Mercurial > repos > cschu > candisnp
changeset 5:9215ffe7d4d5 draft
Fixed issue with INDEL annotations. Changed output to iframe.
| author | cschu |
|---|---|
| date | Wed, 24 Jun 2015 11:42:40 -0400 |
| parents | 28990f586370 |
| children | 564795b5acae |
| files | candisnp.py candisnp.xml tool_dependencies.xml |
| diffstat | 3 files changed, 15 insertions(+), 5 deletions(-) [+] |
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--- a/candisnp.py Fri May 22 13:38:13 2015 -0400 +++ b/candisnp.py Wed Jun 24 11:42:40 2015 -0400 @@ -119,7 +119,8 @@ self.alternate_base = args[4] # info = dict([field.split('=') for field in args[7].strip().split(';')]) - info = dict(field.split('=') for field in args[7].strip().split(';')) + # info = dict(field.split('=') for field in args[7].strip().split(';')) + info = dict(field.split('=') for field in args[7].strip().split(';') if len(field.split('=')) == 2) # self.log.write('***'+str(info.get('EFF', '@@@')+'***\n')) self.allele_frequency = float(info.get('AF', '0.0')) @@ -199,9 +200,12 @@ sys.stderr.write(str(e.reason) + '\n') if candiURL: - body = urllib2.urlopen(candiURL) - fo.write(body.read()) - #fo.write('<iframe src="%s"></iframe>\n' % candiURL) + # body = urllib2.urlopen(candiURL) + # fo.write(body.read()) + #fo.write('<iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="%s"></iframe>' % candiURL) + #fo.write('<iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="%s"></iframe>' % candiURL) + fo.write('<iframe src="%s" frameborder="0" style="position: absolute; width: 100%%; height: 100%%;"></iframe>\n' % candiURL) + # fo.write('<iframe src="%s"></iframe>\n' % candiURL) else: fo.write('I am sorry. CandiSNP does not pick up. Maybe (<a href="%s" target="_blank">try it manually?</a>)\n' % CANDISNP_SERVER)
--- a/candisnp.xml Fri May 22 13:38:13 2015 -0400 +++ b/candisnp.xml Wed Jun 24 11:42:40 2015 -0400 @@ -35,6 +35,6 @@ </outputs> <help> - This tool is a testtool to issue POST requests from Galaxy. + A tool to pull in visualisation output from CandiSNP (candisnp.tsl.ac.uk). </help> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Jun 24 11:42:40 2015 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="snpeff" version="4.0"> + <repository changeset_revision="92b80578fa22" name="snpeff" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>