--- a/deseq2.R	Thu Apr 12 17:29:45 2018 -0400
+++ b/deseq2.R	Sat May 19 03:55:48 2018 -0400
@@ -8,14 +8,14 @@
 #   'factors' a JSON list object from Galaxy
 #
 # the output file has columns:
-# 
+#
 #   baseMean (mean normalized count)
 #   log2FoldChange (by default a moderated LFC estimate)
 #   lfcSE (the standard error)
 #   stat (the Wald statistic)
 #   pvalue (p-value from comparison of Wald statistic to a standard Normal)
 #   padj (adjusted p-value, Benjamini Hochberg correction on genes which pass the mean count filter)
-# 
+#
 # the first variable in 'factors' will be the primary factor.
 # the levels of the primary factor are used in the order of appearance in factors.
 #
@@ -48,6 +48,7 @@
   "help", "h", 0, "logical",
   "outfile", "o", 1, "character",
   "countsfile", "n", 1, "character",
+  "header", "H", 0, "logical",
   "factors", "f", 1, "character",
   "files_to_labels", "l", 1, "character",
   "plots" , "p", 1, "character",
@@ -86,6 +87,12 @@
   FALSE
 }
 
+if (!is.null(opt$header)) {
+  hasHeader <- TRUE
+} else {
+  hasHeader <- FALSE
+}
+
 if (!is.null(opt$tximport)) {
   if (is.null(opt$tx2gene)) stop("A transcript-to-gene map or a GTF file is required for tximport")
   if (tolower(file_ext(opt$tx2gene)) == "gtf") {
@@ -138,15 +145,6 @@
 primaryFactor <- factors[1]
 designFormula <- as.formula(paste("~", paste(rev(factors), collapse=" + ")))
 
-if (verbose) {
-  cat("DESeq2 run information\n\n")
-  cat("sample table:\n")
-  print(sampleTable[,-c(1:2),drop=FALSE])
-  cat("\ndesign formula:\n")
-  print(designFormula)
-  cat("\n\n")
-}
-
 # these are plots which are made once for each analysis
 generateGenericPlots <- function(dds, factors) {
   library("ggplot2")
@@ -202,13 +200,29 @@
 # For JSON input from Galaxy, path is absolute
 dir <- ""
 
-if (!useTXI) {
+if (!useTXI & hasHeader) {
+    countfiles <- lapply(as.character(sampleTable$filename), function(x){read.delim(x, row.names=1)})
+    tbl <- do.call("cbind", countfiles)
+    rownames(sampleTable) <- colnames(tbl) # take sample ids from header
+
+    # check for htseq report lines (from DESeqDataSetFromHTSeqCount function)
+    oldSpecialNames <- c("no_feature", "ambiguous", "too_low_aQual",
+        "not_aligned", "alignment_not_unique")
+    specialRows <- (substr(rownames(tbl), 1, 1) == "_") | rownames(tbl) %in% oldSpecialNames
+    tbl <- tbl[!specialRows, , drop = FALSE]
+
+    dds <- DESeqDataSetFromMatrix(countData = tbl,
+                                  colData = sampleTable[,-c(1:2), drop=FALSE],
+                                  design = designFormula)
+} else if (!useTXI & !hasHeader) {
+
   # construct the object from HTSeq files
   dds <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable,
                                     directory = dir,
                                     design =  designFormula)
   labs <- unname(unlist(filenames_to_labels[colnames(dds)]))
   colnames(dds) <- labs
+
 } else {
     # construct the object using tximport
     # first need to make the tx2gene table
@@ -232,7 +246,16 @@
                                     designFormula)
 }
 
-if (verbose) cat(paste(ncol(dds), "samples with counts over", nrow(dds), "genes\n"))
+if (verbose) {
+  cat("DESeq2 run information\n\n")
+  cat("sample table:\n")
+  print(sampleTable[,-c(1:2),drop=FALSE])
+  cat("\ndesign formula:\n")
+  print(designFormula)
+  cat("\n\n")
+  cat(paste(ncol(dds), "samples with counts over", nrow(dds), "genes\n"))
+}
+
 # optional outlier behavior
 if (is.null(opt$outlier_replace_off)) {
   minRep <- 7
@@ -242,7 +265,7 @@
 }
 if (is.null(opt$outlier_filter_off)) {
   cooksCutoff <- TRUE
-} else {  
+} else {
   cooksCutoff <- FALSE
   if (verbose) cat("outlier filtering off\n")
 }

--- a/deseq2.xml	Thu Apr 12 17:29:45 2018 -0400
+++ b/deseq2.xml	Sat May 19 03:55:48 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="deseq2" name="DESeq2" version="2.11.40.1">
+<tool id="deseq2" name="DESeq2" version="2.11.40.2">
     <description>Determines differentially expressed features from count tables</description>
     <requirements>
         <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement>
@@ -58,6 +58,9 @@
         $temp_factor.reverse()
         $temp_factor_names.append([str($factor.factorName), $temp_factor])
     #end for
+
+    $header
+
     -f '#echo json.dumps(temp_factor_names)#'
     -l '#echo json.dumps(filename_to_element_identifiers)#'
     -t $fit_type
@@ -103,6 +106,8 @@
             </repeat>
         </repeat>
 
+        <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" />
+
         <conditional name="tximport">
             <param name="tximport_selector" type="select" label="Choice of Input data">
                 <option value="count" selected="True">Count data (e.g. from HTSeq-count, featureCounts or StringTie)</option>
@@ -174,7 +179,7 @@
         </data>
     </outputs>
     <tests>
-        <!--Ensure tables output works-->
+        <!--Ensure counts files with header works -->
         <test expect_num_outputs="2">
             <repeat name="rep_factorName">
                 <param name="factorName" value="Treatment"/>
@@ -189,8 +194,45 @@
             </repeat>
             <param name="pdf" value="False"/>
             <param name="normCounts" value="True"/>
-            <output name="counts_out" file="normalized_readcounts.tab"/>
-            <output name="deseq_out" file="deseq2_out.tab"/>
+            <output name="counts_out">
+                <assert_contents>
+                    <has_text_matching expression="untreat1\tuntreat2\tuntreat3\tuntreat4\ttreat1\ttreat2\ttreat3" />
+                    <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
+                </assert_contents>
+            </output>
+            <output name="deseq_out" >
+                <assert_contents>
+                    <has_text_matching expression="FBgn0003360\t1933.9504.*\t-2.8399.*\t0.1309.*-21.6851.*2.831.*8.024" />
+                </assert_contents>
+            </output>
+        </test>
+        <!--Ensure counts files without header works -->
+        <test expect_num_outputs="2">
+            <repeat name="rep_factorName">
+                <param name="factorName" value="Treatment"/>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" value="Treated"/>
+                    <param name="countsFile" value="GSM461179_treat_single.counts.noheader,GSM461180_treat_paired.counts.noheader,GSM461181_treat_paired.counts.noheader"/>
+                </repeat>
+                <repeat name="rep_factorLevel">
+                    <param name="factorLevel" value="Untreated"/>
+                    <param name="countsFile" value="GSM461176_untreat_single.counts.noheader,GSM461177_untreat_paired.counts.noheader,GSM461178_untreat_paired.counts.noheader,GSM461182_untreat_single.counts.noheader"/>
+                </repeat>
+            </repeat>
+            <param name="header" value="False"/>
+            <param name="pdf" value="False"/>
+            <param name="normCounts" value="True"/>
+            <output name="counts_out">
+                <assert_contents>
+                    <has_text_matching expression="GSM461176_untreat_single.counts.noheader\tGSM461177_untreat_paired.counts.noheader\tGSM461178_untreat_paired.counts.noheader\tGSM461182_untreat_single.counts.noheader\tGSM461179_treat_single.counts.noheader\tGSM461180_treat_paired.counts.noheader\tGSM461181_treat_paired.counts.noheader" />
+                    <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
+                </assert_contents>
+            </output>
+            <output name="deseq_out" >
+                <assert_contents>
+                    <has_text_matching expression="FBgn0003360\t1933.9504.*\t-2.8399.*\t0.1309.*-21.6851.*2.831.*8.024" />
+                </assert_contents>
+            </output>
         </test>
         <!--Ensure Sailfish/Salmon input with tx2gene table works-->
         <test expect_num_outputs="1">
@@ -210,8 +252,12 @@
             <param name="txtype" value="sailfish"/>
             <param name="mapping_format_selector" value="tabular"/>
             <param name="tabular_file" value="tx2gene.tab"/>
-            <output name="deseq_out" file="sailfish/out_deseq2_sailfish.tab"/>
-        </test>               
+            <output name="deseq_out" >
+                <assert_contents>
+                    <has_text_matching expression="MIR6859-2\t1.1858.*\t-1.5832.*\t1.2956.*\t-1.2219.*\t0.2217.*\t0.8868.*" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 .. class:: infomark
@@ -226,7 +272,7 @@
 
 **Count Files**
 
-DESeq2_ takes count tables generated from **featureCounts**, **HTSeq-count** or **StringTie** as input. Count tables must be generated for each sample individually, should have no header rows, and rows should be in the same order. DESeq2 is capable of handling multiple factors that affect your experiment. The first factor you input is considered as the primary factor that affects gene expressions. Optionally, you can input one or more 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.
+DESeq2_ takes count tables generated from **featureCounts**, **HTSeq-count** or **StringTie** as input. Count tables must be generated for each sample individually. One header row is assumed, but files with no header (e.g from HTSeq) can be input with the *Files have header?* option set to No. DESeq2 is capable of handling multiple factors that affect your experiment. The first factor you input is considered as the primary factor that affects gene expressions. Optionally, you can input one or more 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:
 
@@ -246,7 +292,7 @@
 
 *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.
 
-DESeq2_ can also take transcript-level counts from quantification tools such as, **kallisto**, **Salmon** and **Sailfish**, and this Galaxy wrapper incorporates the Bioconductor tximport_ package to process the transcript counts for DESeq2. 
+DESeq2_ can also take transcript-level counts from quantification tools such as, **kallisto**, **Salmon** and **Sailfish**, and this Galaxy wrapper incorporates the Bioconductor tximport_ package to process the transcript counts for DESeq2.
 
 **Salmon or Sailfish Files**
 
@@ -275,17 +321,17 @@
 Example:
 
 ============ ========== =============== =========== ===========
-target_id    length     eff_length      est_counts  tpm 
+target_id    length     eff_length      est_counts  tpm
 ------------ ---------- --------------- ----------- -----------
-NR_001526    164        20.4518         0           0          
-NR_001526_1  164        20.4518         0           0          
-NR_001526_2  164        20.4518         0           0          
-NM_130786    1764       1956.04         109.165     2.47415    
-NR_015380    2129       2139.53         85.5821     1.77331    
+NR_001526    164        20.4518         0           0
+NR_001526_1  164        20.4518         0           0
+NR_001526_2  164        20.4518         0           0
+NM_130786    1764       1956.04         109.165     2.47415
+NR_015380    2129       2139.53         85.5821     1.77331
 NM_001198818 9360       7796.58         4.19648e-05 2.38616e-07
-NM_001198819 9527       7964.62         0           0          
-NM_001198820 9410       7855.78         0           0          
-NM_014576    9267       7714.88         8.37255     0.0481114  
+NM_001198819 9527       7964.62         0           0
+NM_001198820 9410       7855.78         0           0
+NM_014576    9267       7714.88         8.37255     0.0481114
 ============ ========== =============== =========== ===========
 
 -----

--- a/test-data/GSM461176_untreat_single.counts	Thu Apr 12 17:29:45 2018 -0400
+++ b/test-data/GSM461176_untreat_single.counts	Sat May 19 03:55:48 2018 -0400
@@ -1,3 +1,4 @@
+GeneID	untreat1
 FBgn0000003	0
 FBgn0000008	15
 FBgn0000014	0

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GSM461176_untreat_single.counts.noheader	Sat May 19 03:55:48 2018 -0400
@@ -0,0 +1,4004 @@
+FBgn0000003	0
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