# HG changeset patch
# User davidvanzessen
# Date 1482333799 18000
# Node ID 44ec2a1009fc7936902be591c3014450e2bf2992
# Parent  cbce7f35f8b0a5557a44f7687f13a3ee9ebaa366
Uploaded

diff -r cbce7f35f8b0 -r 44ec2a1009fc results_footer.html
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/results_footer.html	Wed Dec 21 10:23:19 2016 -0500
@@ -0,0 +1,75 @@
+<style>
+<!--
+ /* Font Definitions */
+ @font-face
+	{font-family:Calibri;
+	panose-1:2 15 5 2 2 2 4 3 2 4;}
+ /* Style Definitions */
+ p.MsoNormal, li.MsoNormal, div.MsoNormal
+	{margin-top:0in;
+	margin-right:0in;
+	margin-bottom:10.0pt;
+	margin-left:0in;
+	line-height:115%;
+	font-size:11.0pt;
+	font-family:"Calibri","sans-serif";}
+p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
+	{margin:0in;
+	margin-bottom:.0001pt;
+	font-size:11.0pt;
+	font-family:"Calibri","sans-serif";}
+.MsoChpDefault
+	{font-family:"Calibri","sans-serif";}
+.MsoPapDefault
+	{margin-bottom:10.0pt;
+	line-height:115%;}
+@page WordSection1
+	{size:8.5in 11.0in;
+	margin:1.0in 1.0in 1.0in 1.0in;}
+div.WordSection1
+	{page:WordSection1;}
+-->
+</style>
+
+<div class=WordSection1>
+
+<p class=MsoNoSpacingCxSpMiddle style='text-align:justify'><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Table showing
+the number of sequences identified for each samples and the number of sequences
+in which no MID tag could be matched. In addition, multiple files can be
+downloaded for each sample.</span></p>
+
+<p class=MsoNoSpacingCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>FASTQ:</span></u><span
+lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
+Downloads a FASTQ file with all the sequences that are linked to the sample.
+Sequences have not been trimmed. </span></p>
+
+<p class=MsoNoSpacingCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>FASTA:</span></u><span
+lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
+Downloads a FASTA file with all the sequences that are linked to the sample.
+Sequences have not been trimmed. </span></p>
+
+<p class=MsoNoSpacingCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Trimmed FASTA:</span></u><span
+lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
+Downloads a trimmed FASTA file with all the sequences that are linked to the
+sample. Sequences are trimmed according to the settings entered at the barcodes
+section of the main page of the demultiplex tool. </span></p>
+
+<p class=MsoNoSpacingCxSpLast style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>FASTQC:</span></u><span
+lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'> The
+sequences of each individual sample automatically is analysed using FASTQC.
+Clicking “Report” opens a new page containing all quality control results of
+the analysis of FASTQC. </span><span style='font-size:12.0pt;font-family:"Times New Roman","serif";
+color:black'>(</span><span lang=EN-GB><a
+href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/" target="_blank"><span
+lang=EN-US style='font-size:12.0pt;font-family:"Times New Roman","serif";
+color:#303030;text-decoration:none'>http://www.bioinformatics.babraham.ac.uk/projects/fastqc/</span></a></span><span
+style='font-size:12.0pt;font-family:"Times New Roman","serif";color:black'>)</span></p>
+
+<p class=MsoNormal>&nbsp;</p>
+
+</div>
diff -r cbce7f35f8b0 -r 44ec2a1009fc wrapper.sh
--- a/wrapper.sh	Wed Dec 21 10:07:42 2016 -0500
+++ b/wrapper.sh	Wed Dec 21 10:23:19 2016 -0500
@@ -64,4 +64,7 @@
 		python $dir/trim.py --input "$file.fasta" --output "${file}_trimmed.fasta" --start "${trim_start[$barcode]}" --end "${trim_end[$barcode]}"
 		echo "<tr><td>$barcode</td><td>$count</td><td><a href='$file.fastq'>$file.fastq</a></td><td><a href='$file.fasta'>$file.fasta</a></td><td><a href='${file}_trimmed.fasta'>${file}_trimmed.fasta</a></td><td><a href='${name}_${barcode}_fastqc.html'>Report</a></td></tr>" >> $output
 done < output.txt
-echo "</tbody></body></html>" >> $output
+
+echo "</tbody></table>" >> $output
+cat $dir/results_footer.html >> $output
+echo "</body></html>" >> $output