Repository revision
3:bf1f8bc4abe6

Repository 'roche454_toolsuite'

runMapping tool metadata
Miscellaneous
runMapping
Map Roche/454 reads to a reference using Newbler
runMapping
toolshed.g2.bx.psu.edu/repos/edward-kirton/roche454_toolsuite/runMapping/1.0.1
1.0.1
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/edward-kirton/roche454_toolsuite/runMapping/1.0.1 (this tool)
toolshed.g2.bx.psu.edu/repos/edward-kirton/roche454_toolsuite/runMapping/1.0.0
toolshed.g2.bx.psu.edu/repos/edward-kirton/roche454_toolsuite/runMapping/1.0.1 (this tool)
toolshed.g2.bx.psu.edu/repos/edward-kirton/roche454_toolsuite/runMapping/1.0.0
runMapping
Requirements (dependencies defined in the <requirements> tag set)
No requirements defined
Additional information about this tool
runMapping_wrapper.pl
$newbler_metrics.extra_files_path
$alignment_info
$all_contigs_fasta
$all_contigs_qual
$all_diffs
$all_struct_vars
$hc_diff
$hc_struct_vars
$mapping_qc
$newbler_metrics
$pair_align
$read_status
$ref_status
$tag_pair_align
$trim_status
$trimmed_reads_fasta
$trimmed_reads_qual
$contigs_ace
$contigs_bam
$large_contigs_fasta
$large_contigs_qual
$gene_status
runAssembly
-o $newbler_metrics.extra_files_path
-cpu 8 
-a $a
-e $e 
-mi $mi 
-ml $ml 
-minlen $minlen 
$pair 
$info 
$notrim 
$tr 
$ace 
$bam
$no 
$qo 
$nor 
$ud 
-ss $ss 
-sl $sl 
-sc $sc 
-ais $ais 
-rst $rst
-hsl $hsl
-mcf $mcf
-vs $vs
-vt $vt
-fi $fi
-fe $fe
-l $l 
$ref_type
-ref
#for $i in $ref_inputs
${i.ref_input}
#end for
-read
#for $i in $sff_paired_inputs
-p ${i.sff_paired_input}
#end for
#for $i in $sanger_paired_inputs
-p ${i.sanger_paired_input}
#end for
#for $i in $sff_inputs
${i.sff_input}
#end for
#for $i in $sanger_inputs
${i.sanger_input}
#end for
perl
False
False
Functional tests
No functional tests defined