_014576 9267 7714.88 8.37255 0.0481114 334 NM_014576 9267 7714.88 8.37255 0.0481114
289 ============ ========== =============== =========== =========== 335 ============ ========== =============== =========== ===========
290 336
291 ----- 337 -----
292 338
293 **Output** 339 **Output**