| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/peterjc/clc_assembly_cell/clc_assembler/0.0.7 (this tool) |
| toolshed.g2.bx.psu.edu/repos/peterjc/clc_assembly_cell/clc_assembler/0.0.2 |
| clc_assembler |
| Requirements (dependencies defined in the <requirements> tag set) |
| Additional information about this tool |
\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler
#for $rg in $read_group
##--------------------------------------
#if str($rg.segments.type) == "paired"
-p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q -i "$rg.segments.filename1" "$rg.segments.filename2"
#end if
##--------------------------------------
#if str($rg.segments.type) == "interleaved"
-p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q "$rg.segments.filename"
#end if
##--------------------------------------
#if str($rg.segments.type) == "none"
-p no -q
#for $f in $rg.segments.filenames
"$f"
#end for
#end if
##--------------------------------------
#end for
-m $min_contig_len
-o "$out_fasta"
--cpus \${GALAXY_SLOTS:-4}
-v | grep -v "^Progress: "
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
read_group_0|segments|placement: fb read_group_0|segments|dist_mode: ss read_group_0|segments|min_size: 1 read_group_0|segments|max_size: 1000 read_group_0|segments|filename: SRR639755_mito_pairs.fastq.gz read_group_0|segments|type: interleaved min_contig_len: 200 |
name: value |
SRR639755_mito_pairs.fastq.gz value |