| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/stacks_clonefilter/stacks_clonefilter/1.46.0 (this tool) |
| stacks_clonefilter |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| stacks | 1.46 | package |
| velvet | 1.2.10 | package |
| stacks_summary | 1.1 | package |
| Additional information about this tool |
#if $data_type.dt_select == "single"
#if $data_type.fname.is_of_type('fastqsanger')
#set $ext = ".fq"
#set inputype = "fastq"
#else
#set $ext = ".fq.gz"
#set inputype = "gzfastq"
#end if
ln -s '$data_type.fname' R1$ext &&
#else
#if $data_type.fwd.is_of_type('fastqsanger')
#set $ext = ".fq"
#set inputype = "fastq"
#else
#set $ext = ".fq.gz"
#set inputype = "gzfastq"
#end if
ln -s '$data_type.fwd' R1$ext &&
ln -s '$data_type.rev' R2$ext &&
#end if
mkdir clone_outputs
&&
clone_filter
#if $data_type.dt_select == 'single':
-f R1$ext
#else
-1 R1$ext
-2 R2$ext
#end if
-i $inputype
-o clone_outputs
#if $oligo_len_1
--oligo_len_1 $oligo_len_1
$data_type.barcode_encoding
#end if
#if $oligo_len_2
--oligo_len_2 $oligo_len_2
#end if
-y gzfastq
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
data_type|fname: clonefilter/R1_0001.1.fq.gz data_type|dt_select: single oligo_len_1: 6 |
name: value |
clonefilter/R1_0001.1.fq.gz value |
| Test-2 |
data_type|fname: clonefilter/R1_0001.1.fq.gz data_type|dt_select: single |
name: value |
clonefilter/R1_0001.1.fq.gz value |
| Test-3 |
data_type|fwd: clonefilter/R1_0001.1.fq.gz data_type|rev: clonefilter/R2_0001.2.fq.gz data_type|dt_select: pair |
name: value name: value |
clonefilter/R1_0001.1.fq.gz clonefilter/R2_0001.2.fq.gz value |
| Test-4 |
data_type|fwd: clonefilter/R1_0001.1.fq.gz data_type|rev: clonefilter/R2_0001.2.fq.gz data_type|dt_select: pair |
name: value name: value |
clonefilter/R1_0001.1.fq.gz clonefilter/R2_0001.2.fq.gz value |