--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/spades_3_5_0/plot_spades_stats.xml	Tue Dec 16 12:57:49 2014 -0500
@@ -0,0 +1,80 @@
+<tool id="plot_spades_stats" name="SPAdes stats" version="0.1">
+  <description>coverage vs. length plot</description>
+  <requirements>
+    <requirement type="package">R</requirement>  
+  </requirements>
+  <command interpreter="bash">r_wrapper.sh $script_file</command>
+
+  <inputs>
+    <param name="input_scaffolds" type="data" format="tabular" label="Scaffold stats"/>
+    <param name="input_contigs" type="data" format="tabular" label="Contig stats"/>
+    <param name="length_co" type="integer" value="1000" min="0" label="Length cut-off" help="Contigs with length under that value are shown in red"/>
+    <param name="coverage_co" type="integer" value="10" min="0" label="Coverage cut-off" help="Contigs with length under that value are shown in red"/>
+  </inputs>
+  <configfiles>
+    <configfile name="script_file">
+## Setup R error handling to go to stderr
+options( show.error.messages=F, 
+  error = function () { 
+    cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) 
+} )
+files = c("${input_contigs}", "${input_scaffolds}")
+types = c("Contigs", "Scaffolds")
+
+## Start plotting device
+png("${out_file}", w=500, h=1000)
+par(mfrow=c(2,1))
+
+## Loop over the two files
+for (i in 1:length(types)){
+  seqs = read.table(files[i], header=FALSE, comment.char="#")
+  colnames = c("name", "length", "coverage")
+  names(seqs) = colnames
+
+  ## Stats over all sequences 
+  sl_all = sort(seqs\$length, decreasing=TRUE)
+  cs_all = cumsum(sl_all)
+  s_all = sum(seqs\$length)
+  n50_idx_all = which.min(sl_all[cs_all &lt; 0.5*s_all])
+  n90_idx_all = which.min(sl_all[cs_all &lt; 0.9*s_all])
+  n50_all = sl_all[n50_idx_all]
+  n90_all = sl_all[n90_idx_all]
+  
+  ## Filter short seqs, redo stats
+  seqs_filt = seqs[seqs\$length >= ${length_co} &amp; seqs\$coverage >= ${coverage_co},]
+  if (nrow(seqs_filt) > 0){
+    sl_filt = sort(seqs_filt\$length, decreasing=TRUE)
+    cs_filt = cumsum(sl_filt)
+    s_filt = sum(seqs_filt\$length)
+    n50_idx_filt = which.min(sl_filt[cs_filt &lt; 0.5*s_filt])
+    n90_idx_filt = which.min(sl_filt[cs_filt &lt; 0.9*s_filt])
+    n50_filt = sl_filt[n50_idx_filt]
+    n90_filt = sl_filt[n90_idx_filt]
+  }
+  seqs_bad = seqs[seqs\$length &lt; ${length_co} | seqs\$coverage &lt; ${coverage_co},]
+
+  ## Length vs coverage
+  plot(length~coverage, data=seqs, log="xy", type="n", main=paste(types[i], ": coverage vs. length", sep=""), xlab="Coverage", ylab="Length")
+  if (nrow(seqs_bad) > 0){
+    points(length~coverage, data=seqs_bad, cex=0.5, col="red")
+  }
+  if (nrow(seqs_filt) > 0){
+    points(length~coverage, data=seqs_filt, cex=0.5, col="black")
+  }
+  abline(v=${coverage_co}, h=${length_co}, lty=2, col=grey(0.3))
+  legend(x="topleft", legend=c("Before/after filtering", paste(c("N50: ", "N90: ", "Median cov.: "), c(n50_all, n90_all, round(median(seqs\$coverage))), rep("/", 3), c(n50_filt, n90_filt, round(median(seqs_filt\$coverage))), sep="")), cex=0.8)
+}
+dev.off()
+    </configfile>
+  </configfiles>
+  <outputs>
+    <data format="png" name="out_file" />
+  </outputs>
+  <help>
+**What it does**
+
+Using the output of SPAdes (a pair of fasta file and stat file for each of the contigs and scaffolds), it produces a coverage vs. contig plot. Each dot represent a contig/scaffold. Given a coverage and a length cutoff, sequences that do not meet those criteria are shown in red. Some statistics are also given (N50, N90, median contig/scaffold length) both before and after filtering.
+
+Use the "filter SPAdes output" tool to actually filter sequences.
+  </help>
+</tool>
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