# HG changeset patch
# User artbio
# Date 1507561629 14400
# Node ID a3be3601bcb3fdf2c1b3e913f89832a4b69f645d
# Parent  12c14642e6ac8db494db906cfd60b4543cae1a60
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d

diff -r 12c14642e6ac -r a3be3601bcb3 small_rna_maps.r
--- a/small_rna_maps.r	Sun Oct 08 17:56:13 2017 -0400
+++ b/small_rna_maps.r	Mon Oct 09 11:07:09 2017 -0400
@@ -12,6 +12,7 @@
 option_list <- list(
     make_option(c("-f", "--first_dataframe"), type="character", help="path to first dataframe"),
     make_option(c("-e", "--extra_dataframe"), type="character", help="path to additional dataframe"),
+    make_option(c("-n", "--normalization"), type="character", help="space-separated normalization/size factors"),
     make_option("--first_plot_method", type = "character", help="How additional data should be plotted"),
     make_option("--extra_plot_method", type = "character", help="How additional data should be plotted"),
     make_option("--output_pdf", type = "character", help="path to the pdf file with plots")
@@ -27,6 +28,21 @@
     Table <- within(Table, Counts[Polarity=="R"] <- (Counts[Polarity=="R"]*-1))
 }
 n_samples=length(unique(Table$Dataset))
+samples = unique(Table$Dataset)
+if (args$normalization != "") {
+    norm_factors = as.numeric(unlist(strsplit(args$normalization, " ")))
+} else {
+    norm_factors = rep(1, n_samples)
+}
+if (args$first_plot_method == "Counts" | args$first_plot_method == "Size" | args$first_plot_method == "Coverage") {
+    i = 1
+    for (sample in samples) {
+        print(norm_factors[i])
+        Table[, length(Table)][Table$Dataset==sample] <- Table[, length(Table)][Table$Dataset==sample]*norm_factors[i]
+        i = i + 1
+    }
+    print(tail(Table))
+}
 genes=unique(levels(Table$Chromosome))
 per_gene_readmap=lapply(genes, function(x) subset(Table, Chromosome==x))
 per_gene_limit=lapply(genes, function(x) c(1, unique(subset(Table, Chromosome==x)$Chrom_length)) )
@@ -36,9 +52,16 @@
     ExtraTable=read.delim(args$extra_dataframe, header=T, row.names=NULL)
     if (args$extra_plot_method == "Counts" | args$extra_plot_method=='Size') {
         ExtraTable <- within(ExtraTable, Counts[Polarity=="R"] <- (Counts[Polarity=="R"]*-1))
+    }
+    if (args$extra_plot_method == "Counts" | args$extra_plot_method == "Size" | args$extra_plot_method == "Coverage") {
+        i = 1
+        for (sample in samples) {
+            ExtraTable[, length(ExtraTable)][ExtraTable$Dataset==sample] <- ExtraTable[, length(ExtraTable)][ExtraTable$Dataset==sample]*norm_factors[i]
+            i = i + 1
         }
+    }
     per_gene_size=lapply(genes, function(x) subset(ExtraTable, Chromosome==x))
-    }
+}
 
 ## functions
 
diff -r 12c14642e6ac -r a3be3601bcb3 small_rna_maps.xml
--- a/small_rna_maps.xml	Sun Oct 08 17:56:13 2017 -0400
+++ b/small_rna_maps.xml	Mon Oct 09 11:07:09 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="small_rna_maps" name="small_rna_maps" version="2.0.0">
+<tool id="small_rna_maps" name="small_rna_maps" version="2.1.0">
   <description></description>
   <requirements>
         <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
@@ -33,6 +33,7 @@
       Rscript '$__tool_directory__'/small_rna_maps.r
           --first_dataframe '$output_tab' 
           --extra_dataframe '$extra_output_tab'
+          --normalization '$normalization'
           #if str($plots_options.plots_options_selector ) == "two_plot":
               --first_plot_method '${plots_options.first_plot}'
               --extra_plot_method '${plots_options.extra_plot}'
@@ -44,20 +45,22 @@
   ]]></command>
  <inputs>
     <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/>
+    <param name="normalization" type="text" label="Enter size/normalization factors as a space-separated list. Leave blank for no normalization (default)"
+           help="e.g. '1 0.75 1.23'. Values of the list map to the above selected files from bottom to top" />
     <conditional name="plots_options">
         <param name="plots_options_selector" type="select" label="Number of plots per chromosome">
             <option value="one_plot">Just one plot per chromosome</option>
             <option value="two_plot" selected="True">Two plots per chromosome</option>
         </param>
         <when value="two_plot">
-            <param name="first_plot" type="select" label="select the type of the first plot">
+            <param name="first_plot" type="select" label="Select the type of the first plot">
                 <option value="Counts">Counts</option> 
                 <option value="Coverage">Coverage</option> 
                 <option value="Mean">Mean Sizes</option> 
                 <option value="Median">Median Sizes</option>
                 <option value="Size">Size Distributions</option>
             </param>
-            <param name="extra_plot" type="select" label="select the type of the second plot">
+            <param name="extra_plot" type="select" label="Select the type of the second plot">
                 <option value="Counts">Counts</option> 
                 <option value="Coverage">Coverage</option> 
                 <option value="Mean">Mean Sizes</option> 
@@ -92,6 +95,7 @@
             <param name="plots_options_selector" value="two_plot" />
             <param name="first_plot" value="Counts" />
             <param name="extra_plot" value="Mean" />
+            <param name="normalization" value="1 1" />
             <output file="count.tab" name="output_tab" />
             <output file="mean.tab" name="extra_output_tab" />
             <output file="count-mean.pdf" name="output_pdf" />
@@ -101,6 +105,7 @@
             <param name="plots_options_selector" value="two_plot" />
             <param name="first_plot" value="Counts" />
             <param name="extra_plot" value="Mean" />
+            <param name="normalization" value="1 1" />
             <output file="doubled_count.tab" name="output_tab" />
             <output file="doubled_mean.tab" name="extra_output_tab" />
             <output file="doubled_count-mean.pdf" name="output_pdf" />
@@ -110,6 +115,7 @@
             <param name="plots_options_selector" value="two_plot" />
             <param name="first_plot" value="Counts" />
             <param name="extra_plot" value="Median" />
+            <param name="normalization" value="1 1" />
             <output file="count.tab" name="output_tab" />
             <output file="median.tab" name="extra_output_tab" />
             <output file="count-median.pdf" name="output_pdf" />
@@ -119,6 +125,7 @@
             <param name="plots_options_selector" value="two_plot" />
             <param name="first_plot" value="Counts" />
             <param name="extra_plot" value="Coverage" />
+            <param name="normalization" value="1 1" />
             <output file="count.tab" name="output_tab" />
             <output file="coverage.tab" name="extra_output_tab" />
             <output file="count-coverage.pdf" name="output_pdf" />
@@ -128,6 +135,7 @@
             <param name="plots_options_selector" value="two_plot" />
             <param name="first_plot" value="Counts" />
             <param name="extra_plot" value="Size" />
+            <param name="normalization" value="1 1" />
             <output file="count.tab" name="output_tab" />
             <output file="size.tab" name="extra_output_tab" />
             <output file="count-size.pdf" name="output_pdf" />
@@ -137,13 +145,25 @@
             <param name="plots_options_selector" value="two_plot" />
             <param name="first_plot" value="Size" />
             <param name="extra_plot" value="Counts" />
+            <param name="normalization" value="1 1" />
             <output file="size.tab" name="output_tab" />
             <output file="count.tab" name="extra_output_tab" />
             <output file="size-count.pdf" name="output_pdf" />
         </test>
         <test>
             <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
+            <param name="plots_options_selector" value="two_plot" />
+            <param name="first_plot" value="Size" />
+            <param name="extra_plot" value="Counts" />
+            <param name="normalization" value="1 0.75" />
+            <output file="size.tab" name="output_tab" />
+            <output file="count.tab" name="extra_output_tab" />
+            <output file="size-count_normed.pdf" name="output_pdf" />
+        </test>
+        <test>
+            <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
             <param name="plots_options_selector" value="one_plot" />
+            <param name="normalization" value="1 1" />
             <param name="first_plot" value="Counts" />
             <output file="count.tab" name="output_tab" />
             <output file="count.pdf" name="output_pdf" />
@@ -152,6 +172,7 @@
             <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
             <param name="plots_options_selector" value="one_plot" />
             <param name="first_plot" value="Size" />
+            <param name="normalization" value="1 1" />
             <output file="size.tab" name="output_tab" />
             <output file="size.pdf" name="output_pdf" />
         </test>
@@ -159,9 +180,18 @@
             <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
             <param name="plots_options_selector" value="one_plot" />
             <param name="first_plot" value="Coverage" />
+            <param name="normalization" value="1 1" />
             <output file="coverage.tab" name="output_tab" />
             <output file="coverage.pdf" name="output_pdf" />
         </test>
+        <test>
+            <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
+            <param name="plots_options_selector" value="one_plot" />
+            <param name="first_plot" value="Coverage" />
+            <param name="normalization" value="1 0.2" />
+            <output file="coverage.tab" name="output_tab" />
+            <output file="coverage_normed.pdf" name="output_pdf" />
+        </test>
     </tests>
 
 
@@ -169,9 +199,19 @@
 
 **What it does**
 
-Generate read count maps from alignment BAM files, using pysam and lattice.
+Plots maps of (1) read counts, (2) mean sizes, (3) median sizes, (4) coverage depth or (5)
+size read distribution along chromosome references.
+
+Mean sizes and median sizes are the mean and the median sizes, respectively, of all reads
+whose 5' end map to a given coordinate in a chromosome reference.
+Coverage depths are computed from the input bam alignment files using the python pysam module.
 
-In addition to the read counts (lower graphs), median size, mean size and coverage depth of reads(lower graphs) mapping at a given position are plotted.	
+The variables mentioned above (1-5) can be plotted either separately or in all possible
+pairwise combinations.
+
+For comparison purpose, values from bam alignment files can be normalized by a size factor
+before plotting. If the normalization field is leaved blank, default normalization of 1
+is assumed.
 
 **Inputs**
 
@@ -180,6 +220,9 @@
   - single-read
   - sorted
   - mapping to the same reference
+  
+Optionally, a space-separated list of normalization/size factors may be added before plotting.
+This list maps to the selected bam alignments from bottom to top.
 
 **Output**
 
diff -r 12c14642e6ac -r a3be3601bcb3 test-data/coverage_normed.pdf
Binary file test-data/coverage_normed.pdf has changed
diff -r 12c14642e6ac -r a3be3601bcb3 test-data/size-count_normed.pdf
Binary file test-data/size-count_normed.pdf has changed