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comparison egsea.xml @ 1:73281fbdf6c1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0
author iuc
date Thu, 15 Feb 2018 02:34:59 -0500
parents a8a083193440
children ba2111ae6eb4
comparison
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0:a8a083193440 1:73281fbdf6c1
1 <tool id="egsea" name="EGSEA" version="1.6.0.0"> 1 <tool id="egsea" name="EGSEA" version="1.6.0.1">
2 <description> easy and efficient ensemble gene set testing</description> 2 <description> easy and efficient ensemble gene set testing</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.6.0">bioconductor-egsea</requirement> 4 <requirement type="package" version="1.6.0">bioconductor-egsea</requirement>
5 <requirement type="package" version="1.4.4">r-optparse</requirement> 5 <requirement type="package" version="1.4.4">r-optparse</requirement>
6 <requirement type="package" version="0.2.15">r-rjson</requirement> 6 <requirement type="package" version="0.2.15">r-rjson</requirement>
7 <!--statmod is required for fry-->
8 <requirement type="package" version="1.4.30">r-statmod</requirement>
7 </requirements> 9 </requirements>
8 <version_command><![CDATA[ 10 <version_command><![CDATA[
9 echo $(R --version | grep version | grep -v GNU)", EGSEA version" $(R --vanilla --slave -e "library(EGSEA); cat(sessionInfo()\$otherPkgs\$EGSEA\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ") 11 echo $(R --version | grep version | grep -v GNU)", EGSEA version" $(R --vanilla --slave -e "library(EGSEA); cat(sessionInfo()\$otherPkgs\$EGSEA\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
10 ]]></version_command> 12 ]]></version_command>
11 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
12 ## EGSEA requires at least 2 threads 14 ## EGSEA requires at least 2 threads
13 SLOTS=\${GALAXY_SLOTS:-2}; 15 SLOTS=\${GALAXY_SLOTS:-2};
14 [ "\$SLOTS" -eq 1 ] && SLOTS=2; 16 [ "\$SLOTS" -eq 1 ] && SLOTS=2;
55 --species $species 57 --species $species
56 58
57 --base_methods $base_methods 59 --base_methods $base_methods
58 --msigdb $msigdb.msigdb_gsets 60 --msigdb $msigdb.msigdb_gsets
59 --keggdb $keggdb.keggdb_gsets 61 --keggdb $keggdb.keggdb_gsets
62 --keggupdated $keggdb.kegg_updated
60 --gsdb $gsdb.gsdb_gsets 63 --gsdb $gsdb.gsdb_gsets
61 64
62 --display_top $advanced.display_top 65 --display_top $advanced.display_top
63 --min_size $advanced.min_size 66 --min_size $advanced.min_size
64 --fdr_cutoff $advanced.fdr_cutoff 67 --fdr_cutoff $advanced.fdr_cutoff
184 <param name="keggdb_gsets" type="select" display="checkboxes" optional="True" multiple="True" label="KEGG Pathways" help="Choose any KEGG Pathways you want to use. Default: None"> 187 <param name="keggdb_gsets" type="select" display="checkboxes" optional="True" multiple="True" label="KEGG Pathways" help="Choose any KEGG Pathways you want to use. Default: None">
185 <option value="keggmet">Metabolism pathways</option> 188 <option value="keggmet">Metabolism pathways</option>
186 <option value="keggsig">Signalling pathways</option> 189 <option value="keggsig">Signalling pathways</option>
187 <option value="keggdis">Disease pathways</option> 190 <option value="keggdis">Disease pathways</option>
188 </param> 191 </param>
192 <param name="kegg_updated" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Download KEGG pathways?" help="Select Yes if you want to download the most recent KEGG pathways, see the Help section below. Default: No"/>
189 </section> 193 </section>
190 194
191 <section name="gsdb" title="GeneSetDB Gene Sets" expanded="True"> 195 <section name="gsdb" title="GeneSetDB Gene Sets" expanded="True">
192 <param name="gsdb_gsets" type="select" display="checkboxes" optional="True" multiple="True" label="GeneSigDB Gene Set Collections" help="Choose any GeneSetDB Gene Set Collections you want to use. Default: None"> 196 <param name="gsdb_gsets" type="select" display="checkboxes" optional="True" multiple="True" label="GeneSigDB Gene Set Collections" help="Choose any GeneSetDB Gene Set Collections you want to use. Default: None">
193 <option value="gsdbpath">Pathway collection</option> 197 <option value="gsdbpath">Pathway collection</option>
257 <filter>advanced['rdaOpt'] is True</filter> 261 <filter>advanced['rdaOpt'] is True</filter>
258 </data> 262 </data>
259 </outputs> 263 </outputs>
260 264
261 <tests> 265 <tests>
262 <!-- Ensure report is output --> 266 <!-- Ensure report is output -->
263 <test expect_num_outputs="1"> 267 <test expect_num_outputs="1">
264 <param name="non_commercial_use" value="True"/> 268 <param name="non_commercial_use" value="True"/>
265 <param name="format" value="matrix" /> 269 <param name="format" value="matrix" />
266 <param name="counts" value="il13.counts"/> 270 <param name="counts" value="il13.counts"/>
267 <param name="genes" value="il13.genes"/> 271 <param name="genes" value="il13.genes"/>
336 </repeat> 340 </repeat>
337 <output_collection name="outTables" count="1"> 341 <output_collection name="outTables" count="1">
338 <element name="ranked-h-gene-sets-IL13Ant-IL13" ftype="tabular" file="ranked-h-gene-sets-IL13Ant-IL13_batch.txt"/> 342 <element name="ranked-h-gene-sets-IL13Ant-IL13" ftype="tabular" file="ranked-h-gene-sets-IL13Ant-IL13_batch.txt"/>
339 </output_collection> 343 </output_collection>
340 </test> 344 </test>
345 <!-- Ensure all gene set methods work -->
346 <test expect_num_outputs="1">
347 <param name="non_commercial_use" value="True"/>
348 <param name="format" value="matrix"/>
349 <param name="counts" value="il13.counts"/>
350 <param name="genes" value="il13.genes"/>
351 <param name="ffile" value="yes"/>
352 <param name="finfo" value="il13.group_batch"/>
353 <repeat name="rep_contrast">
354 <param name="contrast" value="IL13Ant-IL13"/>
355 </repeat>
356 <param name="base_methods" value="camera,safe,gage,zscore,gsva,globaltest,ora,ssgsea,padog,plage,fry,roast"/>
357 <output_collection name="outTables" count="1">
358 <element name="ranked-h-gene-sets-IL13Ant-IL13" ftype="tabular" file="ranked-h-gene-sets-IL13Ant-IL13_batch_all.txt"/>
359 </output_collection>
360 </test>
361 <!-- Ensure KEGG updated works -->
362 <test expect_num_outputs="1">
363 <param name="non_commercial_use" value="True"/>
364 <param name="format" value="matrix"/>
365 <param name="counts" value="il13.counts"/>
366 <param name="genes" value="il13.genes"/>
367 <param name="ffile" value="yes"/>
368 <param name="finfo" value="il13.group_batch"/>
369 <repeat name="rep_contrast">
370 <param name="contrast" value="IL13Ant-IL13"/>
371 </repeat>
372 <param name="keggdb_gsets" value="keggmet"/>
373 <param name="kegg_updated" value="True"/>
374 <output_collection name="outTables" count="2">
375 <element name="ranked-h-gene-sets-IL13Ant-IL13" ftype="tabular" file="ranked-h-gene-sets-IL13Ant-IL13_batch.txt"/>
376 <element name="ranked-kegg-gene-sets-IL13Ant-IL13" ftype="tabular" file="ranked-kegg-gene-sets-IL13Ant-IL13.txt"/>
377 </output_collection>
378 </test>
341 </tests> 379 </tests>
342 380
343 <help><![CDATA[ 381 <help><![CDATA[
344 382
345 .. class:: infomark 383 .. class:: infomark
526 564
527 ----- 565 -----
528 566
529 **KEGG Pathways** 567 **KEGG Pathways**
530 568
531 Obtained by EGSEAdata from the GAGE_ Bioconductor package using the gage function kegg.gsets(). The Pathview_ Bioconductor package is used to visualize the expression data mapped onto the KEGG pathway graphs. Pathview has a GPLv3 licence which means users are required to formally cite the original `Pathview paper`_ (not just mention it) in publications or products. GAGE/Pathview divide the KEGG pathways into 3 categories: Signaling, Metabolism and Disease, listed in this file at the `Pathview website here`_. 569 Obtained by EGSEAdata from the GAGE_ Bioconductor package using the gage function kegg.gsets(). The Pathview_ Bioconductor package is used to visualize the expression data mapped onto the KEGG pathway graphs. Pathview has a GPLv3 licence which means users are required to formally cite the original `Pathview paper`_ (not just mention it) in publications or products. GAGE/Pathview divide the KEGG pathways into 3 categories: Signaling, Metabolism and Disease, listed in this file at the `Pathview website here`_. You can choose if you want to download the most recent KEGG pathways by selecting the ``Download KEGG pathways`` option in the tool form above. Note that downloading the most recent pathways may affect reproducibility as you can't choose what versions of pathways to use.
532 570
533 **Signaling** 571 **Signaling**
534 572
535 * Genetic Information Processing 573 * Genetic Information Processing
536 * Environmental Information Processing 574 * Environmental Information Processing