Mercurial > repos > iuc > dexseq
diff dexseq.xml @ 5:278b189248cd draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
author | iuc |
---|---|
date | Mon, 14 Jan 2019 05:02:19 -0500 |
parents | 251393b72616 |
children | 2872c633f07e |
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--- a/dexseq.xml Tue Dec 11 00:19:18 2018 -0500 +++ b/dexseq.xml Mon Jan 14 05:02:19 2019 -0500 @@ -1,4 +1,4 @@ -<tool id="dexseq" name="DEXSeq" version="@VERSION@.0"> +<tool id="dexseq" name="DEXSeq" version="@VERSION@+galaxy1"> <description>Determines differential exon usage from count tables</description> <macros> <import>macros.xml</import> @@ -54,6 +54,7 @@ -f '#echo json.dumps(temp_factor_names)#' -a $gtf -c $fdr_cutoff + -d $rds #if $report: -r ./html_out @@ -93,6 +94,8 @@ <param name="report" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Visualise the analysis results?" help="Output an additional HTML file." /> + <param name="rds" type="boolean" truevalue="True" falsevalue="False" checked="false" + label="Output rds file for plotDEXSeq?" help="Can be used to generate plots for individual genes with plotDEXSeq" /> <param name="fdr_cutoff" type="float" min="0.0" max="1.0" value="0.05" label="All the genes under this FDR threshold will be shown in the html report"/> </inputs> <outputs> @@ -100,6 +103,9 @@ <data name="htmlreport" format="html" label="DEXSeq report on ${on_string}"> <filter>report is True</filter> </data> + <data name="rds_out" format="rdata" from_work_dir="DEXSeqResults.rds" label="DEXSeq rds file on ${on_string}"> + <filter>rds is True</filter> + </data> </outputs> <tests> <!-- Ensure default output works--> @@ -151,6 +157,22 @@ <param name="fdr_cutoff" value="0.05"/> <output name="dexseq_out" file="dexseq_result_2fact.tabular" ftype="tabular" compare="sim_size"/> </test> + <!-- Ensure rds output works--> + <test expect_num_outputs="2"> + <param name="gtf" value="dexseq.gtf" ftype="gtf"/> + <repeat name="rep_factorName"> + <param name="factorName" value="condition"/> + <param name="factorLevel1" value="knockdown"/> + <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/> + <param name="factorLevel2" value="control"/> + <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/> + </repeat> + <param name="report" value="False"/> + <param name="rds" value="True"/> + <param name="fdr_cutoff" value="0.05"/> + <output name="dexseq_out" ftype="tabular" file="dexseq_result.tabular" compare="sim_size"/> + <output name="rds_out" ftype="rdata" file="dexseq.rds" compare="sim_size"/> + </test> </tests> <help><![CDATA[ .. class:: infomark @@ -188,7 +210,7 @@ **Output** -DEXSeq_ generates a tabular file containing the different columns and an optional html report. +DEXSeq_ generates a tabular file containing the different columns and an optional html report. It can also ouput the DEXSeqResults R object that can be used with the plotDEXSeq tool to visualise individual genes. ====== ========================================================== Column Description