Mercurial > repos > artbio > deseq2_normalization
changeset 0:6b990f6c6ba9 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/deseq2_normalization commit 9dfb5a5331b87d213f495febbfccff0f54becb73
| author | artbio |
|---|---|
| date | Mon, 08 Jan 2018 04:21:24 -0500 |
| parents | |
| children | ca845e480c89 |
| files | deseq2_normalization.xml test-data/counts.tab test-data/norm_factors.tab test-data/norm_table.tab tool_dependencies.xml |
| diffstat | 5 files changed, 1124 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/deseq2_normalization.xml Mon Jan 08 04:21:24 2018 -0500 @@ -0,0 +1,109 @@ +<tool id="deseq2_normalization" name="DESeq2 normalization" version="1.0.0"> + <description>of hit lists (geometric method)</description> + <requirements> + <requirement type="package" version="1.8.2gx=r3.2.1_0">bioconductor-deseq2</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Tool exception" /> + </stdio> + <command detect_errors="exit_code"><![CDATA[ Rscript $normalizationDESeq ]]></command> + <configfiles> + <configfile name="normalizationDESeq"> + ## Setup R error handling to go to stderr + options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + suppressMessages(require(DESeq2)) + countsTable = read.delim("${input}", header=TRUE, check.names=FALSE) + rownames( countsTable )= countsTable[,1] + countsTable= countsTable[ , -1 ] + conds = factor(c(rep ("C", length(countsTable[1,])-1 ), "T")) + cds = DESeqDataSetFromMatrix(countsTable, DataFrame(conds), ~ conds) + cds = estimateSizeFactors( cds ) + write.table (as.data.frame(sizeFactors(cds)), file="${output_factors}", row.names=TRUE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n") + norm_table = as.data.frame(counts( cds, normalized=TRUE )) + norm_table = cbind(rownames(norm_table), norm_table) + colnames(norm_table) = c("gene", colnames(countsTable) ) + write.table (norm_table, file="${norm_hit_table}", row.names=FALSE, col.names=TRUE, quote= FALSE, dec = ".", sep = "\t", eol = "\n") + </configfile> + </configfiles> + <inputs> + <param name="input" type="data" format="tabular" label="Hit lists of items"/> + </inputs> + <outputs> + <data name="output_factors" format="tabular" label="Normalization Factors (Geometric mean method)" /> + <data name="norm_hit_table" format="tabular" label="Normalized Hit Table (Geometric mean method)" /> + </outputs> + <tests> + <test> + <param name="input" value="counts.tab" ftype="tabular"/> + <output name="output_factors" file="norm_factors.tab" ftype="tabular"/> + <output name="norm_hit_table" file="norm_table.tab" ftype="tabular"/> + </test> + </tests> + <help> + +**What it does** + +DESeq2_normalization takes a tabular table of raw read counts (integers), each column corresponding to a sample count, +and returns (1) the DESeq2 Size Factors (geometic mean method) and (2) a normalized table (floatting number) +of counts. + +**Inputs** + +The following table gives an example of the tabular input that has to be provided to the tool: + +<![CDATA[ + +Geneid Oocyte 1 Oocyte 2 Pronuclei 1 pronuclei 2 + +NM_001195025 0 0 0 0 + +NM_028778 0 0 0 0 + +NM_001290393 0 0 0 0 + +NM_008922 3133 2276 2288 2659 + +NM_175370 4 22 7 16 + +NM_001290390 0 0 0 0 + +NM_175642 977 1711 1013 459 + +NM_001290392 0 0 0 0 + +NM_027671 0 0 0 0 + +NM_178884 0 0 0 2 + +NM_199021 332 413 1436 836 + +NM_198680 0 0 0 0 + +NM_011465 0 4 0 0 + +NM_130890 0 0 0 0 + +NM_001113393 0 0 0 0 + +NM_001113392 0 0 0 0 + +NM_001113391 19 3 88 15 + +NM_031162 0 0 0 0 + +NR_103716 0 0 0 0 + +NM_001160371 0 0 0 0 + +NM_177834 1 3 2 0 + +NM_145381 606 445 367 306 + +]]> + + + </help> + <citations> + <citation type="doi">10.1186/s13059-014-0550-8</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/counts.tab Mon Jan 08 04:21:24 2018 -0500 @@ -0,0 +1,500 @@ +Geneid 2: Oocyte 1: accepted_hits 3: Oocyte 2: accepted_hits 4: Pronuclei 1: accepted_hits 5: pronuclei 2: accepted_hits 6: Pronuclei 3: accepted_hits +NM_001195025 0 0 0 0 0 +NM_028778 0 0 0 0 0 +NM_001290393 0 0 0 0 0 +NM_008922 3133 2276 2288 2659 820 +NM_175370 4 22 7 16 9 +NM_001290390 0 0 0 0 0 +NM_175642 977 1711 1013 459 430 +NM_001290392 0 0 0 0 0 +NM_027671 0 0 0 0 0 +NM_178884 0 0 0 2 3 +NM_199021 332 413 1436 836 1018 +NM_198680 0 0 0 0 0 +NM_011465 0 4 0 0 0 +NM_130890 0 0 0 0 0 +NM_001113393 0 0 0 0 0 +NM_001113392 0 0 0 0 0 +NM_001113391 19 3 88 15 31 +NM_031162 0 0 0 0 0 +NR_103716 0 0 0 0 0 +NM_001160371 0 0 0 0 0 +NM_177834 1 3 2 0 1 +NM_145381 606 445 367 306 259 +NM_177173 0 0 0 0 0 +NM_001160369 0 0 0 0 0 +NM_001160370 2 21 9 8 25 +NM_001289497 0 0 0 0 0 +NM_027974 0 0 6 7 8 +NM_133235 74 23 0 2 29 +NM_028096 77 87 2 0 17 +NM_201365 1 0 0 0 0 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/norm_factors.tab Mon Jan 08 04:21:24 2018 -0500 @@ -0,0 +1,6 @@ +sizeFactors(cds) +2: Oocyte 1: accepted_hits 1.06133711644639 +3: Oocyte 2: accepted_hits 1.10788970615123 +4: Pronuclei 1: accepted_hits 1.1873071040134 +5: pronuclei 2: accepted_hits 0.901037373821142 +6: Pronuclei 3: accepted_hits 0.869190376687854
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/norm_table.tab Mon Jan 08 04:21:24 2018 -0500 @@ -0,0 +1,500 @@ +gene 2: Oocyte 1: accepted_hits 3: Oocyte 2: accepted_hits 4: Pronuclei 1: accepted_hits 5: pronuclei 2: accepted_hits 6: Pronuclei 3: accepted_hits +NM_001195025 0 0 0 0 0 +NM_028778 0 0 0 0 0 +NM_001290393 0 0 0 0 0 +NM_008922 2951.93671402921 2054.35612169983 1927.04986963017 2951.04296142972 943.406671303357 +NM_175370 3.7688307871423 19.8575723538648 5.89569453121117 17.7573100349287 10.3544634655247 +NM_001290390 0 0 0 0 0 +NM_175642 920.536919759507 1544.37755897557 853.191222873845 509.412831627018 494.713254463956 +NM_001290392 0 0 0 0 0 +NM_027671 0 0 0 0 0 +NM_178884 0 0 0 2.21966375436609 3.45148782184155 +NM_199021 312.812955332811 372.780790097552 1209.45962097418 927.819449325026 1171.2048675449 +NM_198680 0 0 0 0 0 +NM_011465 0 3.61046770070268 0 0 0 +NM_130890 0 0 0 0 0 +NM_001113393 0 0 0 0 0 +NM_001113392 0 0 0 0 0 +NM_001113391 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Jan 08 04:21:24 2018 -0500 @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="R" version="3.1.2"> + <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="biocbasics" version="2.14"> + <repository changeset_revision="f0ef1a7b157e" name="package_biocbasics_2_14" owner="mvdbeek" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>