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 "
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 ;)
Also not all files might have been copied. To delete this files below from the galaxy installation delete the html page in your history.." >> $html_out
#echo " HTML" >> $html_out
echo "
" >> $html_out
for file in *.vcf *.txt *stderr *stdout
@@ -107,7 +116,7 @@
## 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 $bam_base'.html' $out_path/'out.html' # this is the sample html
cp $bam_base'.falco.vcf' $vcf_out
cp $bam_base'.qc.ann.qual.txt' $qc_ann_qual_out
cp $bam_base'.qc2.ann.txt' $qc2_ann_txt_out
@@ -118,7 +127,9 @@
## ----------
#cp -r ./$bam_base/*png $out_path/$bam_base/
#cp -r ./* $out_path
-cp *.vcf $out_path; cp *.txt $out_path; cp *_std* $out_path
+cp *.vcf $out_path;
+#cp *.txt $out_path;
+cp *_std* $out_path
## ----------
echo "END falco sh"
diff -r cf271f328d5e -r 07c810e4061c falco-call.xml
--- a/falco-call.xml Fri Jul 17 06:02:36 2015 -0400
+++ b/falco-call.xml Fri Jul 17 06:53:45 2015 -0400
@@ -23,6 +23,11 @@
+
+
+ \S+
+
+
@@ -41,18 +46,26 @@
-
-
- \S+
-
-
-
+
+
-
+
+
+
+
+
+
+
+
+
+
+
+
+
@@ -70,6 +83,8 @@
qc_ann_qual_out=$qc_ann_qual_output
qc2_ann_txt_out=$qc2_ann_txt_output
qc_targets_txt_out=$qc_targets_txt_output
+ also_output_txt=$txt2history
+ test_run=$testRun
out_path=${html_output.files_path}
job_name=$jobName
@@ -90,11 +105,19 @@
-
+
+ (txt2history == 'true')
+
-
-
-
+
+ (txt2history == 'true')
+
+
+ (txt2history == 'true')
+
+
+ (txt2history == 'true')
+
@@ -123,13 +146,13 @@
**Notes**
-Because each amplicon is considered separate test, if two amplicons overlap this can cause the same variant position to be present twice in the output VCF. This is intentional, you can use this to evaluate the quality of the variant call beyond the amplicon.
+Because each amplicon is analysed separately, when two amplicons overlap this can cause the same variant position to be present twice in the output VCF. This is intentional, you can use this to evaluate the quality of the variant call beyond the amplicon reads.
-----
**Citation**
-For the underlying tool please cite: Daoud Sie et al. Performance of amplicon-based next generation DNA sequencing for diagnostic gene mutation profiling in oncopathology (Cell Oncol 2014 Oct;37(5):353-61). [Pubmed]
+For the underlying tool please cite: Daoud Sie et al. Performance of amplicon-based next generation DNA sequencing for diagnostic gene mutation profiling in oncopathology (Cell Oncol 2014 Oct;37(5):353-61). Pubmed_
.. _Pubmed: http://www.ncbi.nlm.nih.gov/pubmed/25209392
diff -r cf271f328d5e -r 07c810e4061c falco-filter-report.xml
--- a/falco-filter-report.xml Fri Jul 17 06:02:36 2015 -0400
+++ b/falco-filter-report.xml Fri Jul 17 06:53:45 2015 -0400
@@ -20,41 +20,18 @@
-
-
-
-
\S+
+
-
-
-
-
-
-
-
+
+
+
@@ -113,7 +90,7 @@
**Notes**
-Because each amplicon is considered separate test, if two amplicons overlap this can cause the same variant position to be present twice in the output VCF. This is intentional, you can use this to evaluate the quality of the variant call beyond the amplicon.
+Because each amplicon is analysed separately, when two amplicons overlap this can cause the same variant position to be present twice in the output VCF. This is intentional, you can use this to evaluate the quality of the variant call beyond the amplicon reads.
-----
diff -r cf271f328d5e -r 07c810e4061c tool-data/HCT116_test_ABL1.bam
Binary file tool-data/HCT116_test_ABL1.bam has changed
diff -r cf271f328d5e -r 07c810e4061c tool-data/HCT116_test_ABL1.bam.bai
Binary file tool-data/HCT116_test_ABL1.bam.bai has changed