# HG changeset patch
# User stef
# Date 1425047595 18000
# Node ID 78f10251a484781d264dd6d06fc19438062efba1
# Parent b8751995b54e8ee853a7585496d3059b874ebcff
Uploaded
diff -r b8751995b54e -r 78f10251a484 falco-filter-report.sh
--- a/falco-filter-report.sh Fri Feb 27 09:25:01 2015 -0500
+++ b/falco-filter-report.sh Fri Feb 27 09:33:15 2015 -0500
@@ -37,6 +37,7 @@
## name of file in galaxy not always set so will use a user-set job_name instead
#bam_base=`echo $bam_name | sed 's#.bam$##' - `
vcf_base=$job_name
+sample_html_file=$vcf_base'.html'
## ----------
## Status / debug
@@ -85,17 +86,18 @@
echo "" >> $html_out
echo "" >> $html_out
echo " FALCO
" >> $html_out
-echo " This page is way to get output files that are not implemented in galaxy history, it is not intended to be a user-friendly way of displaying anything ;)
" >> $html_out
+echo " RESULTS" >> $html_out
+#echo " This page is way to get output files that are not implemented in galaxy history, it is not intended to be a user-friendly way of displaying anything ;)
" >> $html_out
#echo " HTML" >> $html_out
-echo " " >> $html_out
-for file in *.vcf *.txt *stderr *stdout
+#echo " " >> $html_out
+#for file in *.vcf *.txt *stderr *stdout
#for file in *
-do
- lineCount=`wc -l $file | cut -f 1 -d " "`
- echo " | $file has $lineCount lines |
" >> $html_out
- echo " | --> " `head -1 $file` " |
" >> $html_out
-done
-echo "
" >> $html_out
+#do
+# lineCount=`wc -l $file | cut -f 1 -d " "`
+# echo " | $file has $lineCount lines |
" >> $html_out
+# echo " | --> " `head -1 $file` " |
" >> $html_out
+#done
+#echo "
" >> $html_out
echo "" >> $html_out
echo "