Repository revision
11:be78e39d56b3

Repository 'stacks_procrad'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad

Stacks: process radtags tool metadata
Miscellaneous
the Stacks demultiplexing script
stacks_procrad
toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.46.0
1.46.0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.46.0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.42.0
toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.40.2
toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.40.1
stacks_procrad
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 $input_type.options_type_selector == "single"

            #if $input_type.input_single.is_of_type('fastqsanger')
                #set $ext = ".fq"
                #set inputype = "fastq"
            #else
                #set $ext = ".fq.gz"
                #set inputype = "gzfastq"
            #end if

            ln -s '$input_type.input_single' R1$ext &&
        #else

            #if $input_type.inputs_paired1.is_of_type('fastqsanger')
                #set $ext = ".fq"
                #set inputype = "fastq"
            #else
                #set $ext = ".fq.gz"
                #set inputype = "gzfastq"
            #end if

            ln -s '$input_type.inputs_paired1' R1$ext &&
            ln -s '$input_type.inputs_paired2' R2$ext &&
        #end if

        mkdir stacks_outputs

        &&

        process_radtags

            #if $input_type.options_type_selector == "single"
                -f R1$ext
            #else
                -1 R1$ext
                -2 R2$ext
            #end if

            -i $inputype
            -b '$barcode'

            $input_type.barcode_encoding

            #if str( $options_enzyme.options_enzyme_selector ) == "1"
                -e $options_enzyme.enzyme
            #else
                --renz_1 $options_enzyme.enzyme --renz_2 $options_enzyme.enzyme2
            #end if

            #if str( $outype ) != "auto"
                -y $outype
            #end if

            $capture

            $options_advanced.retain_header

            #if str($options_advanced.truncate)
                -t $options_advanced.truncate
            #end if

            -w $options_advanced.sliding

            $options_advanced.remove

            $options_advanced.discard
            -s $options_advanced.score

            $options_advanced.rescue

            -o stacks_outputs
    
None
False
Functional tests
name inputs outputs required files
Test-1 input_type|input_single: procrad/R1.fq
input_type|options_type_selector: single
barcode: procrad/barcodes
options_enzyme|enzyme: ecoRI
options_enzyme|options_enzyme_selector: 1
capture: True
options_advanced|discard: True
name: value
procrad/R1.fq
procrad/barcodes
value
Test-2 input_type|input_single: procrad/R1.fq
input_type|options_type_selector: single
barcode: procrad/barcodes
options_enzyme|enzyme: ecoRI
options_enzyme|options_enzyme_selector: 1
capture: True
options_advanced|discard: True
outype: gzfastq
name: value
procrad/R1.fq
procrad/barcodes
value
Test-3 input_type|inputs_paired1: procrad/R1.fq
input_type|inputs_paired2: procrad/R2.fq
input_type|options_type_selector: paired
barcode: procrad/barcodes
options_enzyme|enzyme: ecoRI
options_enzyme|options_enzyme_selector: 1
capture: True
options_advanced|discard: True
name: value
procrad/R1.fq
procrad/R2.fq
procrad/barcodes
value
Test-4 input_type|inputs_paired1: procrad/R1.fq
input_type|inputs_paired2: procrad/R2.fq
input_type|options_type_selector: paired
barcode: procrad/barcodes
options_enzyme|enzyme: ecoRI
options_enzyme|options_enzyme_selector: 1
capture: True
options_advanced|discard: True
options_advanced|retain_header: True
name: value
procrad/R1.fq
procrad/R2.fq
procrad/barcodes
value
Test-5 input_type|inputs_paired1: procrad/R1.fq
input_type|inputs_paired2: procrad/R2.fq
input_type|options_type_selector: paired
barcode: procrad/barcodes
options_enzyme|enzyme: ecoRI
options_enzyme|options_enzyme_selector: 1
capture: True
options_advanced|discard: True
outype: fasta
name: value
procrad/R1.fq
procrad/R2.fq
procrad/barcodes
value
Test-6 input_type|input_single: procrad/R1.fq.gzip
input_type|options_type_selector: single
barcode: procrad/barcodes
options_enzyme|enzyme: ecoRI
options_enzyme|options_enzyme_selector: 1
capture: True
options_advanced|discard: True
name: value
procrad/R1.fq.gzip
procrad/barcodes
value
Test-7 input_type|input_single: procrad/R1.fq.gzip
input_type|options_type_selector: single
barcode: procrad/barcodes
options_enzyme|enzyme: ecoRI
options_enzyme|options_enzyme_selector: 1
capture: True
options_advanced|discard: True
outype: gzfastq
name: value
procrad/R1.fq.gzip
procrad/barcodes
value