comparison tools/sr_assembly/mira.xml @ 5:216bf640baaf draft

Uploaded v0.0.4 which fixes a problem in v0.0.3 with the backbone arguments.

4:117cce3296af

<tool id="mira_assembler" name="Assemble with MIRA" version="0.0.3">
    <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description>
	<command interpreter="python">mira.py mira $out_fasta $out_qual $out_ace $out_caf $out_wig $out_log
##Give the wrapper script list of output filenames, then the mira command...
mira --job=$job_method,$job_type,$job_quality

##Input files
#if $condBackbone.use == "true":
    ## Can this be linked to job_method as well? If mapping we need the backbone...
    -SB:lb=1:bft=1 -FN:bbin=${condBackbone.filename}
#end if
#if $condSanger.use == "true":
    SANGER_SETTINGS
    ## Not easy in Galaxy to add sanger to --job, so use load_sequence_data(lsd) instead
    ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file

5:216bf640baaf

<tool id="mira_assembler" name="Assemble with MIRA" version="0.0.4">
    <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description>
	<command interpreter="python">mira.py mira $out_fasta $out_qual $out_ace $out_caf $out_wig $out_log
##Give the wrapper script list of output filenames, then the mira command...
mira --job=$job_method,$job_type,$job_quality

##Input files
#if $condBackbone.use == "true":
    ## Can this be linked to job_method as well? If mapping we need the backbone...
    -SB:lb=1:bft=fasta -FN:bbin=${condBackbone.filename}
#end if
#if $condSanger.use == "true":
    SANGER_SETTINGS
    ## Not easy in Galaxy to add sanger to --job, so use load_sequence_data(lsd) instead
    ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file