Mercurial > repos > devteam > fastqc
changeset 11:db2dc6bc8f05 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 168f7aeb0f9f38de6dec873f3cbf0c30014fdd72
| author | iuc |
|---|---|
| date | Thu, 20 Apr 2017 11:06:17 -0400 |
| parents | a00a6402d09a |
| children | 484e86282f4b |
| files | rgFastQC.py rgFastQC.xml |
| diffstat | 2 files changed, 13 insertions(+), 8 deletions(-) [+] |
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--- a/rgFastQC.py Wed Feb 08 12:43:43 2017 -0500 +++ b/rgFastQC.py Thu Apr 20 11:06:17 2017 -0400 @@ -48,20 +48,23 @@ # This prevents uncompression of already uncompressed files infname = self.opts.inputfilename linf = infname.lower() + informat = self.opts.informat trimext = False # decompression at upload currently does NOT remove this now bogus ending - fastqc will barf # patched may 29 2013 until this is fixed properly - type = mimetypes.guess_type(self.opts.input) - if linf.endswith('.gz') or linf.endswith('.gzip') or type[-1] == "gzip": + ftype = mimetypes.guess_type(self.opts.input) + if linf.endswith('.gz') or linf.endswith('.gzip') or ftype[-1] == "gzip" or informat.endswith('.gz'): f = gzip.open(self.opts.input) try: f.readline() + ftype = ['gzip'] except: trimext = True f.close() - elif linf.endswith('bz2'): + elif linf.endswith('bz2') or informat.endswith('.bz2'): f = bz2.BZ2File(self.opts.input, 'r') try: + ftype = ['bzip2'] f.readline() except: trimext = True @@ -95,10 +98,12 @@ command_line.append('--limits %s' % self.opts.limits) command_line.append('--quiet') command_line.append('--extract') # to access the output text file - if type[-1] != "gzip": + if ftype[-1] == 'gzip': + self.fastqinfilename += '.gz' + elif ftype[-1] == 'bzip2': + self.fastqinfilename += '.bz2' + else: command_line.append('-f %s' % self.opts.informat) - else: - self.fastqinfilename += ".gz" command_line.append(self.fastqinfilename) self.command_line = ' '.join(command_line)
--- a/rgFastQC.xml Wed Feb 08 12:43:43 2017 -0500 +++ b/rgFastQC.xml Thu Apr 20 11:06:17 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="fastqc" name="FastQC" version="0.67"> +<tool id="fastqc" name="FastQC" version="0.68"> <description>Read Quality reports</description> <requirements> <requirement type="package" version="0.11.5">fastqc</requirement> @@ -124,7 +124,7 @@ - Kmer Content All except Basic Statistics and Overrepresented sequences are plots. - .. _FastQC: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ + .. _FastQC: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ .. _Picard-tools: http://picard.sourceforge.net/index.shtml </help> <citations>