changeset 22:71cb8c5ae8bd draft

Uploaded

--- a/dexseq.R	Thu Sep 03 11:26:08 2015 -0400
+++ b/dexseq.R	Tue Sep 22 11:24:46 2015 -0400
@@ -85,22 +85,28 @@
 
 colData(dxd)
 dxd <- estimateSizeFactors(dxd)
+print("Estimated size factors")
 sizeFactors(dxd)
 BPPARAM=MulticoreParam(workers=opt$threads)
 dxd <- estimateDispersions(dxd, formula=formulaFullModel, BPPARAM=BPPARAM)
-dxd <- testForDEU(dxd, reducedModel=formulaReducedModel, fullModel=formulaFullModel, BPPARAM=BPPARAM)
+print("Estimated dispersions")
+dxd <- testForDEU(dxd, fullModel=formulaFullModel, BPPARAM=BPPARAM)
+print("tested for DEU")
 dxd <- estimateExonFoldChanges(dxd, fitExpToVar=primaryFactor, BPPARAM=BPPARAM)
+print("Estimated fold changes")
 res <- DEXSeqResults(dxd)
+print("Results")
 table(res$padj <= opt$fdr)
 resSorted <- res[order(res$padj),]
 head(resSorted)
 
 write.table(as.data.frame(resSorted), file = opt$outfile, sep="\t", quote = FALSE, col.names = FALSE)
+print("Written Results")
 
 if ( !is.null(opt$reportdir) ) {
     save(dxd, resSorted, file = file.path(opt$reportdir,"DEXSeq_analysis.RData"))
     save.image()
-    DEXSeqHTML(res, path=opt$reportdir, FDR=opt$fdr, color=c("#C3EEE7","#B7FEA0","#F1E7A1","#CEAEFF","#FF8F43","#EDC3C5","#AAA8AA","#FF0000","#637EE9","#FBFBFB"))
+    DEXSeqHTML(res, path=opt$reportdir, FDR=opt$fdr, color=c("#B7FEA0", "#FF8F43", "#637EE9", "#FF0000", "#F1E7A1", "#C3EEE7","#CEAEFF", "#EDC3C5", "#AAA8AA"))
     unlink(file.path(opt$reportdir,"DEXSeq_analysis.RData"))
 }
 sessionInfo()

--- a/dexseq.xml	Thu Sep 03 11:26:08 2015 -0400
+++ b/dexseq.xml	Tue Sep 22 11:24:46 2015 -0400
@@ -11,7 +11,7 @@
         #import json
         Rscript $__tool_directory__/dexseq.R
             -o "$dexseq_out"
-            -p 12
+            -p 6
             #set $temp_factor_names = list()
             #for $factor in $rep_factorName:
                 #set $temp_factor = list()
@@ -49,7 +49,7 @@
            description="An undefined error occured, please check your intput carefully and contact your administrator." />
     </stdio>
     <inputs>
-        <param name="gtf" type="data" label="GTF file created from dexseq_count tool"/>
+        <param name="gtf" type="data" label="GTF file created from DEXSeq-Count tool"/>
         <repeat name="rep_factorName" title="Factor" min="1">
             <param name="factorName" type="text" value="FactorName" label="Specify a factor name" 
                 help="Only letters, numbers and underscores will be retained in this field">
@@ -79,7 +79,78 @@
             <filter>report == True</filter>
         </data>
     </outputs>
+    
     <code file="dexseq_helper.py" />
+    <tests>
+        <test>
+            <param name="gtf" value="flattened.filtered.gtf" ftype="bed"/>
+            <repeat name="rep_factorName">
+                <param name="factorName" value="condition" ftype="bed"/>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" type="text" value="knockdown"/>
+                    <param name="countsFile" ftype="tabular" value="treated1fb.txt"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" type="text" value="knockdown"/>
+                    <param name="countsFile" ftype="tabular" value="treated2fb.txt"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" type="text" value="knockdown"/>
+                    <param name="countsFile" ftype="tabular" value="treated3fb.txt"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" type="text" value="control"/>
+                    <param name="countsFile" ftype="tabular" value="untreated1fb.txt"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" type="text" value="control"/>
+                    <param name="countsFile" ftype="tabular" value="untreated2fb.txt"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" type="text" value="control"/>
+                    <param name="countsFile" ftype="tabular" value="untreated2fb.txt"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" type="text" value="control"/>
+                    <param name="countsFile" ftype="tabular" value="untreated3fb.txt"/>
+                </repeat>
+            </repeat>
+            <repeat name="rep_factorName">
+                <param name="factorName" value="libtype" ftype="bed"/>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" type="text" value="singleend"/>
+                    <param name="countsFile" ftype="tabular" value="treated1fb.txt"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" type="text" value="singleend"/>
+                    <param name="countsFile" ftype="tabular" value="untreated1fb.txt"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" type="text" value="singleend"/>
+                    <param name="countsFile" ftype="tabular" value="untreated2fb.txt"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" type="text" value="pairedend"/>
+                    <param name="countsFile" ftype="tabular" value="treated2fb.txt"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" type="text" value="pairedend"/>
+                    <param name="countsFile" ftype="tabular" value="treated3fb.txt"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" type="text" value="pairedend"/>
+                    <param name="countsFile" ftype="tabular" value="untreated3fb.txt"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" type="text" value="pairedend"/>
+                    <param name="countsFile" ftype="tabular" value="untreated4fb.txt"/>
+                </repeat>
+            </repeat>
+            <param name="report" type="boolean" value="False"/>
+            <param name="fdr_cutoff" value="0.05"/>
+            <output name="dexseq_out" file="DEXSeq_result_file.tabular" ftype="tabular"/>
+        </test>
+    </tests>
     <help>
 
 .. class:: infomark

--- a/dexseq_count.xml	Thu Sep 03 11:26:08 2015 -0400
+++ b/dexseq_count.xml	Tue Sep 22 11:24:46 2015 -0400
@@ -2,15 +2,25 @@
     <description>Prepare and count exon abundancies from RNA-seq data</description>
     <requirements>
         <requirement type="package" version="3.1.0">R</requirement>
-        <requirement type="package" version="1.14.2">DEXSeq</requirement> 
+        <requirement type="package" version="1.14.2">DEXSeq</requirement>
+        <requirement type="package">htseq</requirement>
+        <requirement type="package">pysam</requirement>
     </requirements>
-    <command interpreter="python">
+    <command>
         #if $mode.mode_select == "prepare":
-            dexseq_prepare_annotation.py -r $aggregate $gtffile $flattened_gtf_out
+            python \$DEXSEQ_ROOT/python_scripts/dexseq_prepare_annotation.py -r $mode.aggregate $mode.gtffile $flattened_gtf_out
         #elif $mode.mode_select == "count":
-            dexseq_count.py -f bam -p $paired -r $order -s $stranded $flattened_gtf_in $bamfile $counts_file
+            python \$DEXSEQ_ROOT/python_scripts/dexseq_count.py -f bam -p $mode.paired -s $mode.stranded -a $mode.qual -r $mode.order $mode.flattened_gtf_in $mode.bamfile $counts_file
         #end if
     </command>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+        <!-- In case the return code has not been set propery check stderr too -->
+        <regex match="Error:" />
+        <regex match="Exception:" />
+    </stdio>
     <inputs>
         <conditional name="mode">
             <param name="mode_select" type="select" label="Mode of operation">

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test_data/DEXSeq_result_file.tabular	Tue Sep 22 11:24:46 2015 -0400
@@ -0,0 +1,307 @@
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+FBgn0000120:E003	FBgn0000120	E003	0	NA	NA	NA	NA	NA	NA	NA	2L	18079957	18080086	130	+	0	0	0	0	0	0	0	c("FBtr0307350", "FBtr0081030")
+FBgn0000120:E004	FBgn0000120	E004	0	NA	NA	NA	NA	NA	NA	NA	2L	18080147	18080415	269	+	0	0	0	0	0	0	0	c("FBtr0307350", "FBtr0081030")
+FBgn0000137:E001	FBgn0000137	E001	0	NA	NA	NA	NA	NA	NA	NA	X	354533	357209	2677	+	0	0	0	0	0	0	0	FBtr0070075

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test_data/flattened.filtered.gtf	Tue Sep 22 11:24:46 2015 -0400
@@ -0,0 +1,397 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test_data/treated2fb.txt	Tue Sep 22 11:24:46 2015 -0400
@@ -0,0 +1,307 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test_data/treated3fb.txt	Tue Sep 22 11:24:46 2015 -0400
@@ -0,0 +1,307 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test_data/untreated1fb.txt	Tue Sep 22 11:24:46 2015 -0400
@@ -0,0 +1,307 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test_data/untreated2fb.txt	Tue Sep 22 11:24:46 2015 -0400
@@ -0,0 +1,307 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test_data/untreated3fb.txt	Tue Sep 22 11:24:46 2015 -0400
@@ -0,0 +1,307 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test_data/untreated4fb.txt	Tue Sep 22 11:24:46 2015 -0400
@@ -0,0 +1,307 @@
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--- a/tool_dependencies.xml	Thu Sep 03 11:26:08 2015 -0400
+++ b/tool_dependencies.xml	Tue Sep 22 11:24:46 2015 -0400
@@ -81,7 +81,7 @@
                     <package>https://github.com/bgruening/download_store/raw/master/DEXSeq_1.14.2/DEXSeq_1.14.2.tar.gz</package>
                 </action>
                 <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/DEXSeq/python_scripts/</environment_variable>
+                    <environment_variable action="set_to" name="DEXSEQ_ROOT">$INSTALL_DIR/DEXSeq/</environment_variable>
                 </action>
             </actions>
         </install>