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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
author iuc
date Fri, 21 Apr 2023 14:09:17 +0000
parents d1f7fa5bb3cb
children
comparison
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3:d1f7fa5bb3cb 4:3a083c78896e
1 <tool id="ruvseq" name="Remove Unwanted Variation" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@"> 1 <tool id="ruvseq" name="Remove Unwanted Variation" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@">
2 <description>from RNA-seq data</description> 2 <description>from RNA-seq data</description>
3 <xrefs>
4 <xref type="bio.tools">ruvseq</xref>
5 <xref type="bioconductor">ruvseq</xref>
6 </xrefs>
3 <macros> 7 <macros>
4 <token name="@TOOL_VERSION@">1.26.0</token> 8 <token name="@TOOL_VERSION@">1.26.0</token>
5 <token name="@WRAPPER_VERSION@">0</token> 9 <token name="@WRAPPER_VERSION@">1</token>
6 </macros> 10 </macros>
7 <requirements> 11 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">bioconductor-ruvseq</requirement> 12 <requirement type="package" version="@TOOL_VERSION@">bioconductor-ruvseq</requirement>
9 <requirement type="package" version="1.32.0">bioconductor-deseq2</requirement> 13 <requirement type="package" version="1.32.0">bioconductor-deseq2</requirement>
10 <requirement type="package" version="1.20.0">bioconductor-tximport</requirement> 14 <requirement type="package" version="1.20.0">bioconductor-tximport</requirement>
58 --tx2gene mapping.gtf 62 --tx2gene mapping.gtf
59 #else: 63 #else:
60 --tx2gene mapping.txt 64 --tx2gene mapping.txt
61 #end if 65 #end if
62 #end if 66 #end if
67
68 #if $ruv_ncounts == 1:
69 --ruv_ncounts
70 #end if
63 ]]></command> 71 ]]></command>
64 <configfiles> 72 <configfiles>
65 <configfile name="sampleTable"> 73 <configfile name="sampleTable">
66 #import json 74 #import json
67 #set sample_table = [] 75 #set sample_table = []
115 <when value="count" /> 123 <when value="count" />
116 </conditional> 124 </conditional>
117 <param name="pdf" type="boolean" truevalue="1" falsevalue="0" checked="true" 125 <param name="pdf" type="boolean" truevalue="1" falsevalue="0" checked="true"
118 label="Visualising the analysis results" 126 label="Visualising the analysis results"
119 help="output an additional PDF files" /> 127 help="output an additional PDF files" />
128 <param name="ruv_ncounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
129 label="Output RUVSeq normalized count tables"
130 help="If this option is set to Yes, the tool will generate RUVseq normalized count files. Default: No" />
120 </inputs> 131 </inputs>
121 <outputs> 132 <outputs>
122 <collection name="unwanted_variation" type="list" label="RUVSeq covariate files on ${on_string}"> 133 <collection name="unwanted_variation" type="list" label="RUVSeq covariate files on ${on_string}">
123 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tabular" format="tabular" directory="." visible="false"/> 134 <discover_datasets pattern="uv_(?P&lt;designation&gt;.+)\.tabular" format="tabular" directory="." visible="false"/>
135 </collection>
136 <collection name="ruv_normcounts" type="list" label="RUVSeq normalized counts on ${on_string}">
137 <filter>ruv_ncounts == True</filter>
138 <discover_datasets pattern="ruv_(?P&lt;designation&gt;.+)\.tabular" format="tabular" directory="." visible="false"/>
124 </collection> 139 </collection>
125 <data format="pdf" name="plots" label="RUVSeq diagonstic plots on ${on_string}"> 140 <data format="pdf" name="plots" label="RUVSeq diagonstic plots on ${on_string}">
126 <filter>pdf == True</filter> 141 <filter>pdf == True</filter>
127 </data> 142 </data>
128 </outputs> 143 </outputs>
230 <has_text_matching expression=".*sailfish_quant.sf1.tab\tTreated\t.+"/> 245 <has_text_matching expression=".*sailfish_quant.sf1.tab\tTreated\t.+"/>
231 </assert_contents> 246 </assert_contents>
232 </element> 247 </element>
233 </output_collection> 248 </output_collection>
234 </test> 249 </test>
250 <!--Ensure Normalized counts files are generated -->
251 <test>
252 <repeat name="rep_factorLevel">
253 <param name="factorLevel" value="Treated"/>
254 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
255 </repeat>
256 <repeat name="rep_factorLevel">
257 <param name="factorLevel" value="Untreated"/>
258 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
259 </repeat>
260 <param name="pdf" value="true"/>
261 <param name="ruv_ncounts" value="true"/>
262 <output name="plots" file="ruvseq_diag.pdf" ftype="pdf" compare="sim_size"/>
263 <output_collection name="ruv_normcounts" type="list">
264 <element name="norm_counts_control_method_k1">
265 <assert_contents>
266 <has_text_matching expression="geneID\tGSM461179_treat_single.counts\tGSM461180_treat_paired.counts\t.+"/>
267 </assert_contents>
268 </element>
269 <element name="norm_counts_replicate_method_k1">
270 <assert_contents>
271 <has_text_matching expression="geneID\tGSM461179_treat_single.counts\tGSM461180_treat_paired.counts\t.+"/>
272 </assert_contents>
273 </element>
274 <element name="norm_counts_residual_method_k1">
275 <assert_contents>
276 <has_text_matching expression="geneID\tGSM461179_treat_single.counts\tGSM461180_treat_paired.counts\t.+"/>
277 </assert_contents>
278 </element>
279 </output_collection>
280 </test>
281 <!--Ensure Normalized counts are generated with sailfish files -->
282 <test>
283 <repeat name="rep_factorLevel">
284 <param name="factorLevel" value="Treated"/>
285 <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/>
286 </repeat>
287 <repeat name="rep_factorLevel">
288 <param name="factorLevel" value="Untreated"/>
289 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/>
290 </repeat>
291 <param name="pdf" value="true"/>
292 <param name="tximport_selector" value="tximport"/>
293 <param name="txtype" value="sailfish"/>
294 <param name="mapping_format_selector" value="tabular"/>
295 <param name="tabular_file" value="tx2gene.tab"/>
296 <param name="min_mean_count" value="0"/>
297 <param name="ruv_ncounts" value="true"/>
298 <output name="plots" file="ruvseq_diag_sailfish.pdf" ftype="pdf" compare="sim_size"/>
299 <output_collection name="ruv_normcounts" type="list">
300 <element name="norm_counts_control_method_k1">
301 <assert_contents>
302 <has_text_matching expression="geneID\tsailfish_quant.sf1.tab\tsailfish_quant.sf2.tab\t.+"/>
303 </assert_contents>
304 </element>
305 <element name="norm_counts_replicate_method_k1">
306 <assert_contents>
307 <has_text_matching expression="geneID\tsailfish_quant.sf1.tab\tsailfish_quant.sf2.tab\t.+"/>
308 </assert_contents>
309 </element>
310 <element name="norm_counts_residual_method_k1">
311 <assert_contents>
312 <has_text_matching expression="geneID\tsailfish_quant.sf1.tab\tsailfish_quant.sf2.tab\t.+"/>
313 </assert_contents>
314 </element>
315 </output_collection>
316 </test>
235 </tests> 317 </tests>
236 <help><![CDATA[ 318 <help><![CDATA[
237 .. class:: infomark 319 .. class:: infomark
238 320
239 **What it does** 321 **What it does**
304 386
305 **Output** 387 **Output**
306 388
307 RUVSeq_ generates a tabular file for each method and each k of variation as well as a summary PDF. 389 RUVSeq_ generates a tabular file for each method and each k of variation as well as a summary PDF.
308 390
391 RUVSeq can also generate RUVSeq normalized count tables. However, *these counts should be used only for exploration. It is important that subsequent DE analysis be done on the original counts, as removing the unwanted factors from the counts can also remove part of a factor of interest*.
392
393
309 .. _RUVSeq: http://master.bioconductor.org/packages/release/bioc/html/RUVSeq.html 394 .. _RUVSeq: http://master.bioconductor.org/packages/release/bioc/html/RUVSeq.html
310 .. _tximport: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html 395 .. _tximport: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html
311 ]]></help> 396 ]]></help>
312 <citations> 397 <citations>
313 <citation type="doi">10.1038/nbt.2931</citation> 398 <citation type="doi">10.1038/nbt.2931</citation>