comparison tools/mira4/mira4_mapping.xml @ 13:7fcabeeca5df draft

Uploaded v0.0.2 preview 5, fixes for MIRA 4.0 (final), more verbose error if $MIRA4 path wrong

12:a6a56440567c

    </outputs>
    <configfiles>
        <configfile name="manifest">
project = MIRA
job = mapping,${job_type},${job_quality}
parameters = -GE:not=1 -NW:cmrnl -DI:trt=/tmp
## -GE:not is short for -GENERAL:number_of_threads and using one (1)
## can be useful for repeatability of assemblies and bug hunting.
##
## -NW:cmrnl is short for -NAG_AND_WARN:check_maxreadnamelength
## and without this MIRA aborts with read names over 40 characters
## due to limitations of some downstream tools.
##

##This is perhaps redundant as MIRA defaults to StrainX for the reads:
strain = StrainX
#end if
##Record the segment placement (if any)
#if str($rg.segments.type) == "paired"
segmentplacement = ${rg.segments.placement}
segmentnaming = ${rg.segments.naming}
#end if
#if str($rg.segments.type) == "none"
segmentplacement = ?
#end if
##MIRA will accept multiple filenames on one data line, or multiple data lines
#for $f in $rg.filenames
##Must now map Galaxy datatypes to MIRA file types...
#if $f.ext.startswith("fastq")
##MIRA doesn't like fastqsanger etc, just plain old fastq:

13:7fcabeeca5df

    </outputs>
    <configfiles>
        <configfile name="manifest">
project = MIRA
job = mapping,${job_type},${job_quality}
parameters = -NW:cmrnl=no -DI:trt=/tmp
## -GE:not is short for -GENERAL:number_of_threads and using one (1)
## can be useful for repeatability of assemblies and bug hunting.
## This is overriden by the command line -t switch which is easier
## to set from within Galaxy.
##
## -NW:cmrnl is short for -NAG_AND_WARN:check_maxreadnamelength
## and without this MIRA aborts with read names over 40 characters
## due to limitations of some downstream tools.
##

##This is perhaps redundant as MIRA defaults to StrainX for the reads:
strain = StrainX
#end if
##Record the segment placement (if any)
#if str($rg.segments.type) == "paired"
segment_placement = ${rg.segments.placement}
segment_naming = ${rg.segments.naming}
#end if
##if str($rg.segments.type) == "none"
##MIRA4 manual says use segment_placement = unknown or ? for unpaired data
##but this stopped working in MIRA 4.0 RC5 and 4.0 (final). See:
##http://www.freelists.org/post/mira_talk/Unpaired-reads-and-segment-placement--or-unknown
##segment_placement = ?
##end if
##MIRA will accept multiple filenames on one data line, or multiple data lines
#for $f in $rg.filenames
##Must now map Galaxy datatypes to MIRA file types...
#if $f.ext.startswith("fastq")
##MIRA doesn't like fastqsanger etc, just plain old fastq: