Repository revision
5:216bf640baaf

Repository 'mira_assembler'

Assemble with MIRA tool metadata
Miscellaneous
Takes Sanger, Roche, Illumina, and Ion Torrent data
mira_assembler
toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler/mira_assembler/0.0.4
0.0.4
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler/mira_assembler/0.0.5
toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler/mira_assembler/0.0.4 (this tool)
toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler/mira_assembler/0.0.3
toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler/mira_assembler/0.0.2
toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler/mira_assembler/0.0.1
toolshed.g2.bx.psu.edu/repos/peterjc/mira_assembler/mira_assembler/0.0.2
mira_assembler
Requirements (dependencies defined in the <requirements> tag set)
name version type
Bio not provided python-module
Additional information about this tool
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 $condSanger.use == "true":
    SANGER_SETTINGS
    ## Not easy in Galaxy to add sanger to --job, so use load_sequence_data(lsd) instead
    ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
    -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condSanger.filename}
#end if
#if $condRoche.use == "true":
    454_SETTINGS
    ## Not easy in Galaxy to add 454 to --job, so use load_sequence_data(lsd) instead
    ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
    -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condRoche.filename}
#end if
#if $condIllumina.use == "true":
    SOLEXA_SETTINGS
    ## Not easy in Galaxy to add solexa to --job, so use load_sequence_data(lsd) instead
    -LR:lsd=1:ft=fastq -FN:fqi=${condIllumina.filename}
    ##TODO - Look at -LR FASTQ qual offset (fqqo)
#end if
#if $condIonTorrent.use == "true":
    IONTOR_SETTINGS
    ## Not easy in Galaxy to add iontor to --job, so use load_sequence_data(lsd) instead
    ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
    -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condIonTorrent.filename}
#end if

##Output files
COMMON_SETTINGS
##Explicitly request the FASTA (+QUAL), CAF, ACE, WIG output
##Explicitly disable formats we won't use like MAF (reduce IO)
-OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0
##remove_rollover_tmps, remove_tmp_directory
-OUT:rrot=1:rtd=1

    
python
False
False
Functional tests
No functional tests defined