# HG changeset patch
# User mvdbeek
# Date 1454435227 18000
# Node ID 44a0b0fa52a9e3c47231914b23c036b72ca693f4
# Parent  4e7f59d5ee18a293fbe285a57cebcc99d02414ac
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit e27d18d58ae095e7fad4b08b04370857a1d37964-dirty

diff -r 4e7f59d5ee18 -r 44a0b0fa52a9 readmap.xml
--- a/readmap.xml	Tue Feb 02 11:50:13 2016 -0500
+++ b/readmap.xml	Tue Feb 02 12:47:07 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.0.5">
+<tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.1.0">
   <description>from sRbowtie aligment</description>
   <requirements>
         <requirement type="package" version="0.12.7">bowtie</requirement>
@@ -77,145 +77,151 @@
                 <param name="maxquery" type="integer" size="3" value="28" label="Max size of query small RNAs" help="'28' = 28 nucleotides"/>
                 <param name="title" type="text" size="15" value= "Readmaps and size distributions" label="Main Titles"/>
                 <param name="xlabel" type="text" size="15" value="Coordinates/read size" label="x axis label"/>
-                <param name="yrange" type="integer" size="6" value="0" label="y axis range" help="leave at 0 for autoscaling"/>
+                <param name="yrange" type="integer" size="6" value="0" label="y axis range for readmap tool" help="leave at 0 for autoscaling"/>
                 <param name="ylabel" type="text" size="15" value="Number of reads" label="y axis label"/>
                 <param name="rows_per_page" type="text" size="9" value="8" label="How many items to display per page?">
 		  <validator type="in_range" min="6" max="20" message="Select between 6 and 20 rows, as the readability will suffer otherwise."/>
                 </param>
   </inputs>
    <configfiles>
-     <configfile name="plotCode">
+     <configfile name="plotCode"><![CDATA[
       ## Setup R error handling to go to stderr
-      options( show.error.messages=F,
-               error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
-      library(RColorBrewer)
-      library(lattice)
-      library(latticeExtra)
-      library(grid)
-      library(gridExtra)
-      
-      ## data frames implementation
+    options( show.error.messages=F,
+             error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+    library(RColorBrewer)
+    library(lattice)
+    library(latticeExtra)
+    library(grid)
+    library(gridExtra)
+
+    ## data frames implementation
 
-      rm=read.delim("${readmap_dataframe}", header=T, row.names=NULL)
-      n_samples=length(unique(rm\$sample))
-      genes=unique(levels(rm\$gene))
-      per_gene_readmap=lapply(genes, function(x) subset(rm, gene==x)) ####### ?
-      n_genes=length(per_gene_readmap)
-      
-      size=read.delim("${size_distribution_dataframe}", header=T, row.names=NULL)
-      per_gene_size=lapply(genes, function(x) subset(size, gene==x)) ###### ?
+    rm=read.delim("${readmap_dataframe}", header=T, row.names=NULL)
+    n_samples=length(unique(rm$sample))
+    genes=unique(levels(rm$gene))
+    per_gene_readmap=lapply(genes, function(x) subset(rm, gene==x)) ####### ?
+    n_genes=length(per_gene_readmap)
 
-      ## end of data frames implementation
-      
-      ## functions
-      
-      plot_readmap=function(df, ...) {
-      combineLimits(xyplot(count~coord|factor(sample, levels=unique(sample))+reorder(gene, count, function(x) -sum(abs(x))), 
-      data=df, 
-      type='h', 
-      scales= list(relation="free", x=list(rot=0, cex=0.7, axs="i", tck=0.5), y=list(tick.number=4, rot=90, cex=0.7)),
-      xlab=NULL, main=NULL, ylab=NULL, 
-      as.table=T, 
-      origin = 0, 
-      horizontal=FALSE, 
-      group=polarity,
-      col=c("red","blue"),
-      par.strip.text = list(cex=0.7),
-      ...))
-      }
+    size=read.delim("${size_distribution_dataframe}", header=T, row.names=NULL)
+    per_gene_size=lapply(genes, function(x) subset(size, gene==x)) ###### ?
+
+    ## end of data frames implementation
+
+    ## functions
 
-      plot_size_distribution= function(df, ...) {
-          smR.prepanel=function(x,y,...){; yscale=c(-max(abs(y)), max(abs(y)));list(ylim=yscale);}
-          bc= barchart(count~as.factor(size)|factor(sample, levels=unique(sample))+gene, data = df, origin = 0,
-            horizontal=FALSE,
-            group=polarity,
-            stack=TRUE,
-            col=c('red', 'blue'),
-            cex=0.75,
-            scales=list(y=list(tick.number=4, rot=90, relation="free", cex=0.7), x=list(cex=0.7) ),
-            prepanel=smR.prepanel,
-            xlab = NULL,
-            ylab = NULL,
-            main = NULL,
-            as.table=TRUE,
-            newpage = T,
-            par.strip.text = list(cex=0.7),
-            ...)
-          combineLimits(bc)
-          }
-          
-      ## end of functions
-      
-      ## function parameters'
-      
-      par.settings.readmap=list(layout.heights=list(top.padding=0, bottom.padding=-2.5), strip.background = list(col=c("lightblue","lightgreen")) )
-      par.settings.size=list(layout.heights=list(top.padding=-1, bottom.padding=-2.5), strip.background = list(col=c("lightblue","lightgreen")) )
-      par.settings.combination.readmap=list(layout.heights=list(top.padding=0, bottom.padding=-3), strip.background=list(col=c("lightblue","lightgreen")) )
-      par.settings.combination.size=list(layout.heights=list(top.padding=-2, bottom.padding=-0.5), strip.background=list(col=c("lightblue", "lightgreen")) )
+    plot_readmap=function(df, ...) {
+      combineLimits(xyplot(count~coord|factor(sample, levels=unique(sample))+reorder(gene, count, function(x) -sum(abs(x))),
+                           data=df,
+                           type='h',
+                           scales= list(relation="free", x=list(rot=0, cex=0.7, axs="i", tck=0.5), y=list(tick.number=4, rot=90, cex=0.7)),
+                           xlab=NULL, main=NULL, ylab=NULL,
+                           as.table=T,
+                           origin = 0,
+                           horizontal=FALSE,
+                           group=polarity,
+                           col=c("red","blue"),
+                           par.strip.text = list(cex=0.7),
+                           ...))
+    }
 
-      ## end of function parameters'
-      
-      ## GRAPHS
-
-      if (n_genes > 7) {page_height_simple = 11.69; page_height_combi=11.69; rows_per_page=${rows_per_page}; extrarow=0 } else {
-                         rows_per_page= 8; page_height_simple = 11.69; page_height_combi=11.69; extrarow=0 }
-                         ## rows_per_page= 8; page_height_simple = 11.69/7*n_genes; page_height_combi=11.69/9*(n_genes*2); extrarow=0 }
-                         ## rows_per_page= n_genes; page_height_simple = 11.69/n_genes/4; page_height_combi=11.69/(n_genes*2); extrarow=1 }
-     if (n_samples > 4) {page_width = 8.2677*n_samples/4} else {page_width = 8.2677*n_samples/3} # to test
+    plot_size_distribution= function(df, ...) {
+      smR.prepanel=function(x,y,...){; yscale=c(-max(abs(y)), max(abs(y)));list(ylim=yscale);}
+      bc= barchart(count~as.factor(size)|factor(sample, levels=unique(sample))+gene, data = df, origin = 0,
+                   horizontal=FALSE,
+                   group=polarity,
+                   stack=TRUE,
+                   col=c('red', 'blue'),
+                   cex=0.75,
+                   scales=list(y=list(tick.number=4, rot=90, relation="free", cex=0.7), x=list(cex=0.7) ),
+                   prepanel=smR.prepanel,
+                   xlab = NULL,
+                   ylab = NULL,
+                   main = NULL,
+                   as.table=TRUE,
+                   newpage = T,
+                   par.strip.text = list(cex=0.7),
+                   ...)
+      combineLimits(bc)
+    }
 
-      pdf(file="${readmap_PDF}", paper="special", height=page_height_simple, width=page_width)
-      for (i in seq(1,n_genes,rows_per_page)) {
-        start=i
-        end=i+rows_per_page-1
-        if (end>n_genes) {end=n_genes}
-        readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap))
-        args.list=c(readmap_plot.list, list(nrow=rows_per_page, ncol=1,
-                                            main=textGrob("Read Maps (nucleotide coordinates)", gp=gpar(cex=1), just="top"),
-                                            left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90)
-                                            #sub=textGrob("readmap coordinates", gp=gpar(cex=.75), just="bottom")
-                                            )
-                   )
-        do.call(grid.arrange, args.list)
-      }
-      devname=dev.off()
+    ## end of functions
+
+    ## function parameters'
+
+    par.settings.readmap=list(layout.heights=list(top.padding=0, bottom.padding=-2.5), strip.background = list(col=c("lightblue","lightgreen")) )
+    par.settings.size=list(layout.heights=list(top.padding=-1, bottom.padding=-2.5), strip.background = list(col=c("lightblue","lightgreen")) )
+    par.settings.combination.readmap=list(layout.heights=list(top.padding=0, bottom.padding=-3), strip.background=list(col=c("lightblue","lightgreen")) )
+    par.settings.combination.size=list(layout.heights=list(top.padding=-2, bottom.padding=-0.5), strip.background=list(col=c("lightblue", "lightgreen")) )
+
+    ## end of function parameters'
+
+    ## GRAPHS
+
+    if (n_genes > 7) {page_height_simple = 11.69; page_height_combi=11.69; rows_per_page=${rows_per_page}; extrarow=0 } else {
+      rows_per_page= 8; page_height_simple = 11.69; page_height_combi=11.69; extrarow=0 }
+    ## rows_per_page= 8; page_height_simple = 11.69/7*n_genes; page_height_combi=11.69/9*(n_genes*2); extrarow=0 }
+    ## rows_per_page= n_genes; page_height_simple = 11.69/n_genes/4; page_height_combi=11.69/(n_genes*2); extrarow=1 }
+    if (n_samples > 4) {page_width = 8.2677*n_samples/4} else {page_width = 8.2677*n_samples/3} # to test
 
 
-      pdf(file="${size_PDF}", paper="special", height=page_height_simple, width=page_width)
-      for (i in seq(1,n_genes,rows_per_page)) {
-        start=i
-        end=i+rows_per_page-1
-        if (end>n_genes) {end=n_genes}
-        plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, par.settings=par.settings.size) )
-        args.list=c(plot.list, list(nrow=rows_per_page, ncol=1,
-                                    main=textGrob("Size distributions (in nucleotides)", gp=gpar(cex=1), just="top"),
-                                    left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90)
-                                    #sub="readsize in nucleotides"
-                                    )
-                    )
-        do.call(grid.arrange, args.list)
-      }
-      devname=dev.off()
+    }
 
-      pdf(file="${combi_PDF}", paper="special", height=page_height_combi, width=page_width)
-      for (i in seq(1,n_genes,rows_per_page/2)) {
-        start=i
-        end=i+rows_per_page/2-1
-        if (end>n_genes) {end=n_genes}
-	read_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.combination.readmap))
-        size_plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, strip=FALSE, par.settings=par.settings.combination.size))
-	plot.list=rbind(read_plot.list, size_plot.list )
-        args.list=c(plot.list, list(nrow=rows_per_page + extrarow, ncol=1,
-                                    main=textGrob("${title}", gp=gpar(cex=1), just="top"),
-                                    left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90),
-                                    sub=textGrob("${xlabel}", gp=gpar(cex=1), just="bottom")
-                                    )
-                    )
-        do.call(grid.arrange, args.list)
+    pdf(file="${readmap_PDF}", paper="special", height=page_height_simple, width=page_width)
+    for (i in seq(1,n_genes,rows_per_page)) {
+      start=i
+      end=i+rows_per_page-1
+      if (end>n_genes) {end=n_genes}
+      if ("${yrange}" != 0) {
+        readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap))
+      } else {
+        readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-"{$yrange}", "{$yrange}"), par.settings=par.settings.readmap))
       }
-      devname=dev.off()
+      args.list=c(readmap_plot.list, list(nrow=rows_per_page, ncol=1,
+                                          main=textGrob("Read Maps (nucleotide coordinates)", gp=gpar(cex=1), just="top"),
+                                          left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90)
+                                          #sub=textGrob("readmap coordinates", gp=gpar(cex=.75), just="bottom")
+      )
+      )
+      do.call(grid.arrange, args.list)
+    }
+    devname=dev.off()
 
 
-     </configfile>
+    pdf(file="${size_PDF}", paper="special", height=page_height_simple, width=page_width)
+    for (i in seq(1,n_genes,rows_per_page)) {
+      start=i
+      end=i+rows_per_page-1
+      if (end>n_genes) {end=n_genes}
+      plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, par.settings=par.settings.size) )
+      args.list=c(plot.list, list(nrow=rows_per_page, ncol=1,
+                                  main=textGrob("Size distributions (in nucleotides)", gp=gpar(cex=1), just="top"),
+                                  left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90)
+                                  #sub="readsize in nucleotides"
+      )
+      )
+      do.call(grid.arrange, args.list)
+    }
+    devname=dev.off()
+
+    pdf(file="${combi_PDF}", paper="special", height=page_height_combi, width=page_width)
+    for (i in seq(1,n_genes,rows_per_page/2)) {
+      start=i
+      end=i+rows_per_page/2-1
+      if (end>n_genes) {end=n_genes}
+      read_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.combination.readmap))
+      size_plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, strip=FALSE, par.settings=par.settings.combination.size))
+      plot.list=rbind(read_plot.list, size_plot.list )
+      args.list=c(plot.list, list(nrow=rows_per_page + extrarow, ncol=1,
+                                  main=textGrob("${title}", gp=gpar(cex=1), just="top"),
+                                  left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90),
+                                  sub=textGrob("${xlabel}", gp=gpar(cex=1), just="bottom")
+      )
+      )
+      do.call(grid.arrange, args.list)
+    }
+    devname=dev.off()
+
+     ]]></configfile>
    </configfiles>
 
    <outputs>