| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/sickle/sickle/1.33.3 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/sickle/sickle/1.33.2 |
| toolshed.g2.bx.psu.edu/repos/iuc/sickle/sickle/1.33.1 |
| toolshed.g2.bx.psu.edu/repos/iuc/sickle/sickle/1.33 |
| sickle |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| sickle-trim | 1.33 | package |
| Additional information about this tool |
## Link in the input files, which also determines the type of the output
#set compressed = ""
#if str($readtype.single_or_paired) == "se":
#if $readtype.input_single.is_of_type('fastq.gz'):
#set read1 = "input_1.fastq.gz"
#set compressed = "-g"
#else
#set read1 = "input_1.fastq"
#end if
ln -f -s '${readtype.input_single}' ${read1} &&
#else if str($readtype.single_or_paired) == "pe_combo":
#if $readtype.input_combo.is_of_type('fastq.gz'):
#set read1 = "input_1.fastq.gz"
#set compressed = "-g"
#else
#set read1 = "input_1.fastq"
#end if
ln -f -s '${readtype.input_combo}' ${read1} &&
#else if str($readtype.single_or_paired) == "pe_sep":
#if $readtype.input_paired1.is_of_type('fastq.gz'):
#set read1 = "input_1.fastq.gz"
#set compressed = "-g"
#else
#set read1 = "input_1.fastq"
#end if
ln -f -s '${readtype.input_paired1}' ${read1} &&
#if $readtype.input_paired2.is_of_type('fastq.gz'):
#set read2 = "input_2.fastq.gz"
#else
#set read2 = "input_2.fastq"
#end if
ln -f -s '${readtype.input_paired2}' ${read2} &&
#else
#if $readtype.input_paired.forward.is_of_type('fastq.gz'):
#set read1 = "input_1.fastq.gz"
#set compressed = "-g"
#else
#set read1 = "input_1.fastq"
#end if
ln -f -s '${readtype.input_paired.forward}' ${read1} &&
#if $readtype.input_paired.reverse.is_of_type('fastq.gz'):
#set read2 = "input_2.fastq.gz"
#else
#set read2 = "input_2.fastq"
#end if
ln -f -s '${readtype.input_paired.reverse}' ${read2} &&
#end if
sickle
#if str($readtype.single_or_paired) == "se":
se -f ${read1} -o '${output_single}'
#if $readtype.input_single.is_of_type('fastqillumina', 'fastqillumina.gz'):
-t illumina
#else if $readtype.input_single.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
-t solexa
#else:
-t sanger
#end if
#else if str($readtype.single_or_paired) == "pe_combo":
#if $readtype.output_n:
pe -c ${read1} -M '${output_combo}'
#else
pe -c ${read1} -m '${output_combo}' -s '${output_combo_single}'
#end if
#if $readtype.input_combo.is_of_type('fastqillumina', 'fastqillumina.gz'):
-t illumina
#else if $readtype.input_combo.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
-t solexa
#else:
-t sanger
#end if
#else if str($readtype.single_or_paired) == "pe_sep":
pe -f ${read1} -r ${read2} -o '${output_paired1}' -p '${output_paired2}' -s '${output_paired_single}'
#if $readtype.input_paired1.is_of_type('fastqillumina', 'fastqillumina.gz'):
-t illumina
#else if $readtype.input_paired1.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
-t solexa
#else:
-t sanger
#end if
#else if str($readtype.single_or_paired) == "pe_collection":
pe -f ${read1} -r ${read2} -o '${output_paired_coll.forward}' -p '${output_paired_coll.reverse}' -s '${output_paired_coll_single}'
#if $readtype.input_paired.forward.is_of_type('fastqillumina', 'fastqillumina.gz'):
-t illumina
#else if $readtype.input_paired.forward.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
-t solexa
#else:
-t sanger
#end if
#end if
$compressed
#if str($qual_threshold) != "":
-q $qual_threshold
#end if
#if str($length_threshold) != "":
-l $length_threshold
#end if
#if $no_five_prime:
-x
#end if
#if $trunc_n:
-n
#end if
#if $log_out
2>&1 | tee '${log}'
#end if
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
readtype|input_combo: test.fastq readtype|single_or_paired: pe_combo qual_threshold: 3 |
name: value name: value |
test.fastq value |
| Test-2 |
readtype|input_combo: test.fastq readtype|output_n: True readtype|single_or_paired: pe_combo qual_threshold: 3 |
name: value |
test.fastq value |
| Test-3 |
readtype|input_paired1: test.f.fastq readtype|input_paired2: test.r.fastq readtype|single_or_paired: pe_sep qual_threshold: 3 |
name: value name: value name: value |
test.f.fastq test.r.fastq value |
| Test-4 |
readtype|input_paired1: test.f.fastq.gz readtype|input_paired2: test.r.fastq.gz readtype|single_or_paired: pe_sep qual_threshold: 3 |
name: value name: value name: value |
test.f.fastq.gz test.r.fastq.gz value |
| Test-5 |
readtype|input_paired: paired collection readtype|single_or_paired: pe_collection qual_threshold: 3 |
name: value |
test.f.fastq test.r.fastq value |
| Test-6 |
readtype|input_paired: paired collection readtype|single_or_paired: pe_collection qual_threshold: 3 |
name: value |
test.f.fastq.gz test.r.fastq.gz value |
| Test-7 |
readtype|input_combo: test.fastq readtype|single_or_paired: pe_combo qual_threshold: 3 log_out: True |
name: value name: value name: value |
test.fastq value |