Mercurial > repos > iuc > limma_voom

comparison limma_voom.xml @ 11:7e8af58c8052 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
author iuc
date Mon, 11 Jun 2018 08:18:25 -0400
parents e26047c4562d
children 81796eb60bd0
comparison
equal deleted inserted replaced
10:e26047c4562d 11:7e8af58c8052
1 <tool id="limma_voom" name="limma" version="3.34.9.6"> 1 <tool id="limma_voom" name="limma" version="3.34.9.7">
2 <description> 2 <description>
3 Perform differential expression with limma-voom or limma-trend 3 Perform differential expression with limma-voom or limma-trend
4 </description> 4 </description>
5 5
6 <requirements> 6 <requirements>
79 79
80 #if $out.normCounts: 80 #if $out.normCounts:
81 -x 81 -x
82 #end if 82 #end if
83 83
84 #if $out.libinfo:
85 -L
86 #end if
87
84 #if $out.rdaOption: 88 #if $out.rdaOption:
85 -r 89 -r
86 #end if 90 #end if
91
87 92
88 -l '$adv.lfc' 93 -l '$adv.lfc'
89 -p '$adv.pVal' 94 -p '$adv.pVal'
90 -d '$adv.pAdjust' 95 -d '$adv.pAdjust'
91 -G '$adv.topgenes' 96 -G '$adv.topgenes'
269 </param> 274 </param>
270 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false" 275 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
271 label="Output Normalised Counts Table?" 276 label="Output Normalised Counts Table?"
272 help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No"> 277 help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No">
273 </param> 278 </param>
279 <param name="libinfo" type="boolean" truevalue="1" falsevalue="0" checked="false"
280 label="Output Library information file?"
281 help="Output a tabular file showing the library sizes, normalisation factors and effective library sizes for the samples. Default: No">
282 </param>
274 <param name="rscript" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used will be provided as a text file in the output. Default: No"/> 283 <param name="rscript" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used will be provided as a text file in the output. Default: No"/>
275 <param name="rdaOption" type="boolean" truevalue="1" falsevalue="0" checked="false" 284 <param name="rdaOption" type="boolean" truevalue="1" falsevalue="0" checked="false"
276 label="Output RData file?" 285 label="Output RData file?"
277 help="Output all the data used by R to construct the plots and tables, can be loaded into R. A link to the RData file will be provided in the HTML report. Default: No"> 286 help="Output all the data used by R to construct the plots and tables, can be loaded into R. A link to the RData file will be provided in the HTML report. Default: No">
278 </param> 287 </param>
314 <collection name="outTables" type="list" label="${tool.name} on ${on_string}: Tables"> 323 <collection name="outTables" type="list" label="${tool.name} on ${on_string}: Tables">
315 <discover_datasets pattern="(?P&lt;name&gt;.+)\.tsv$" format="tabular" directory="output_dir" visible="false" /> 324 <discover_datasets pattern="(?P&lt;name&gt;.+)\.tsv$" format="tabular" directory="output_dir" visible="false" />
316 </collection> 325 </collection>
317 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript"> 326 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript">
318 <filter>out['rscript']</filter> 327 <filter>out['rscript']</filter>
328 </data>
329 <data name="libinfo" format="tabular" from_work_dir="libsizeinfo" label="${tool.name} on ${on_string}: Library information">
330 <filter>out['libinfo']</filter>
319 </data> 331 </data>
320 </outputs> 332 </outputs>
321 333
322 <tests> 334 <tests>
323 <!-- Ensure report is output --> 335 <!-- Ensure report is output -->
794 * an interactive Glimma MD plot and table (if annotation file provided) 806 * an interactive Glimma MD plot and table (if annotation file provided)
795 807
796 Optionally, under **Output Options** you can choose to output 808 Optionally, under **Output Options** you can choose to output
797 809
798 * a normalised counts table 810 * a normalised counts table
811 * a library size information file
799 * the R script used by this tool 812 * the R script used by this tool
800 * an RData file 813 * an RData file
801 814
802 ----- 815 -----
803 816