Mercurial > repos > jdv > nanopore_qc

changeset 4:4b7d1bcf210c draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopore_qc commit dfa6f9934da27ffddc4da6c16d97d4057662ef65
author jdv
date Mon, 12 Mar 2018 15:04:45 -0400
parents 5c571ad2803e
children f2081dc93880
files nanopore_qc.R nanopore_qc.xml
diffstat 2 files changed, 10 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- a/nanopore_qc.R	Mon Dec 04 15:23:55 2017 -0500
+++ b/nanopore_qc.R	Mon Mar 12 15:04:45 2018 -0400
@@ -143,6 +143,9 @@
         d$num_events_template = as.numeric(as.character(d$num_events_template))
         d$start_time = as.numeric(as.character(d$start_time))
     }
+
+    # ignore 0-length reads
+    d <- d[d$sequence_length_template > 0,]
         
     d$events_per_base = d$num_events_template/d$sequence_length_template
 
@@ -334,6 +337,7 @@
     # make plots
     flog.info(paste(sep = "", flowcell, ": plotting length histogram"))
     len.lims <- quantile(d$sequence_length_template,c(0.01,0.99))
+    len.lims[1] <- max(1,len.lims[1])
     
     p1 = ggplot(d, aes(x = sequence_length_template)) + 
         geom_histogram(bins = 200, fill="steelblue") + 
--- a/nanopore_qc.xml	Mon Dec 04 15:23:55 2017 -0500
+++ b/nanopore_qc.xml	Mon Mar 12 15:04:45 2018 -0400
@@ -71,6 +71,12 @@
     </tests>
     <help>
 <![CDATA[
+
+    `NanoporeQC` produces a summary report on nanopore read data called by
+    Albacore. It acts on the summary table produced by Albacore and produces
+    HTML output. It was originally forked from the MinionQC code by Robert
+    Lanfear.
+
 ]]>
     </help>
     <citations>