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better tool naming in outputs for all picard tools and finally found where the picard log was hiding

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Ross Lazarus
2011-05-08 22:16:18 -04:00
parent 8ef61a22c8
commit db5d90222e
1 changed files with 3 additions and 3 deletions
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tools/picard/picard_wrapper.py
+3 -3
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@@ -22,7 +22,7 @@ galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
<body>
<div class="document">
"""
galhtmlattr = """Galaxy tool wrapper run %s at %s</b><br/>"""
galhtmlattr = """Galaxy tool wrapper %s at %s</b><br/>"""
galhtmlpostfix = """</div></body></html>\n"""
@@ -68,7 +68,7 @@ class PicardBase():
os.makedirs(opts.tmpdir)
except:
pass
self.log_filename = '%s.log' % self.picname
self.log_filename = os.path.join(opts.outdir,'%s.log' % self.picname)
self.metricsOut = os.path.join(opts.outdir,'%s.metrics.txt' % self.picname)
def baseName(self,name=None):
@@ -237,7 +237,7 @@ class PicardBase():
tr.d1 td {background-color: aliceblue; color: black;}
</style>"""
res = [rstyle,]
res.append(galhtmlprefix % self.progname)
res.append(galhtmlprefix % self.picname)
res.append(galhtmlattr % (self.progname,timenow()))
flist = [x for x in os.listdir(self.opts.outdir) if not x.startswith('.')]
pdflist = [x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf']