details: http://www.bx.psu.edu/hg/galaxy/rev/b633d836ce07 changeset: 3701:b633d836ce07 user: Dan Blankenberg <dan@bx.psu.edu> date: Tue Apr 27 10:59:46 2010 -0400 description: Add eland and elandmulti formats. Enhance MACs peakcaller to properly handle these formats. diffstat: datatypes_conf.xml.sample | 2 ++ lib/galaxy/datatypes/tabular.py | 12 ++++++++++++ tools/peak_calling/macs_wrapper.xml | 20 +++++++++++--------- 3 files changed, 25 insertions(+), 9 deletions(-) diffs (77 lines): diff -r c2a80b197ba5 -r b633d836ce07 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample Tue Apr 27 10:12:59 2010 -0400 +++ b/datatypes_conf.xml.sample Tue Apr 27 10:59:46 2010 -0400 @@ -42,6 +42,8 @@ <datatype extension="fastqsolexa" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true"/> <datatype extension="fastqcssanger" type="galaxy.datatypes.sequence:FastqCSSanger" display_in_upload="true"/> <datatype extension="fastqillumina" type="galaxy.datatypes.sequence:FastqIllumina" display_in_upload="true"/> + <datatype extension="eland" type="galaxy.datatypes.tabular:Eland" display_in_upload="true"/> + <datatype extension="elandmulti" type="galaxy.datatypes.tabular:ElandMulti" display_in_upload="true"/> <datatype extension="genetrack" type="galaxy.datatypes.tracks:GeneTrack"> <!-- <display file="genetrack.xml" /> --> </datatype> diff -r c2a80b197ba5 -r b633d836ce07 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py Tue Apr 27 10:12:59 2010 -0400 +++ b/lib/galaxy/datatypes/tabular.py Tue Apr 27 10:59:46 2010 -0400 @@ -420,3 +420,15 @@ return True except: return False + +class Eland( Tabular ): + file_ext = 'eland' + + def sniff( self, filename ): + return False + +class ElandMulti( Tabular ): + file_ext = 'elandmulti' + + def sniff( self, filename ): + return False diff -r c2a80b197ba5 -r b633d836ce07 tools/peak_calling/macs_wrapper.xml --- a/tools/peak_calling/macs_wrapper.xml Tue Apr 27 10:12:59 2010 -0400 +++ b/tools/peak_calling/macs_wrapper.xml Tue Apr 27 10:59:46 2010 -0400 @@ -9,19 +9,19 @@ <param name="experiment_name" type="text" value="MACS in Galaxy" size="50" label="Experiment Name"/> <conditional name="input_type"> <param name="input_type_selector" type="select" label="Paired End Sequencing"> - <option value="paired_end">Paired End (requires elandmultipet format)</option> + <option value="paired_end">Paired End (requires elandmulti format)</option> <option value="single_end" selected="true">Single End</option> </param> <when value="paired_end"> - <param name="input_chipseq_file1" type="data" format="elandmultipet" label="ChIP-Seq Tag File 1" /> - <param name="input_chipseq_file2" type="data" format="elandmultipet" label="ChIP-Seq Tag File 2" /> - <param name="input_control_file1" type="data" format="elandmultipet" optional="True" label="ChIP-Seq Control File 1" /> - <param name="input_control_file2" type="data" format="elandmultipet" optional="True" label="ChIP-Seq Control File 2" /> + <param name="input_chipseq_file1" type="data" format="elandmulti" label="ChIP-Seq Tag File 1" /> + <param name="input_chipseq_file2" type="data" format="elandmulti" label="ChIP-Seq Tag File 2" /> + <param name="input_control_file1" type="data" format="elandmulti" optional="True" label="ChIP-Seq Control File 1" /> + <param name="input_control_file2" type="data" format="elandmulti" optional="True" label="ChIP-Seq Control File 2" /> <param name="petdist" type="integer" label="Best distance between Pair-End Tags" value="200"/> </when> <when value="single_end"> - <param name="input_chipseq_file1" type="data" format="bed,sam,bam" label="ChIP-Seq Tag File" /> - <param name="input_control_file1" type="data" format="bed,sam,bam" optional="True" label="ChIP-Seq Control File" /> + <param name="input_chipseq_file1" type="data" format="bed,sam,bam,eland,elandmulti" label="ChIP-Seq Tag File" /> + <param name="input_control_file1" type="data" format="bed,sam,bam,eland,elandmulti" optional="True" label="ChIP-Seq Control File" /> </when> </conditional> <param name="gsize" type="float" label="Effective genome size" value="2.7e+9" help="default: 2.7e+9"/> @@ -101,11 +101,13 @@ #else: #set $__options['xls_to_interval'] = False #end if -#set $__options['format'] = $input_type['input_chipseq_file1'].extension.upper() -##treatment/tag input files +##treatment/tag input files and format #set $__options['input_chipseq'] = [ str( $input_type['input_chipseq_file1'] ) ] #if $input_type['input_type_selector'] == 'paired_end': #set $_hole = __options['input_chipseq'].append( str( $input_type['input_chipseq_file2'] ) ) +#set $__options['format'] = 'ELANDMULTIPET' +#else: +#set $__options['format'] = $input_type['input_chipseq_file1'].extension.upper() #end if ##control/input files #set $__options['input_control'] = []