Mercurial > repos > sblanck > smagexp
comparison MetaRNAseq.xml @ 0:1024245abc70 draft
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
| author | sblanck |
|---|---|
| date | Thu, 22 Feb 2018 08:38:22 -0500 |
| parents | |
| children | f18413a94742 |
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| -1:000000000000 | 0:1024245abc70 |
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| 1 <tool id="metarnaseq" name="RNA-seq data meta-analysis" version="1.0.0"> | |
| 2 | |
| 3 <description>Performs meta-analysis thanks to metaRNAseq</description> | |
| 4 | |
| 5 <requirements> | |
| 6 <requirement type="package">bioconductor-affy</requirement> | |
| 7 <requirement type="package">bioconductor-annaffy</requirement> | |
| 8 <requirement type="package">bioconductor-geoquery</requirement> | |
| 9 <requirement type="package">r-venndiagram</requirement> | |
| 10 <requirement type="package">r-jsonlite</requirement> | |
| 11 <requirement type="package">r-metarnaseq</requirement> | |
| 12 <requirement type="package">r-optparse</requirement> | |
| 13 </requirements> | |
| 14 | |
| 15 <stdio> | |
| 16 <exit_code range="1:" /> | |
| 17 <regex match="Warning" source="both" level="warning"/> | |
| 18 </stdio> | |
| 19 | |
| 20 <command> | |
| 21 | |
| 22 <![CDATA[ | |
| 23 Rscript | |
| 24 ${__tool_directory__}/MetaRNASeq.R | |
| 25 --input "#for $input in $inputs# $input;$input.name, #end for#" | |
| 26 --result $top_table | |
| 27 --htmloutput $result_html | |
| 28 --htmloutputpath $result_html.extra_files_path | |
| 29 --htmltemplate ${__tool_directory__}/MetaRNASeq_tpl.html | |
| 30 ]]> | |
| 31 </command> | |
| 32 | |
| 33 <inputs> | |
| 34 <param format="tabular" name="inputList" multiple="true" type="data" optional="false" label="Counts file" help="Must have the same number of row in each study. The experimental conditions must be specified in the header of each file"/> | |
| 35 </inputs> | |
| 36 | |
| 37 <outputs> | |
| 38 <data format="tabular" name="top_table" label="Summary of meta-analysis and single studie analysis from ${tool.name} on ${on_string}"/> | |
| 39 <data format="html" name="diagnostic_html" label="Charts for ${tool.name} on ${on_string}"/> | |
| 40 </outputs> | |
| 41 | |
| 42 <tests> | |
| 43 | |
| 44 </tests> | |
| 45 | |
| 46 <help> | |
| 47 | |
| 48 </help> | |
| 49 | |
| 50 </tool> |