Mercurial > repos > stef > falco
changeset 73:78f10251a484 draft
Uploaded
| author | stef |
|---|---|
| date | Fri, 27 Feb 2015 09:33:15 -0500 |
| parents | b8751995b54e |
| children | 00f63511d177 |
| files | falco-filter-report.sh |
| diffstat | 1 files changed, 13 insertions(+), 11 deletions(-) [+] |
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--- 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 "</head>" >> $html_out echo "<body>" >> $html_out echo " <h1>FALCO</h1>" >> $html_out -echo " <p>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 ;)</p>" >> $html_out +echo " <a href=\"$sample_html_file\">RESULTS</a>" >> $html_out +#echo " <p>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 ;)</p>" >> $html_out #echo " <a href=\"index.html\">HTML</a>" >> $html_out -echo " <table><tbody>" >> $html_out -for file in *.vcf *.txt *stderr *stdout +#echo " <table><tbody>" >> $html_out +#for file in *.vcf *.txt *stderr *stdout #for file in * -do - lineCount=`wc -l $file | cut -f 1 -d " "` - echo " <tr><td><a href=\"$file\">$file</a> has $lineCount lines</td></tr>" >> $html_out - echo " <tr><td> --> " `head -1 $file` "</td></tr>" >> $html_out -done -echo " </tbody></table>" >> $html_out +#do +# lineCount=`wc -l $file | cut -f 1 -d " "` +# echo " <tr><td><a href=\"$file\">$file</a> has $lineCount lines</td></tr>" >> $html_out +# echo " <tr><td> --> " `head -1 $file` "</td></tr>" >> $html_out +#done +#echo " </tbody></table>" >> $html_out echo "</body>" >> $html_out echo "</html>" >> $html_out @@ -103,8 +105,8 @@ ## creating galaxy history outputs ## ---------- #cp 'index.html' $html_out # this is the overview of samples html -#cp $bam_base'.html' $out_path/'out.html' # this is the sample html -cp $vcf_base'.html' $html_out # this is the sample html +cp $sample_html_file $out_path # this is the sample html +#cp $vcf_base'.html' $html_out # this is the sample html ## ---------- ## copy files to keep to output path