diff dexseq.xml @ 19:b7235a9b1881 draft

Uploaded

--- a/dexseq.xml	Tue Sep 01 11:08:29 2015 -0400
+++ b/dexseq.xml	Thu Sep 03 05:25:49 2015 -0400
@@ -2,14 +2,14 @@
     <description>Determines differential exon usage from count tables</description>
     <requirements>
         <requirement type="package" version="3.2.0">R</requirement>
-        <requirement type="binary">Rscript</requirement>
+        <requirement type="package" version="4.0.3">tiff</requirement>
         <requirement type="package" version="1.14.2">DEXSeq</requirement>
     </requirements>
     <code file="dexseq_helper.py" />
     <command>
+    mkdir ./html_out ;
         #import json
-        Rscript /usr/local/galaxy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/pavanvidem/dexseq/cbd118202fd1/dexseq/dexseq.R
-            #set $reportdir = str($dexseq_out).replace('.dat','_files')
+        Rscript $__tool_directory__/dexseq.R
             -o "$dexseq_out"
             -p 12
             #set $temp_factor_names = list()
@@ -27,12 +27,12 @@
             -f '#echo json.dumps(temp_factor_names)#'
             -a $gtf
             #if $report:
-                -x "$htmlreport"
-                -r "$reportdir"
+                -r ./html_out
             #end if
             -c $fdr_cutoff;
-            
-##            cp #echo os.path.join($reportdir, 'testForDEU.html')# $htmlreport;
+        mkdir $htmlreport.extra_files_path;
+        cp ./html_out/testForDEU.html $htmlreport ;
+        cp -r ./html_out/* $htmlreport.extra_files_path ;
     </command>
     <stdio>
         <regex match="Execution halted" 
@@ -91,52 +91,54 @@
 
 **Inputs**
 
-DESeq2_ takes count tables that generated from the htseq-count as input. Count tables must be generated for each sample individually. DESeq2 is capable of handling multiple factors that effect your experiment. The first factor you input is considered as the primary factor that affects gene expressions. You also input several secondary factors that might influence your experiment. But the final output will be changes in genes due to primary factor in presence of secondary factors. Each factor has two levels/states. You need to select appropriate count table from your history for each factor level.
+DEXSeq_ takes count tables that generated from the dexseq_count as input. Count tables must be generated for each sample individually. DEXSeq is capable of handling multiple factors that effect your experiment. The first factor you input is considered as the primary factor that affects gene expressions. Primary factor should always be named as 'condition'. You also input several secondary factors that might influence your experiment. But the final output will be changes in genes due to primary factor in presence of secondary factors. Each factor has two levels/states. You need to select appropriate count table from your history for each factor level.
 
 The following table gives some examples of factors and their levels:
 
 ========= ============== ===============
 Factor    Factor level 1 Factor level 2 
 --------- -------------- ---------------
-Treatment Treated        Untreated
+condition Knockdown      Wildtype
 --------- -------------- ---------------
-Condition Knockdown      Wildtype
+treatment Treated        Untreated
 --------- -------------- ---------------
-TimePoint Day4           Day1
+timePoint Day4           Day1
 --------- -------------- ---------------
 SeqType   SingleEnd      PairedEnd
 --------- -------------- ---------------
 Gender    Female         Male
 ========= ============== ===============
 
-*Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level2. Here the order of factor levels is important. For example, for the factor 'Treatment' given in above table, DESeq2 computes fold changes of 'Treated' samples against 'Untreated', i.e. the values correspond to up or down regulations of genes in Treated samples.
+*Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level2. Here the order of factor levels is important. For example, for the factor 'condition' given in above table, DEXSeq computes fold changes of 'Knockdown' samples against 'Wildtype', i.e. the values correspond to up or down regulations of genes in Knockdown samples.
 
 **Output**
 
-DESeq2_ generates a tabular file containing the different columns and optional visualized results as PDF.
+DEXSeq_ generates a tabular file containing the different columns and an optional html report.
 
 ====== ==========================================================
 Column Description
 ------ ----------------------------------------------------------
-     1 Gene Identifiers
-     2 mean normalised counts, averaged over all samples from both conditions
-     3 the logarithm (to basis 2) of the fold change (See the note in inputs section)
-     4 standard error estimate for the log2 fold change estimate
-     5 Wald statistic
-     6 p value for the statistical significance of this change
-     7 p value adjusted for multiple testing with the Benjamini-Hochberg procedure
-       which controls false discovery rate (FDR)
+     1 Gene and exon Identifiers
+     2 group/gene identifier
+     3 feature/exon identifier
+     4 mean of the counts across samples in each feature/exon
+     5 exon dispersion estimate
+     6 LRT statistic
+     7 LRT p-value
+     8 BH adjusted p-values
+     9 exon usage coefficient factorLevel 2
+    10 exon usage coefficient factorLevel 1
+    11 relative exon usage fold changes
+    12 GRanges object of the coordinates of the exon/feature
+    13 matrix of integer counts, of each column containing a sample
+    14 list of transcripts overlapping with the exon
 ====== ==========================================================
 
 
-
-
-
-.. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html
-
+.. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html
 
     </help>
     <citations>
-        <citation type="doi">10.1101/002832</citation>
+        <citation type="doi">10.1101/gr.133744.111</citation>
     </citations>
 </tool>