Mercurial > repos > mingchen0919 > aurora_deseq2

changeset 18:81dd7b8c8118 draft

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planemo upload commit c3ae92f8087d0c69a7b9dd447d6060090a784bb1-dirty
author mingchen0919
date Thu, 13 Sep 2018 11:01:36 -0400
parents 508f582a1f1d
children af52576472bc
files command-line-arguments.csv rmarkdown_report.Rmd rmarkdown_report.xml
diffstat 3 files changed, 8 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/command-line-arguments.csv	Sat Jun 09 22:58:53 2018 -0400
+++ b/command-line-arguments.csv	Thu Sep 13 11:01:36 2018 -0400
@@ -7,7 +7,6 @@
 D,1,character,treatment_name
 E,1,character,treated
 F,1,character,untreated
-G,1,character,test_type
 H,1,character,fit_type
 I,1,character,alpha
 J,1,character,significant_genes
--- a/rmarkdown_report.Rmd	Sat Jun 09 22:58:53 2018 -0400
+++ b/rmarkdown_report.Rmd	Thu Sep 13 11:01:36 2018 -0400
@@ -66,6 +66,11 @@
 dds = DESeqDataSetFromMatrix(countData = count_data,
                              colData = coldata,
                              design = formula(opt$X_C))
+
+# prefiltering
+keep <- rowSums(counts(dds)) >= 10
+dds <- dds[keep,]
+
 dds = DESeq(dds, test = opt$X_G, fitType = opt$X_H)
 ## Differential expression test results
 res = results(dds, contrast = c(opt$X_D, opt$X_E, opt$X_F), alpha = opt$X_I)
--- a/rmarkdown_report.xml	Sat Jun 09 22:58:53 2018 -0400
+++ b/rmarkdown_report.xml	Thu Sep 13 11:01:36 2018 -0400
@@ -1,4 +1,4 @@
-<tool name="aurora_deseq2" id='aurora_deseq2_report' version="2.2.1">
+<tool name="aurora_deseq2" id='aurora_deseq2_report' version="2.2.2">
     <description>
         Differential analysis of count data with the DESeq2 package
     </description>
@@ -6,7 +6,7 @@
         <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
         <requirement type="package" version="1.20.0">r-getopt</requirement>
         <requirement type="package" version="1.6">r-rmarkdown</requirement>
-        <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
+        <requirement type="package" version="v1.18.1">bioconductor-deseq2</requirement>
         <requirement type="package" version="4.5.6">r-plotly</requirement>
         <requirement type="package" version="2.2.1">r-ggplot2</requirement>
         <requirement type="package" version="1.0.8">r-pheatmap</requirement>
@@ -38,7 +38,6 @@
             -D '$treatment_name'
             -E '$treated'
             -F '$untreated'
-            -G '$test_type'
             -H '$fit_type'
             -I '$alpha'
             -J '$significant_genes'
@@ -70,10 +69,6 @@
         <param type="text" name="untreated" label="Untreated"
                help="A level from the specified treatment column that will be used as the untreated group in the DESeq2 analysis."
                optional="False"/>
-        <param type="select" name="test_type" label="Test type" optional="False">
-            <option value="Wald" selected="true">Wald</option>
-            <option value="LRT" selected="false">Likelihood Ratio Test (LRT)</option>
-        </param>
         <param type="select" name="fit_type" label="Fitting of dispersions"
                help="either &quot;parametric&quot;, &quot;local&quot;, or &quot;mean&quot; for the type of fitting of dispersions to the mean intensity"
                optional="False">
@@ -86,7 +81,7 @@
                optional="False" value="0.1" min="0" max="1"/>
     </inputs>
     <outputs>
-        <data format="html" name="report" label="${tool.name} on ${on_string}"/>
+        <data format="html" name="report" label="${tool.name} report on ${on_string}"/>
         <data name="significant_genes" format="tabular" label="${tool.name} signficant genes on ${on_string} "
               hidden="false"/>
     </outputs>