# HG changeset patch
# User estrain
# Date 1539788960 14400
# Node ID 7d62c324d642402b9fbae4adb46ca3aba57ed289
# Parent  17652c6a7517255608d37b559799f4fff0608087
Deleted selected files

diff -r 17652c6a7517 -r 7d62c324d642 sum_fastqc-b769c810924e/sum_fastqc.pl
--- a/sum_fastqc-b769c810924e/sum_fastqc.pl	Wed Oct 17 11:09:06 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,79 +0,0 @@
-#!/usr/bin/perl
-
-####################################################
-## 
-## sum_fastqc.pl
-## 
-## Errol Strain (estrain@gmail.com) 
-##
-## Description: Takes raw FASTQC output and produces
-## simple table summary
-##
-#################################################### 
-
-my($inname)=shift(@ARGV);
-my($qscore)=shift(@ARGV);
-$qscore=~s/\s+//g;
-my(@qlist)=split(/\,/,$qscore);
-
-print "Input\tFile\tFastQC\tPass-Fail\tReads\tPoor_Reads\tGC";
-foreach(@qlist) {
-  print "\tQ".$_;
-}
-print "\n";
-
-foreach (@ARGV) {
-  print_stats($_);
-}
-
-sub print_stats {
-  $infile = shift;
-  # First 10 lines of raw FASTQC contain basic overview
-  @sumlines=`head -n 10 $infile`;
-  chomp(@sumlines);
-
-  # Sequence level Q scores are buried in the middle of the file
-  @qlines=`awk '/#Quality\tCount/,/>>END_MODULE/' $infile | head -n -1 | tail -n +2`;
-  chomp(@qlines);
-
-  @fastqc = split(/[\n\t]/,shift(@sumlines));
-  @pass = split(/\t/,shift(@sumlines));
-  shift(@sumlines);
-  @fn = split(/\t/,shift(@sumlines));
-  shift(@sumlines);
-  shift(@sumlines);
-  @nreads = split(/\t/,shift(@sumlines));
-  @npoor = split(/\t/,shift(@sumlines));
-  shift(@sumlines);
-  @gc = split(/\t/,shift(@sumlines));
-
-  print $inname."\t";
-  print $fn[1]."\t";
-  print $fastqc[1]."\t";
-  print $pass[1]."\t";
-  print $nreads[1]."\t";
-  print $npoor[1]."\t";
-  print $gc[1];
-  foreach $qs (@qlist) {
-    print "\t";
-    print qcal($nreads[1],$qs,\@qlines);
-  }
-  print "\n";
-}
-
-# Sum reads w/ Q scores > cutoff and divide by number of reads
-sub qcal {
-   $nreads=shift(@_);
-   $cutoff=shift(@_);
-   @qarray=@{$_[0]};
-   $sum = 0;
-  
-   foreach $item (@qarray) {
-      my($qval,$q)=split(/\t/,$item);
-      if($qval>=$cutoff) {
-        $sum += $q;
-      }
-   }
-   $qmean = sprintf("%.2f", 100 * $sum / $nreads);
-   return $qmean;
-}
diff -r 17652c6a7517 -r 7d62c324d642 sum_fastqc-b769c810924e/sum_fastqc.xml
--- a/sum_fastqc-b769c810924e/sum_fastqc.xml	Wed Oct 17 11:09:06 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,55 +0,0 @@
-<tool id="sum_fastqc" name="sum_fastqc" version="0.2">
-    <requirements>
-    </requirements>
-    <command detect_errors="exit_code"><![CDATA[
-
-      #if $jobtype.select == "single"
-        #set inname = $jobtype.file
-        #set infile = $jobtype.file
-        perl $__tool_directory__/sum_fastqc.pl "$inname" $qset.qscore $infile > sum_fastqc.tab
-      #else if $jobtype.select == "col"
-        #set inname = $jobtype.coll.name
-        #set infile = $jobtype.coll.forward
-        #set infile2 = $jobtype.coll.reverse
-        perl $__tool_directory__/sum_fastqc.pl "$inname" $qset.qscore $infile $infile2 > sum_fastqc.tab;
-      #end if
-
-    ]]></command>
-    <inputs>
-      <conditional name="jobtype">
-        <param name="select" type="select" label="Select Input">
-          <option value="single">Raw FASTQC output File</option>
-          <option value="col">Pair of raw FASTQC Files</option>
-        </param>
-        <when value="single">
-          <param name="file" type="data" format="txt" label="Raw FASTQC" />
-        </when>
-        <when value="col">
-          <param name="coll" label="Raw FASTQC pair" type="data_collection" format="txt" collection_type="paired" />
-        </when>
-      </conditional>
-      <conditional name="qset">
-        <param name="selectq" type="select" label="Single or multiple Q scores">
-          <option value="single">Single Q score</option>
-          <option value="mul">Multiple Q scores</option>
-        </param>
-        <when value="single">
-          <param name="qscore" type="integer" label="Q score threshold (i.e. reads >= Q score)" value="30">
-            <validator type="in_range" message="Must be integer(0,40)." min="0" max="40"/>
-          </param>
-        </when>
-        <when value="mul">
-          <param name="qscore" type="text" label="Comma delimited Q score list (e.g. 25,30,35)" value="30"/>
-        </when>
-      </conditional>
-    </inputs>
-    <outputs>
-      <data format="tabular" name="FASTQC Summary" label="${tool.name} on ${on_string}: Contigs" from_work_dir="*.tab"/>
-    </outputs>
-
-    <help><![CDATA[
-
-    ]]></help>
-     <citations>
-    </citations>
-</tool>