| Previous changeset 26:6a3a025714d3 (2021-01-08) Next changeset 28:7ff33c2d525b (2021-11-19) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05" |
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modified:
deseq2.R deseq2.xml deseq2_macros.xml |
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| diff -r 6a3a025714d3 -r d027d1f4984e deseq2.R --- a/deseq2.R Fri Jan 08 20:29:54 2021 +0000 +++ b/deseq2.R Mon Jun 28 05:14:25 2021 +0000 |
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| @@ -67,7 +67,8 @@ "outlier_replace_off", "a", 0, "logical", "outlier_filter_off", "b", 0, "logical", "auto_mean_filter_off", "c", 0, "logical", - "beta_prior_off", "d", 0, "logical" + "beta_prior_off", "d", 0, "logical", + "alpha_ma", "A", 1, "numeric" ), byrow = TRUE, ncol = 4) opt <- getopt(spec) @@ -200,7 +201,7 @@ text(x = c(0, length(h1$counts)), y = 0, label = paste(c(0, 1)), adj = c(0.5, 1.7), xpd = NA) legend("topright", fill = rev(colori), legend = rev(names(colori)), bg = "white") } - plotMA(res, main = paste("MA-plot for", title_suffix), ylim = range(res$log2FoldChange, na.rm = TRUE)) + plotMA(res, main = paste("MA-plot for", title_suffix), ylim = range(res$log2FoldChange, na.rm = TRUE), alpha = opt$alpha_ma) } if (verbose) { |
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| diff -r 6a3a025714d3 -r d027d1f4984e deseq2.xml --- a/deseq2.xml Fri Jan 08 20:29:54 2021 +0000 +++ b/deseq2.xml Mon Jun 28 05:14:25 2021 +0000 |
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| b'@@ -1,20 +1,11 @@\n-<tool id="deseq2" name="DESeq2" version="2.11.40.6+galaxy1">\n+<tool id="deseq2" name="DESeq2" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@">\n <description>Determines differentially expressed features from count tables</description>\n <macros>\n <import>deseq2_macros.xml</import>\n </macros>\n- <requirements>\n- <requirement type="package" version="1.22.1">bioconductor-deseq2</requirement>\n- <!-- Optional dependency of tximport, needed to import kallisto results https://github.com/galaxyproject/usegalaxy-playbook/issues/161 -->\n- <requirement type="package" version="2.26.2">bioconductor-rhdf5</requirement>\n- <requirement type="package" version="1.10.0">bioconductor-tximport</requirement>\n- <requirement type="package" version="1.34.1">bioconductor-genomicfeatures</requirement>\n- <requirement type="package" version="1.20.2">r-getopt</requirement>\n- <requirement type="package" version="0.8.0">r-ggrepel</requirement>\n- <requirement type="package" version="3.0.1">r-gplots</requirement>\n- <requirement type="package" version="1.0.10">r-pheatmap</requirement>\n- <requirement type="package" version="0.2.20">r-rjson</requirement>\n- </requirements>\n+ <expand macro=\'requirements\'/>\n+ <expand macro=\'edam_ontology\' />\n+ <expand macro=\'xrefs\'/>\n <stdio>\n <regex match="Execution halted"\n source="both"\n@@ -49,16 +40,17 @@\n Rscript \'${__tool_directory__}/deseq2.R\'\n --cores \\${GALAXY_SLOTS:-1}\n -o \'$deseq_out\'\n- #if $pdf:\n+ #if \'pdf\' in $output_options.output_selector:\n -p \'$plots\'\n #end if\n- #if $normCounts:\n+ -A $output_options.alpha_ma\n+ #if \'normCounts\' in $output_options.output_selector:\n -n \'$counts_out\'\n #end if\n- #if $normRLog:\n+ #if \'normRLog\' in $output_options.output_selector:\n -r \'$rlog_out\'\n #end if\n- #if $normVST:\n+ #if \'normVST\' in $output_options.output_selector:\n -v \'$vst_out\'\n #end if\n #set $filename_to_element_identifiers = {}\n@@ -90,23 +82,23 @@\n \n -f \'#echo json.dumps(temp_factor_names)#\'\n -l \'#echo json.dumps(filename_to_element_identifiers)#\'\n- #if $esf:\n- -e $esf\n+ #if $advanced_options.esf:\n+ -e $advanced_options.esf\n #end if\n- -t $fit_type\n+ -t $advanced_options.fit_type\n #if $batch_factors:\n --batch_factors \'$batch_factors\'\n #end if\n- #if $outlier_replace_off:\n+ #if $advanced_options.outlier_replace_off:\n -a\n #end if\n- #if $outlier_filter_off:\n+ #if $advanced_options.outlier_filter_off:\n -b\n #end if\n- #if $auto_mean_filter_off:\n+ #if $advanced_options.auto_mean_filter_off:\n -c\n #end if\n- #if $many_contrasts:\n+ #if \'many_contrasts\' in $output_options.output_selector\n -m\n #end if\n #if $tximport.tximport_selector == \'tximport\':\n@@ -168,71 +160,71 @@\n </when>\n <when value="count" />\n </conditional>\n- <param name="pdf" type="boolean" truevalue="1" falsevalue="0" checked="true"\n- label="Visualising the analysis results"\n- help="output an additional PDF files" />\n- <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"\n- label="Output normalized counts table" />\n- <param name="normRLog" type="boolean" truevalue="1" falsevalue="0" checked="false"\n- label="Output rLog normalized table" />\n- <param name="normVST" type="boolean" truevalue="1" falsevalue="0" checked="false"\n- label="Output VST normalized table" />\n- <param name="many_contrasts" type="boolean" truevalue="1" falsevalue="0" checked="false"\n- label="Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)"\n- help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a'..b'le" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/>\n </repeat>\n </repeat>\n- <param name="pdf" value="False"/>\n+ <section name="output_options">\n+ <param name="output_selector" value=""/>\n+ </section> \n <param name="tximport_selector" value="tximport"/>\n <param name="txtype" value="sailfish"/>\n <param name="mapping_format_selector" value="gtf"/>\n@@ -437,7 +434,9 @@\n <param name="groups" value="primary:untreated"/>\n </repeat>\n </repeat>\n- <param name="pdf" value="False"/>\n+ <section name="output_options">\n+ <param name="output_selector" value=""/>\n+ </section> \n <param name="tximport_selector" value="tximport"/>\n <param name="txtype" value="sailfish"/>\n <param name="mapping_format_selector" value="tabular"/>\n@@ -472,12 +471,13 @@\n <param name="groups" value="primary:untreated"/>\n </repeat>\n </repeat>\n- <param name="pdf" value="False"/>\n+ <section name="output_options">\n+ <param name="output_selector" value="many_contrasts"/>\n+ </section> \n <param name="tximport_selector" value="tximport"/>\n <param name="txtype" value="sailfish"/>\n <param name="mapping_format_selector" value="tabular"/>\n <param name="tabular_file" value="tx2gene.tab"/>\n- <param name="many_contrasts" value="true"/>\n <output_collection name="split_output" type="list" count="1">\n <element name="Treatment_Treated_vs_Untreated">\n <assert_contents>\n@@ -486,6 +486,33 @@\n </element>\n </output_collection>\n </test>\n+ <!--Test alpha_ma option-->\n+ <test expect_num_outputs="1">\n+ <repeat name="rep_factorName">\n+ <param name="factorName" value="Treatment"/>\n+ <repeat name="rep_factorLevel">\n+ <param name="factorLevel" value="Treated"/>\n+ <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/>\n+ </repeat>\n+ <repeat name="rep_factorLevel">\n+ <param name="factorLevel" value="Untreated"/>\n+ <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/>\n+ </repeat>\n+ </repeat>\n+ <section name="output_options">\n+ <param name="output_selector" value=""/>\n+ <param name="alpha_ma" value="0.05"/>\n+ </section> \n+ <param name="tximport_selector" value="tximport"/>\n+ <param name="txtype" value="sailfish"/>\n+ <param name="mapping_format_selector" value="gtf"/>\n+ <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/>\n+ <output name="deseq_out" >\n+ <assert_contents>\n+ <has_text_matching expression="ENSG00000168671\\t1.8841.*\\t-0.1180.*\\t0.7429.*\\t-0.1589.*\\t0.8737.*\\t0.9999.*" />\n+ </assert_contents>\n+ </output>\n+ </test>\n </tests>\n <help><![CDATA[\n .. class:: infomark\n@@ -584,7 +611,5 @@\n .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html\n .. _tximport: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html\n ]]></help>\n- <citations>\n- <citation type="doi">10.1186/s13059-014-0550-8</citation>\n- </citations>\n+ <expand macro="citations" />\n </tool>\n' |
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| diff -r 6a3a025714d3 -r d027d1f4984e deseq2_macros.xml --- a/deseq2_macros.xml Fri Jan 08 20:29:54 2021 +0000 +++ b/deseq2_macros.xml Mon Jun 28 05:14:25 2021 +0000 |
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| @@ -18,4 +18,38 @@ </repeat> </repeat> </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.22.1">bioconductor-deseq2</requirement> + <!-- Optional dependency of tximport, needed to import kallisto results https://github.com/galaxyproject/usegalaxy-playbook/issues/161 --> + <requirement type="package" version="2.26.2">bioconductor-rhdf5</requirement> + <requirement type="package" version="1.10.0">bioconductor-tximport</requirement> + <requirement type="package" version="1.34.1">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> + </xml> + <token name="@TOOL_VERSION@">2.11.40.6</token> + <token name="@SUFFIX_VERSION@">2</token> + <xml name="edam_ontology"> + <edam_topics> + <edam_topic>topic_3308</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_3800</edam_operation> + </edam_operations> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1186/s13059-014-0550-8</citation> + </citations> + </xml> + <xml name="xrefs"> + <xrefs> + <xref type='bio.tools'>DESeq2</xref> + </xrefs> + </xml> </macros> \ No newline at end of file |