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comparison deseq2.xml @ 19:c56e0689e46e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
author iuc
date Tue, 04 Dec 2018 08:19:06 -0500
parents 3bf1b3ec1ddf
children 89d26b11d452
comparison
equal deleted inserted replaced
18:3bf1b3ec1ddf 19:c56e0689e46e
1 <tool id="deseq2" name="DESeq2" version="2.11.40.3"> 1 <tool id="deseq2" name="DESeq2" version="2.11.40.4">
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="1.20.0">bioconductor-deseq2</requirement>
5 <requirement type="package" version="1.6.0">bioconductor-tximport</requirement> 5 <!-- Optional dependency of tximport, needed to import kallisto results https://github.com/galaxyproject/usegalaxy-playbook/issues/161 -->
6 <requirement type="package" version="1.30.0">bioconductor-genomicfeatures</requirement> 6 <requirement type="package" version="2.24.0">bioconductor-rhdf5</requirement>
7 <requirement type="package" version="0.6.5">r-ggrepel</requirement> 7 <requirement type="package" version="1.8.0">bioconductor-tximport</requirement>
8 <requirement type="package" version="1.0.8">r-pheatmap</requirement> 8 <requirement type="package" version="1.32.3">bioconductor-genomicfeatures</requirement>
9 <requirement type="package" version="1.20.2">r-getopt</requirement>
10 <requirement type="package" version="0.8.0">r-ggrepel</requirement>
11 <requirement type="package" version="3.0.1">r-gplots</requirement>
12 <requirement type="package" version="1.0.10">r-pheatmap</requirement>
13 <requirement type="package" version="0.2.20">r-rjson</requirement>
9 </requirements> 14 </requirements>
10 <stdio> 15 <stdio>
11 <regex match="Execution halted" 16 <regex match="Execution halted"
12 source="both" 17 source="both"
13 level="fatal" 18 level="fatal"
25 echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ") 30 echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
26 ]]></version_command> 31 ]]></version_command>
27 <command><![CDATA[ 32 <command><![CDATA[
28 #if $tximport.tximport_selector == 'tximport': 33 #if $tximport.tximport_selector == 'tximport':
29 #if $tximport.mapping_format.mapping_format_selector == 'gtf': 34 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
30 ln -s '$tximport.mapping_format.gtf_file' mapping.gtf && 35 ln -s '$tximport.mapping_format.gtf_file' mapping.gff &&
31 #else: 36 #else:
32 ln -s '$tximport.mapping_format.tabular_file' mapping.txt && 37 ln -s '$tximport.mapping_format.tabular_file' mapping.txt &&
33 #end if 38 #end if
34 #end if 39 #end if
35 40
90 #end if 95 #end if
91 #if $tximport.tximport_selector == 'tximport': 96 #if $tximport.tximport_selector == 'tximport':
92 -i 97 -i
93 -y $tximport.txtype 98 -y $tximport.txtype
94 #if $tximport.mapping_format.mapping_format_selector == 'gtf': 99 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
95 -x mapping.gtf 100 -x mapping.gff
96 #else: 101 #else:
97 -x mapping.txt 102 -x mapping.txt
98 #end if 103 #end if
99 104
100 #end if 105 #end if
131 <option value="sailfish">Sailfish</option> 136 <option value="sailfish">Sailfish</option>
132 <option value="salmon">Salmon</option> 137 <option value="salmon">Salmon</option>
133 </param> 138 </param>
134 <conditional name="mapping_format"> 139 <conditional name="mapping_format">
135 <param name="mapping_format_selector" type="select" label="Gene mapping format"> 140 <param name="mapping_format_selector" type="select" label="Gene mapping format">
136 <option value="gtf" selected="True">GTF</option> 141 <option value="gtf" selected="True">GTF/GFF3</option>
137 <option value="tabular">Transcript-ID and Gene-ID mapping file</option> 142 <option value="tabular">Transcript-ID to Gene-ID mapping file</option>
138 </param> 143 </param>
139 <when value="gtf"> 144 <when value="gtf">
140 <param name="gtf_file" type="data" format="gtf,gff3" label="GTF/GFF3 file with Transcript - Gene mapping"/> 145 <param name="gtf_file" type="data" format="gtf,gff3" label="GTF/GFF3 annotation file"/>
141 </when> 146 </when>
142 <when value="tabular"> 147 <when value="tabular">
143 <param name="tabular_file" type="data" format="tabular" label="Tabular file with Transcript - Gene mapping"/> 148 <param name="tabular_file" type="data" format="tabular" label="Tabular file with Transcript-ID to Gene-ID mapping"/>
144 </when> 149 </when>
145 </conditional> 150 </conditional>
146 </when> 151 </when>
147 <when value="count" /> 152 <when value="count" />
148 </conditional> 153 </conditional>
188 <param name="auto_mean_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false" 193 <param name="auto_mean_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
189 label="Turn off independent filtering" 194 label="Turn off independent filtering"
190 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" /> 195 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
191 </inputs> 196 </inputs>
192 <outputs> 197 <outputs>
193 <data format="tabular" name="deseq_out" label="DESeq2 result file on ${on_string}"> 198 <data name="deseq_out" format="tabular" label="DESeq2 result file on ${on_string}">
194 <filter>many_contrasts is False</filter> 199 <filter>many_contrasts is False</filter>
195 <actions> 200 <actions>
196 <action name="column_names" type="metadata" default="GeneID,Base mean,log2(FC),StdErr,Wald-Stats,P-value,P-adj" /> 201 <action name="column_names" type="metadata" default="GeneID,Base mean,log2(FC),StdErr,Wald-Stats,P-value,P-adj" />
197 </actions> 202 </actions>
198 </data> 203 </data>
199 <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}"> 204 <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}">
200 <filter>many_contrasts is True</filter> 205 <filter>many_contrasts is True</filter>
201 <discover_datasets pattern="None.(?P&lt;designation&gt;.+_vs_.+)" format="tabular" directory="." visible="false"/> 206 <discover_datasets pattern="None.(?P&lt;designation&gt;.+_vs_.+)" format="tabular" directory="." visible="false"/>
202 </collection> 207 </collection>
203 <data format="pdf" name="plots" label="DESeq2 plots on ${on_string}"> 208 <data name="plots" format="pdf" label="DESeq2 plots on ${on_string}">
204 <filter>pdf == True</filter> 209 <filter>pdf == True</filter>
205 </data> 210 </data>
206 <data format="tabular" name="counts_out" label="Normalized counts file on ${on_string}"> 211 <data name="counts_out" format="tabular" label="Normalized counts file on ${on_string}">
207 <filter>normCounts == True</filter> 212 <filter>normCounts == True</filter>
208 </data> 213 </data>
209 <data format="tabular" name="rlog_out" label="rLog-Normalized counts file on ${on_string}"> 214 <data name="rlog_out" format="tabular" label="rLog-Normalized counts file on ${on_string}">
210 <filter>normRLog == True</filter> 215 <filter>normRLog == True</filter>
211 </data> 216 </data>
212 <data format="tabular" name="vst_out" label="VST-Normalized counts file on ${on_string}"> 217 <data name="vst_out" format="tabular" label="VST-Normalized counts file on ${on_string}">
213 <filter>normVST == True</filter> 218 <filter>normVST == True</filter>
214 </data> 219 </data>
215 </outputs> 220 </outputs>
216 <tests> 221 <tests>
217 <!--Ensure counts files with header works --> 222 <!--Ensure counts files with header works -->
249 <has_text_matching expression="FBgn0000003\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*" /> 254 <has_text_matching expression="FBgn0000003\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*" />
250 </assert_contents> 255 </assert_contents>
251 </output> 256 </output>
252 <output name="deseq_out" > 257 <output name="deseq_out" >
253 <assert_contents> 258 <assert_contents>
254 <has_text_matching expression="FBgn0003360\t1933.9504.*\t-2.8399.*\t0.1309.*-21.6851.*2.831.*8.024" /> 259 <has_text_matching expression="FBgn0003360\t1933\.9504.*\t-2\.8399.*\t0\.1309.*\t-21\.68.*\t.*e-104\t.*e-101" />
255 </assert_contents> 260 </assert_contents>
256 </output> 261 </output>
257 </test> 262 </test>
258 <!--Ensure additional batch factor correction works --> 263 <!--Ensure additional batch factor correction works -->
259 <test expect_num_outputs="2"> 264 <test expect_num_outputs="2">
313 <has_text_matching expression="FBgn0000003\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*" /> 318 <has_text_matching expression="FBgn0000003\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*" />
314 </assert_contents> 319 </assert_contents>
315 </output> 320 </output>
316 <output name="deseq_out" > 321 <output name="deseq_out" >
317 <assert_contents> 322 <assert_contents>
318 <has_text_matching expression="FBgn0003360\t1933.9504.*\t-2.8399.*\t0.1309.*-21.6851.*2.831.*8.024" /> 323 <has_text_matching expression="FBgn0003360\t1933\.9504.*\t-2\.8399.*\t0\.1309.*\t-21\.68.*\t.*e-104\t.*e-101" />
319 </assert_contents> 324 </assert_contents>
320 </output> 325 </output>
321 </test> 326 </test>
322 <!--Ensure Sailfish/Salmon input with tx2gene table works--> 327 <!--Ensure Sailfish/Salmon input with tx2gene table works-->
323 <test expect_num_outputs="1"> 328 <test expect_num_outputs="1">
337 <param name="txtype" value="sailfish"/> 342 <param name="txtype" value="sailfish"/>
338 <param name="mapping_format_selector" value="tabular"/> 343 <param name="mapping_format_selector" value="tabular"/>
339 <param name="tabular_file" value="tx2gene.tab"/> 344 <param name="tabular_file" value="tx2gene.tab"/>
340 <output name="deseq_out" > 345 <output name="deseq_out" >
341 <assert_contents> 346 <assert_contents>
342 <has_text_matching expression="MIR6859-2\t1.1858.*\t-1.5832.*\t1.2956.*\t-1.2219.*\t0.2217.*\t0.8868.*" /> 347 <has_text_matching expression="UGT3A2\t1.8841.*\t-0.1329.*\t0.6936.*\t-0.1917.*\t0.8479.*\t0.9999.*" />
348 </assert_contents>
349 </output>
350 </test>
351 <!--Ensure Sailfish/Salmon input with GFF3 annotation works-->
352 <test expect_num_outputs="1">
353 <repeat name="rep_factorName">
354 <param name="factorName" value="Treatment"/>
355 <repeat name="rep_factorLevel">
356 <param name="factorLevel" value="Treated"/>
357 <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/>
358 </repeat>
359 <repeat name="rep_factorLevel">
360 <param name="factorLevel" value="Untreated"/>
361 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/>
362 </repeat>
363 </repeat>
364 <param name="pdf" value="False"/>
365 <param name="tximport_selector" value="tximport"/>
366 <param name="txtype" value="sailfish"/>
367 <param name="mapping_format_selector" value="gtf"/>
368 <param name="gtf_file" value="GRCh38_latest_genomic.gff"/>
369 <output name="deseq_out" >
370 <assert_contents>
371 <has_text_matching expression="UGT3A2\t1.8841.*\t-0.1329.*\t0.6936.*\t-0.1917.*\t0.8479.*\t0.9999.*" />
343 </assert_contents> 372 </assert_contents>
344 </output> 373 </output>
345 </test> 374 </test>
346 </tests> 375 </tests>
347 <help><![CDATA[ 376 <help><![CDATA[