Mercurial > repos > iuc > deseq2
diff deseq2.xml @ 19:c56e0689e46e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
author | iuc |
---|---|
date | Tue, 04 Dec 2018 08:19:06 -0500 |
parents | 3bf1b3ec1ddf |
children | 89d26b11d452 |
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--- a/deseq2.xml Fri Nov 16 14:47:19 2018 -0500 +++ b/deseq2.xml Tue Dec 04 08:19:06 2018 -0500 @@ -1,11 +1,16 @@ -<tool id="deseq2" name="DESeq2" version="2.11.40.3"> +<tool id="deseq2" name="DESeq2" version="2.11.40.4"> <description>Determines differentially expressed features from count tables</description> <requirements> - <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement> - <requirement type="package" version="1.6.0">bioconductor-tximport</requirement> - <requirement type="package" version="1.30.0">bioconductor-genomicfeatures</requirement> - <requirement type="package" version="0.6.5">r-ggrepel</requirement> - <requirement type="package" version="1.0.8">r-pheatmap</requirement> + <requirement type="package" version="1.20.0">bioconductor-deseq2</requirement> + <!-- Optional dependency of tximport, needed to import kallisto results https://github.com/galaxyproject/usegalaxy-playbook/issues/161 --> + <requirement type="package" version="2.24.0">bioconductor-rhdf5</requirement> + <requirement type="package" version="1.8.0">bioconductor-tximport</requirement> + <requirement type="package" version="1.32.3">bioconductor-genomicfeatures</requirement> + <requirement type="package" version="1.20.2">r-getopt</requirement> + <requirement type="package" version="0.8.0">r-ggrepel</requirement> + <requirement type="package" version="3.0.1">r-gplots</requirement> + <requirement type="package" version="1.0.10">r-pheatmap</requirement> + <requirement type="package" version="0.2.20">r-rjson</requirement> </requirements> <stdio> <regex match="Execution halted" @@ -27,7 +32,7 @@ <command><![CDATA[ #if $tximport.tximport_selector == 'tximport': #if $tximport.mapping_format.mapping_format_selector == 'gtf': - ln -s '$tximport.mapping_format.gtf_file' mapping.gtf && + ln -s '$tximport.mapping_format.gtf_file' mapping.gff && #else: ln -s '$tximport.mapping_format.tabular_file' mapping.txt && #end if @@ -92,7 +97,7 @@ -i -y $tximport.txtype #if $tximport.mapping_format.mapping_format_selector == 'gtf': - -x mapping.gtf + -x mapping.gff #else: -x mapping.txt #end if @@ -133,14 +138,14 @@ </param> <conditional name="mapping_format"> <param name="mapping_format_selector" type="select" label="Gene mapping format"> - <option value="gtf" selected="True">GTF</option> - <option value="tabular">Transcript-ID and Gene-ID mapping file</option> + <option value="gtf" selected="True">GTF/GFF3</option> + <option value="tabular">Transcript-ID to Gene-ID mapping file</option> </param> <when value="gtf"> - <param name="gtf_file" type="data" format="gtf,gff3" label="GTF/GFF3 file with Transcript - Gene mapping"/> + <param name="gtf_file" type="data" format="gtf,gff3" label="GTF/GFF3 annotation file"/> </when> <when value="tabular"> - <param name="tabular_file" type="data" format="tabular" label="Tabular file with Transcript - Gene mapping"/> + <param name="tabular_file" type="data" format="tabular" label="Tabular file with Transcript-ID to Gene-ID mapping"/> </when> </conditional> </when> @@ -190,7 +195,7 @@ help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" /> </inputs> <outputs> - <data format="tabular" name="deseq_out" label="DESeq2 result file on ${on_string}"> + <data name="deseq_out" format="tabular" label="DESeq2 result file on ${on_string}"> <filter>many_contrasts is False</filter> <actions> <action name="column_names" type="metadata" default="GeneID,Base mean,log2(FC),StdErr,Wald-Stats,P-value,P-adj" /> @@ -200,16 +205,16 @@ <filter>many_contrasts is True</filter> <discover_datasets pattern="None.(?P<designation>.+_vs_.+)" format="tabular" directory="." visible="false"/> </collection> - <data format="pdf" name="plots" label="DESeq2 plots on ${on_string}"> + <data name="plots" format="pdf" label="DESeq2 plots on ${on_string}"> <filter>pdf == True</filter> </data> - <data format="tabular" name="counts_out" label="Normalized counts file on ${on_string}"> + <data name="counts_out" format="tabular" label="Normalized counts file on ${on_string}"> <filter>normCounts == True</filter> </data> - <data format="tabular" name="rlog_out" label="rLog-Normalized counts file on ${on_string}"> + <data name="rlog_out" format="tabular" label="rLog-Normalized counts file on ${on_string}"> <filter>normRLog == True</filter> </data> - <data format="tabular" name="vst_out" label="VST-Normalized counts file on ${on_string}"> + <data name="vst_out" format="tabular" label="VST-Normalized counts file on ${on_string}"> <filter>normVST == True</filter> </data> </outputs> @@ -251,7 +256,7 @@ </output> <output name="deseq_out" > <assert_contents> - <has_text_matching expression="FBgn0003360\t1933.9504.*\t-2.8399.*\t0.1309.*-21.6851.*2.831.*8.024" /> + <has_text_matching expression="FBgn0003360\t1933\.9504.*\t-2\.8399.*\t0\.1309.*\t-21\.68.*\t.*e-104\t.*e-101" /> </assert_contents> </output> </test> @@ -315,7 +320,7 @@ </output> <output name="deseq_out" > <assert_contents> - <has_text_matching expression="FBgn0003360\t1933.9504.*\t-2.8399.*\t0.1309.*-21.6851.*2.831.*8.024" /> + <has_text_matching expression="FBgn0003360\t1933\.9504.*\t-2\.8399.*\t0\.1309.*\t-21\.68.*\t.*e-104\t.*e-101" /> </assert_contents> </output> </test> @@ -339,7 +344,31 @@ <param name="tabular_file" value="tx2gene.tab"/> <output name="deseq_out" > <assert_contents> - <has_text_matching expression="MIR6859-2\t1.1858.*\t-1.5832.*\t1.2956.*\t-1.2219.*\t0.2217.*\t0.8868.*" /> + <has_text_matching expression="UGT3A2\t1.8841.*\t-0.1329.*\t0.6936.*\t-0.1917.*\t0.8479.*\t0.9999.*" /> + </assert_contents> + </output> + </test> + <!--Ensure Sailfish/Salmon input with GFF3 annotation works--> + <test expect_num_outputs="1"> + <repeat name="rep_factorName"> + <param name="factorName" value="Treatment"/> + <repeat name="rep_factorLevel"> + <param name="factorLevel" value="Treated"/> + <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/> + </repeat> + <repeat name="rep_factorLevel"> + <param name="factorLevel" value="Untreated"/> + <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/> + </repeat> + </repeat> + <param name="pdf" value="False"/> + <param name="tximport_selector" value="tximport"/> + <param name="txtype" value="sailfish"/> + <param name="mapping_format_selector" value="gtf"/> + <param name="gtf_file" value="GRCh38_latest_genomic.gff"/> + <output name="deseq_out" > + <assert_contents> + <has_text_matching expression="UGT3A2\t1.8841.*\t-0.1329.*\t0.6936.*\t-0.1917.*\t0.8479.*\t0.9999.*" /> </assert_contents> </output> </test>