2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5c3675b6d1bd/ changeset: 5c3675b6d1bd user: fubar date: 2012-10-26 07:00:13 summary: Fix parameters for fastqc to work properly with bam and with a contaminants file Been b0rken for a long time - probably not much used.. affected #: 3 files diff -r f156b9e144437e541127009c2a32efc1019af5c7 -r 5c3675b6d1bd44f27225d4bef1d2ea7096cedee9 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -911,7 +911,7 @@ self.ref_input = None self.default_value = elem.get( "default_value", None ) self.is_dynamic = True - self.usecolnames = string_as_bool( elem.get( "use_header_names", False )) + self.usecolnames = string_as_bool( elem.get( "use_header_names", True )) # much easier for the user - make default if not overridden def from_html( self, value, trans=None, context={} ): """ diff -r f156b9e144437e541127009c2a32efc1019af5c7 -r 5c3675b6d1bd44f27225d4bef1d2ea7096cedee9 tools/filters/sorter.xml --- a/tools/filters/sorter.xml +++ b/tools/filters/sorter.xml @@ -15,7 +15,7 @@ </command><inputs><param format="tabular" name="input" type="data" label="Sort Query" /> - <param name="column" label="on column" type="data_column" data_ref="input" accept_default="true" /> + <param name="column" label="on column" type="data_column" data_ref="input" accept_default="true"/><param name="style" type="select" label="with flavor"><option value="num">Numerical sort</option><option value="alpha">Alphabetical sort</option> diff -r f156b9e144437e541127009c2a32efc1019af5c7 -r 5c3675b6d1bd44f27225d4bef1d2ea7096cedee9 tools/rgenetics/rgFastQC.py --- a/tools/rgenetics/rgFastQC.py +++ b/tools/rgenetics/rgFastQC.py @@ -51,9 +51,9 @@ fastq = os.path.basename(self.opts.input) cl = [self.opts.executable,'--outdir=%s' % self.opts.outputdir] if self.opts.informat in ['sam','bam']: - cl.append('-f %s' % self.opts.informat) + cl.append('--f=%s' % self.opts.informat) if self.opts.contaminants <> None : - cl.append('-c %s' % self.opts.contaminants) + cl.append('--contaminants=%s' % self.opts.contaminants) # patch suggested by bwlang https://bitbucket.org/galaxy/galaxy-central/pull-request/30 # use a symlink in a temporary directory so that the FastQC report reflects the history input file name fastqinfilename = re.sub(ur'[^a-zA-Z0-9_\-\.]', '_', os.path.basename(self.opts.inputfilename)) https://bitbucket.org/galaxy/galaxy-central/changeset/720b4067ab5e/ changeset: 720b4067ab5e user: fubar date: 2012-10-26 07:03:10 summary: Revert use_header_names to default false - breaks a couple of existing tests - would need to repair those too. affected #: 1 file diff -r 5c3675b6d1bd44f27225d4bef1d2ea7096cedee9 -r 720b4067ab5e5b617569278155ab21216c0de176 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -911,7 +911,7 @@ self.ref_input = None self.default_value = elem.get( "default_value", None ) self.is_dynamic = True - self.usecolnames = string_as_bool( elem.get( "use_header_names", True )) # much easier for the user - make default if not overridden + self.usecolnames = string_as_bool( elem.get( "use_header_names", False )) def from_html( self, value, trans=None, context={} ): """ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.