| Previous changeset 30:8fe98f7094de (2022-08-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf |
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modified:
deseq2.R deseq2.xml |
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added:
macros.xml test-data/size_factors_out.tsv |
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removed:
deseq2_macros.xml |
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| diff -r 8fe98f7094de -r 9a882d108833 deseq2.R --- a/deseq2.R Fri Aug 26 11:16:15 2022 +0000 +++ b/deseq2.R Tue Jul 18 14:58:52 2023 +0000 |
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| @@ -36,9 +36,6 @@ q("no", 1, FALSE) }) -# we need that to not crash galaxy with an UTF8 error on German LC settings. -loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") - library("getopt") library("tools") options(stringAsFactors = FALSE, useFancyQuotes = FALSE) @@ -69,7 +66,7 @@ "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", + "use_beta_priors", "d", 0, "logical", "alpha_ma", "A", 1, "numeric", "prefilter", "P", 0, "logical", "prefilter_value", "V", 1, "numeric" @@ -217,11 +214,27 @@ } dds <- get_deseq_dataset(sample_table, header = opt$header, design_formula = design_formula, tximport = opt$tximport, txtype = opt$txtype, tx2gene = opt$tx2gene) -# estimate size factors for the chosen method + +# use/estimate size factors with the chosen method if (!is.null(opt$esf)) { - dds <- estimateSizeFactors(dds, type = opt$esf) + if (opt$esf %in% list("ratio", "poscounts", "iterate")) { + cat("Calculating size factors de novo\n") + dds <- estimateSizeFactors(dds, type = opt$esf) + } else { + sf_table <- read.table(opt$esf) + # Sort the provided size factors just in case the order differs from the input file order. + merged_table <- merge(sample_table, sf_table, by.x = 0, by.y = 1, sort = FALSE) + sf_values <- as.numeric(unlist(merged_table[5])) + "sizeFactors"(dds) <- sf_values + + cat("Using user-provided size factors:\n") + print(sf_values) + } +} else { + cat("No size factor was used\n") } + # estimate size factors for each sample # - https://support.bioconductor.org/p/97676/ if (!is.null(opt$sizefactorsfile)) { @@ -312,12 +325,15 @@ } # shrinkage of LFCs -if (is.null(opt$beta_prior_off)) { - beta_prior <- TRUE +if (is.null(opt$use_beta_priors)) { + beta_prior <- FALSE + if (verbose) + cat("Applied default - beta prior off\n") } else { - beta_prior <- FALSE - if (verbose) cat("beta prior off\n") + beta_prior <- opt$use_beta_priors } +sprintf("use_beta_prior is set to %s", beta_prior) + # dispersion fit type if (is.null(opt$fit_type)) { |
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| diff -r 8fe98f7094de -r 9a882d108833 deseq2.xml --- a/deseq2.xml Fri Aug 26 11:16:15 2022 +0000 +++ b/deseq2.xml Tue Jul 18 14:58:52 2023 +0000 |
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| b'@@ -1,24 +1,24 @@\n-<tool id="deseq2" name="DESeq2" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@">\n+<tool id="deseq2" name="DESeq2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n <description>Determines differentially expressed features from count tables</description>\n <macros>\n- <import>deseq2_macros.xml</import>\n+ <import>macros.xml</import>\n </macros>\n+ <expand macro=\'edam_ontology\'/>\n+ <expand macro=\'xrefs\'/>\n <expand macro=\'requirements\'/>\n- <expand macro=\'edam_ontology\' />\n- <expand macro=\'xrefs\'/>\n <stdio>\n <regex match="Execution halted"\n source="both"\n level="fatal"\n- description="Execution halted." />\n+ description="Execution halted."/>\n <regex match="Error in"\n source="both"\n level="fatal"\n- description="An undefined error occurred, please check your input carefully and contact your administrator." />\n+ description="An undefined error occurred, please check your input carefully and contact your administrator."/>\n <regex match="Fatal error"\n source="both"\n level="fatal"\n- description="An undefined error occurred, please check your input carefully and contact your administrator." />\n+ description="An undefined error occurred, please check your input carefully and contact your administrator."/>\n </stdio>\n <version_command><![CDATA[\n echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\\$otherPkgs\\$DESeq2\\$Version)" 2> /dev/null | grep -v -i "WARNING: ")\n@@ -85,8 +85,12 @@\n \n -f \'#echo json.dumps(temp_factor_names)#\'\n -l \'#echo json.dumps(filename_to_element_identifiers)#\'\n- #if $advanced_options.esf:\n- -e $advanced_options.esf\n+ #if $advanced_options.esf_cond.esf:\n+ #if $advanced_options.esf_cond.esf == "user":\n+ -e $advanced_options.esf_cond.size_factor_input\n+ #else:\n+ -e $advanced_options.esf_cond.esf\n+ #end if\n #end if\n -t $advanced_options.fit_type\n #if $batch_factors:\n@@ -96,15 +100,12 @@\n $advanced_options.prefilter_conditional.prefilter\n -V $advanced_options.prefilter_conditional.prefilter_value\n #end if\n- #if $advanced_options.outlier_replace_off:\n- -a\n- #end if\n- #if $advanced_options.outlier_filter_off:\n- -b\n- #end if\n- #if $advanced_options.auto_mean_filter_off:\n- -c\n- #end if\n+ \n+ $advanced_options.outlier_replace_off\n+ $advanced_options.outlier_filter_off\n+ $advanced_options.auto_mean_filter_off\n+ $advanced_options.use_beta_priors\n+\n #if \'many_contrasts\' in $output_options.output_selector\n -m\n #end if\n@@ -116,7 +117,6 @@\n #else:\n -x mapping.txt\n #end if\n-\n #end if\n ]]></command>\n <inputs>\n@@ -139,7 +139,7 @@\n </conditional>\n \n <param name="batch_factors" type="data" format="tabular" optional="true" label="(Optional) provide a tabular file with additional batch factors to include in the model." help="You can produce this file using RUVSeq or svaseq."/>\n- <param name="header" type="boolean" truevalue="-H" falsevalue="" checked="true" label="Files have header?" help="If this option is set to Yes, the tool will assume that the count files have column headers in the first row. Default: Yes" />\n+ <param name="header" type="boolean" truevalue="-H" falsevalue="" checked="true" label="Files have header?" help="If this option is set to Yes, the tool will assume that the count files have column headers in the first row. Default: Yes"/>\n \n <conditional name="tximport">\n <param name="tximport_selector" type="select" label="Choice of Input data">\n@@ -165,39 +165,49 @@\n </when>\n </conditional>\n </when>\n- <when value="'..b'ching expression="sailfish_quant\\.sf3\\.tab\\t1\\.0\\d+" />\n+ <has_text_matching expression="sailfish_quant\\.sf4\\.tab\\t0\\.8\\d+"/>\n+ <has_text_matching expression="sailfish_quant\\.sf3\\.tab\\t1\\.0\\d+"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <!--Test alpha_ma option, but with user-provided size factors -->\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="advanced_options">\n+ <param name="use_beta_priors" value="1"/>\n+ <conditional name="esf_cond">\n+ <param name="esf" value="user"/>\n+ <param name="size_factor_input" value="size_factors_out.tsv"/>\n+ </conditional>\n+ </section>\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\\t1.90.*\\t-0.05.*\\t0.75.*\\t-0.07.*\\t0.94.*\\t0.95.*"/>\n </assert_contents>\n </output>\n </test>\n@@ -580,7 +680,7 @@\n </repeat>\n </repeat>\n <section name="advanced_options">\n- <param name="esf" value="poscounts" />\n+ <param name="esf" value="poscounts"/>\n </section>\n <section name="output_options">\n <param name="output_selector" value="sizefactors"/>\n@@ -592,8 +692,8 @@\n <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/>\n <output name="sizefactors_out" >\n <assert_contents>\n- <has_text_matching expression="sailfish_quant\\.sf4\\.tab\\t0\\.8\\d+" />\n- <has_text_matching expression="sailfish_quant\\.sf3\\.tab\\t1\\.0\\d+" />\n+ <has_text_matching expression="sailfish_quant\\.sf4\\.tab\\t0\\.8\\d+"/>\n+ <has_text_matching expression="sailfish_quant\\.sf3\\.tab\\t1\\.0\\d+"/>\n </assert_contents>\n </output>\n </test>\n@@ -636,7 +736,7 @@\n \n **What it does**\n \n-Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution\n+Uses DESeq2 version @DESEQ2_VERSION@ to estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.\n \n -----\n \n@@ -732,5 +832,5 @@\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- <expand macro="citations" />\n+ <expand macro="citations"/>\n </tool>\n' |
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| diff -r 8fe98f7094de -r 9a882d108833 deseq2_macros.xml --- a/deseq2_macros.xml Fri Aug 26 11:16:15 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,55 +0,0 @@ -<macros> - <xml name="factor_repeat"> - <repeat name="rep_factorName" title="Factor" min="1"> - <param name="factorName" type="text" value="FactorName" label="Specify a factor name, e.g. effects_drug_x or cancer_markers" - help="Only letters, numbers and underscores will be retained in this field"> - <sanitizer> - <valid initial="string.letters,string.digits"><add value="_" /></valid> - </sanitizer> - </param> - <repeat name="rep_factorLevel" title="Factor level" min="2" default="2"> - <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'" - help="Only letters, numbers and underscores will be retained in this field"> - <sanitizer> - <valid initial="string.letters,string.digits"><add value="_" /></valid> - </sanitizer> - </param> - <yield/> - </repeat> - </repeat> - </xml> - <xml name="requirements"> - <requirements> - <requirement type="package" version="1.34.0">bioconductor-deseq2</requirement> - <!-- Optional dependency of tximport, needed to import kallisto results https://github.com/galaxyproject/usegalaxy-playbook/issues/161 --> - <requirement type="package" version="2.38.0">bioconductor-rhdf5</requirement> - <requirement type="package" version="1.22.0">bioconductor-tximport</requirement> - <requirement type="package" version="1.46.1">bioconductor-genomicfeatures</requirement> - <requirement type="package" version="1.20.3">r-getopt</requirement> - <requirement type="package" version="0.9.1">r-ggrepel</requirement> - <requirement type="package" version="3.1.1">r-gplots</requirement> - <requirement type="package" version="1.0.12">r-pheatmap</requirement> - <requirement type="package" version="0.2.20">r-rjson</requirement> - </requirements> - </xml> - <token name="@TOOL_VERSION@">2.11.40.7</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 |
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| diff -r 8fe98f7094de -r 9a882d108833 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Jul 18 14:58:52 2023 +0000 |
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| @@ -0,0 +1,58 @@ +<macros> + <xml name="factor_repeat"> + <repeat name="rep_factorName" title="Factor" min="1"> + <param name="factorName" type="text" value="FactorName" label="Specify a factor name, e.g. effects_drug_x or cancer_markers" + help="Only letters, numbers and underscores will be retained in this field"> + <sanitizer> + <valid initial="string.letters,string.digits"><add value="_" /></valid> + </sanitizer> + </param> + <repeat name="rep_factorLevel" title="Factor level" min="2" default="2"> + <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'" + help="Only letters, numbers and underscores will be retained in this field"> + <sanitizer> + <valid initial="string.letters,string.digits"><add value="_" /></valid> + </sanitizer> + </param> + <yield/> + </repeat> + </repeat> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@DESEQ2_VERSION@">bioconductor-deseq2</requirement> + <!-- Optional dependency of tximport, needed to import kallisto results https://github.com/galaxyproject/usegalaxy-playbook/issues/161 --> + <requirement type="package" version="2.44.0">bioconductor-rhdf5</requirement> + <requirement type="package" version="1.28.0">bioconductor-tximport</requirement> + <requirement type="package" version="1.52.1">bioconductor-genomicfeatures</requirement> + <requirement type="package" version="1.20.3">r-getopt</requirement> + <requirement type="package" version="0.9.3">r-ggrepel</requirement> + <requirement type="package" version="3.1.3">r-gplots</requirement> + <requirement type="package" version="1.0.12">r-pheatmap</requirement> + <requirement type="package" version="0.2.21">r-rjson</requirement> + </requirements> + </xml> + <token name="@TOOL_VERSION@">2.11.40.8</token> + <token name="@DESEQ2_VERSION@">1.40.2</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">22.01</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> + <xref type="bioconductor">deseq2</xref> + </xrefs> + </xml> +</macros> |
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| diff -r 8fe98f7094de -r 9a882d108833 test-data/size_factors_out.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/size_factors_out.tsv Tue Jul 18 14:58:52 2023 +0000 |
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| @@ -0,0 +1,6 @@ +sailfish_quant.sf4.tab 0.84800690799672 +sailfish_quant.sf5.tab 1.10790786350701 +sailfish_quant.sf6.tab 1.21319523337605 +sailfish_quant.sf1.tab 1.19061589081921 +sailfish_quant.sf2.tab 0.712203801356132 +sailfish_quant.sf3.tab 1.03464248515867 |