sickle: sickle.xml annotate

annotate sickle.xml @ 6:6756c87dc2d4 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c"

author	iuc
date	Thu, 05 Sep 2019 13:14:23 -0400
parents	3905ccd5c631
children

rev	line source
6 6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	1 <tool id="sickle" name="Sickle" version="1.33.2" profile="17.01">
0 a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	2 <description>windowed adaptive trimming of FASTQ data</description>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	3 <requirements>
2 013275060443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 9cf2e1454bf23a11ca0e7eeb26b4eaa446832bf8-dirty iuc parents: 1 diff changeset	4 <requirement type="package" version="1.33">sickle-trim</requirement>
0 a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	5 </requirements>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	6 <version_command>sickle --version \| head -n 1</version_command>
5 3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	7 <command><![CDATA[
6 6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	8 ## Link in the input files, which also determines the type of the output
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	9 #set compressed = ""
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	10 #if str($readtype.single_or_paired) == "se":
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	11 #if $readtype.input_single.is_of_type('fastq.gz'):
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	12 #set read1 = "input_1.fastq.gz"
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	13 #set compressed = "-g"
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	14 #else
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	15 #set read1 = "input_1.fastq"
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	16 #end if
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	17 ln -f -s '${readtype.input_single}' ${read1} &&
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	18 #else if str($readtype.single_or_paired) == "pe_combo":
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	19 #if $readtype.input_combo.is_of_type('fastq.gz'):
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	20 #set read1 = "input_1.fastq.gz"
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	21 #set compressed = "-g"
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	22 #else
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	23 #set read1 = "input_1.fastq"
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	24 #end if
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	25 ln -f -s '${readtype.input_combo}' ${read1} &&
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	26 #else if str($readtype.single_or_paired) == "pe_sep":
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	27 #if $readtype.input_paired1.is_of_type('fastq.gz'):
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	28 #set read1 = "input_1.fastq.gz"
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	29 #set compressed = "-g"
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	30 #else
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	31 #set read1 = "input_1.fastq"
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	32 #end if
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	33 ln -f -s '${readtype.input_paired1}' ${read1} &&
5 3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	34
6 6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	35 #if $readtype.input_paired2.is_of_type('fastq.gz'):
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	36 #set read2 = "input_2.fastq.gz"
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	37 #else
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	38 #set read2 = "input_2.fastq"
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	39 #end if
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	40 ln -f -s '${readtype.input_paired2}' ${read2} &&
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	41 #else
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	42 #if $readtype.input_paired.forward.is_of_type('fastq.gz'):
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	43 #set read1 = "input_1.fastq.gz"
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	44 #set compressed = "-g"
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	45 #else
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	46 #set read1 = "input_1.fastq"
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	47 #end if
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	48 ln -f -s '${readtype.input_paired.forward}' ${read1} &&
5 3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	49
6 6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	50 #if $readtype.input_paired.reverse.is_of_type('fastq.gz'):
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	51 #set read2 = "input_2.fastq.gz"
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	52 #else
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	53 #set read2 = "input_2.fastq"
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	54 #end if
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	55 ln -f -s '${readtype.input_paired.reverse}' ${read2} &&
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	56 #end if
5 3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	57
6 6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	58 sickle
0 a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	59
6 6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	60 #if str($readtype.single_or_paired) == "se":
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	61 se -f ${read1} -o '${output_single}'
5 3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	62
6 6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	63 #if $readtype.input_single.is_of_type('fastqillumina', 'fastqillumina.gz'):
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	64 -t illumina
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	65 #else if $readtype.input_single.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	66 -t solexa
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	67 #else:
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	68 -t sanger
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	69 #end if
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	70 #else if str($readtype.single_or_paired) == "pe_combo":
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	71 #if $readtype.output_n:
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	72 pe -c ${read1} -M '${output_combo}'
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	73 #else
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	74 pe -c ${read1} -m '${output_combo}' -s '${output_combo_single}'
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	75 #end if
0 a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	76
6 6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	77 #if $readtype.input_combo.is_of_type('fastqillumina', 'fastqillumina.gz'):
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	78 -t illumina
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	79 #else if $readtype.input_combo.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	80 -t solexa
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	81 #else:
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	82 -t sanger
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	83 #end if
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	84 #else if str($readtype.single_or_paired) == "pe_sep":
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	85 pe -f ${read1} -r ${read2} -o '${output_paired1}' -p '${output_paired2}' -s '${output_paired_single}'
5 3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	86
6 6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	87 #if $readtype.input_paired1.is_of_type('fastqillumina', 'fastqillumina.gz'):
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	88 -t illumina
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	89 #else if $readtype.input_paired1.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	90 -t solexa
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	91 #else:
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	92 -t sanger
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	93 #end if
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	94 #else if str($readtype.single_or_paired) == "pe_collection":
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	95 pe -f ${read1} -r ${read2} -o '${output_paired_coll.forward}' -p '${output_paired_coll.reverse}' -s '${output_paired_coll_single}'
5 3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	96
6 6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	97 #if $readtype.input_paired.forward.is_of_type('fastqillumina', 'fastqillumina.gz'):
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	98 -t illumina
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	99 #else if $readtype.input_paired.forward.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	100 -t solexa
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	101 #else:
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	102 -t sanger
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	103 #end if
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	104 #end if
0 a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	105
6 6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	106 $compressed
1 43e081d32f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	107
6 6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	108 #if str($qual_threshold) != "":
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	109 -q $qual_threshold
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	110 #end if
0 a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	111
6 6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	112 #if str($length_threshold) != "":
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	113 -l $length_threshold
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	114 #end if
0 a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	115
6 6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	116 #if $no_five_prime:
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	117 -x
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	118 #end if
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	119
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	120 #if $trunc_n:
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	121 -n
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	122 #end if
6756c87dc2d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	123 ]]></command>
0 a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	124
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	125 <inputs>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	126 <conditional name="readtype">
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	127 <param name="single_or_paired" type="select" label="Single-end or paired-end reads?" help="Note: Sickle will infer the quality type of the file from its datatype. I.e., if the datatype is fastqsanger, then the quality type is sanger. The default is fastqsanger.">
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	128 <option value="se" selected="true">Single-end</option>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	129 <option value="pe_combo">Paired-end (one interleaved input file)</option>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	130 <option value="pe_sep">Paired-end (two separate input files)</option>
1 43e081d32f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	131 <option value="pe_collection">Paired-end (as collection)</option>
0 a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	132 </param>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	133
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	134 <when value="se">
5 3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	135 <param format="fastq,fastq.gz" name="input_single" type="data" label="Single-end FASTQ reads" help="(-f)" />
0 a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	136 </when>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	137
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	138 <when value="pe_combo">
5 3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	139 <param format="fastq,fastq.gz" name="input_combo" type="data" label="Paired-end interleaved FASTQ reads" help="(-c)" />
0 a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	140 <param name="output_n" type="boolean" label="Output only one file with all reads" help="This will output only one file with all the reads, where the reads that did not pass filter will be replaced with a single 'N', rather than discarded."/>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	141 </when>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	142
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	143 <when value="pe_sep">
5 3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	144 <param format="fastq,fastq.gz" name="input_paired1" type="data" label="Paired-end forward strand FASTQ reads" help="(-f)" />
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	145 <param format="fastq,fastq.gz" name="input_paired2" type="data" label="Paired-end reverse strand FASTQ reads" help="(-r)" />
0 a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	146 </when>
1 43e081d32f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	147
43e081d32f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	148 <when value="pe_collection">
5 3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	149 <param format="fastq,fastq.gz" name="input_paired" type="data_collection" collection_type="paired" label="Paired-end FASTQ reads as paired collection" />
1 43e081d32f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	150 </when>
0 a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	151 </conditional>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	152
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	153 <param name="qual_threshold" value="20" min="0" type="integer" optional="true" label="Quality threshold" help="Threshold for trimming based on average quality in a window (-q)" />
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	154
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	155 <param name="length_threshold" value="20" min="0" type="integer" optional="true" label="Length threshold" help="Threshold to keep a read based on length after trimming (-l)" />
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	156
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	157 <param name="no_five_prime" type="boolean" label="Don't do 5' trimming" help="(-x)" />
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	158 <param name="trunc_n" type="boolean" label="Truncate sequences with Ns at first N position" help="(-n)" />
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	159 </inputs>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	160
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	161 <outputs>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	162 <data name="output_single" format_source="input_single" label="Single-end output of ${tool.name} on ${on_string}">
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	163 <filter>readtype['single_or_paired'] == 'se'</filter>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	164 </data>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	165
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	166 <data name="output_combo" format_source="input_combo" label="Paired-end interleaved output of ${tool.name} on ${on_string}">
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	167 <filter>readtype['single_or_paired'] == 'pe_combo'</filter>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	168 </data>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	169
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	170 <data name="output_combo_single" format_source="input_combo" label="Singletons from paired-end interleaved output of ${tool.name} on ${on_string}">
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	171 <filter>readtype['single_or_paired'] == 'pe_combo' and not readtype['output_n']</filter>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	172 </data>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	173
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	174 <data name="output_paired1" format_source="input_paired1" label="Paired-end forward strand output of ${tool.name} on ${on_string}">
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	175 <filter>readtype['single_or_paired'] == 'pe_sep'</filter>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	176 </data>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	177
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	178 <data name="output_paired2" format_source="input_paired2" label="Paired-end reverse strand output of ${tool.name} on ${on_string}">
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	179 <filter>readtype['single_or_paired'] == 'pe_sep'</filter>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	180 </data>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	181
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	182 <data name="output_paired_single" format_source="input_paired1" label="Singletons from paired-end output of ${tool.name} on ${on_string}">
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	183 <filter>readtype['single_or_paired'] == 'pe_sep'</filter>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	184 </data>
1 43e081d32f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	185
43e081d32f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	186 <collection name="output_paired_coll" type="paired" structured_like="input_paired" inherit_format="true" label="Paired-end output of ${tool.name} on ${on_string}">
43e081d32f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	187 <filter>readtype['single_or_paired'] == 'pe_collection'</filter>
43e081d32f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	188 </collection>
43e081d32f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	189
43e081d32f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	190 <data name="output_paired_coll_single" format_source="input_paired['forward']" label="Singletons from paired-end output of ${tool.name} on ${on_string}">
43e081d32f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	191 <filter>readtype['single_or_paired'] == 'pe_collection'</filter>
43e081d32f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	192 </data>
0 a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	193 </outputs>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	194 <tests>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	195 <test>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	196 <param name="single_or_paired" value="pe_combo" />
5 3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	197 <param name="input_combo" ftype="fastqillumina" value="test.fastq" />
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	198 <param name="qual_threshold" value="3" />
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	199 <output name="output_combo" ftype="fastqillumina" file="output.c1.fastq" />
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	200 <output name="output_combo_single" ftype="fastqillumina" file="output.s.fastq" />
0 a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	201 </test>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	202 <test>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	203 <param name="single_or_paired" value="pe_combo" />
5 3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	204 <param name="input_combo" ftype="fastqillumina" value="test.fastq" />
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	205 <param name="qual_threshold" value="3" />
0 a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	206 <param name="output_n" value="true" />
5 3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	207 <output name="output_combo" ftype="fastqillumina" file="output.c2.fastq" />
0 a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	208 </test>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	209 <test>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	210 <param name="single_or_paired" value="pe_sep" />
5 3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	211 <param name="input_paired1" ftype="fastqillumina" value="test.f.fastq" />
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	212 <param name="input_paired2" ftype="fastqillumina" value="test.r.fastq" />
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	213 <param name="qual_threshold" value="3" />
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	214 <output name="output_paired1" ftype="fastqillumina" file="output.f.fastq" />
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	215 <output name="output_paired2" ftype="fastqillumina" file="output.r.fastq" />
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	216 <output name="output_paired_single" ftype="fastqillumina" file="output.s.fastq" />
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	217 </test>
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	218 <test> <!-- as above, but gzipped -->
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	219 <param name="single_or_paired" value="pe_sep" />
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	220 <param name="input_paired1" ftype="fastqillumina.gz" value="test.f.fastq.gz" />
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	221 <param name="input_paired2" ftype="fastqillumina.gz" value="test.r.fastq.gz" />
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	222 <param name="qual_threshold" value="3" />
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	223 <output name="output_paired1" ftype="fastqillumina.gz" file="output.f.fastq.gz" />
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	224 <output name="output_paired2" ftype="fastqillumina.gz" file="output.r.fastq.gz" />
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	225 <output name="output_paired_single" ftype="fastqillumina.gz" file="output.s.fastq.gz" />
1 43e081d32f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	226 </test>
43e081d32f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	227 <test>
43e081d32f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	228 <param name="single_or_paired" value="pe_collection" />
43e081d32f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	229 <param name="input_paired">
43e081d32f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	230 <collection type="paired">
5 3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	231 <element name="forward" ftype="fastqillumina" value="test.f.fastq" />
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	232 <element name="reverse" ftype="fastqillumina" value="test.r.fastq" />
1 43e081d32f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	233 </collection>
43e081d32f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	234 </param>
5 3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	235 <param name="qual_threshold" value="3" />
1 43e081d32f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	236 <output_collection name="output_paired_coll" type="paired">
5 3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	237 <element name="forward" ftype="fastqillumina" file="output.f.fastq" />
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	238 <element name="reverse" ftype="fastqillumina" file="output.r.fastq" />
1 43e081d32f90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	239 </output_collection>
5 3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	240 <output name="output_paired_coll_single" ftype="fastqillumina" file="output.s.fastq" />
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	241 </test>
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	242
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	243 <test> <!-- as above, but gzipped -->
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	244 <param name="single_or_paired" value="pe_collection" />
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	245 <param name="input_paired">
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	246 <collection type="paired">
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	247 <element name="forward" ftype="fastqillumina.gz" value="test.f.fastq.gz" />
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	248 <element name="reverse" ftype="fastqillumina.gz" value="test.r.fastq.gz" />
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	249 </collection>
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	250 </param>
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	251 <param name="qual_threshold" value="3" />
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	252 <output_collection name="output_paired_coll" type="paired">
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	253 <element name="forward" ftype="fastqillumina.gz" file="output.f.fastq.gz" />
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	254 <element name="reverse" ftype="fastqillumina.gz" file="output.r.fastq.gz" />
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	255 </output_collection>
3905ccd5c631 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	256 <output name="output_paired_coll_single" ftype="fastqillumina.gz" file="output.s.fastq.gz" />
0 a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	257 </test>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	258 </tests>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	259 <help>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	260 What it does
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	261
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	262 Most modern sequencing technologies produce reads that have
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	263 deteriorating quality towards the 3'-end and some towards the 5'-end
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	264 as well. Incorrectly called bases in both regions negatively impact
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	265 assembles, mapping, and downstream bioinformatics analyses.
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	266
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	267 Sickle is a tool that uses sliding windows along with quality and
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	268 length thresholds to determine when quality is sufficiently low to
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	269 trim the 3'-end of reads and also determines when the quality is
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	270 sufficiently high enough to trim the 5'-end of reads. It will also
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	271 discard reads based upon the length threshold. It takes the quality
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	272 values and slides a window across them whose length is 0.1 times the
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	273 length of the read. If this length is less than 1, then the window is
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	274 set to be equal to the length of the read. Otherwise, the window
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	275 slides along the quality values until the average quality in the
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	276 window rises above the threshold, at which point the algorithm
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	277 determines where within the window the rise occurs and cuts the read
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	278 and quality there for the 5'-end cut. Then when the average quality
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	279 in the window drops below the threshold, the algorithm determines
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	280 where in the window the drop occurs and cuts both the read and quality
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	281 strings there for the 3'-end cut. However, if the length of the
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	282 remaining sequence is less than the minimum length threshold, then the
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	283 read is discarded entirely (or replaced with an "N" record). 5'-end
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	284 trimming can be disabled. Sickle also has an option to truncate reads
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	285 with Ns at the first N position.
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	286
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	287 Sickle supports three types of quality values: Illumina, Solexa, and
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	288 Sanger. Note that the Solexa quality setting is an approximation (the
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	289 actual conversion is a non-linear transformation). The end
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	290 approximation is close. Illumina quality refers to qualities encoded
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	291 with the CASAVA pipeline between versions 1.3 and 1.7. Illumina
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	292 quality using CASAVA >= 1.8 is Sanger encoded. The quality value will
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	293 be determined from the datatype of the data, i.e. a fastqsanger datatype
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	294 is assumed to be Sanger encoded.
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	295
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	296 Note that Sickle will remove the 2nd FASTQ record header (on the "+"
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	297 line) and replace it with simply a "+". This is the default format for
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	298 CASAVA >= 1.8.
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	299
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	300 -----
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	301
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	302 Options
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	303
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	304 Single-end
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	305
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	306 This option takes one single-end input file and outputs one single-end
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	307 output file of reads that passed the filters.
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	308
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	309 Paired-End (one interleaved input file)
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	310
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	311 This option takes as input one interleaved paired-end file. If you then
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	312 check the "Output only one file with all reads" checkbox, it will output
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	313 one interleaved file where any read that did not pass filter will be replaced
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	314 with a FASTQ record where the sequence is a single "N" and the quality is the
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	315 lowest quality possible for that quality type. This will preserve the paired
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	316 nature of the data. If you leave the checkbox unchecked, it will output two files,
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	317 one interleaved file with all the passed pairs and one singletons file where only
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	318 one of the pair passed filter.
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	319
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	320 Paired-End (two separate input files)
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	321
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	322 This option takes two separate (forward and reverse) paired-end files as input.
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	323 The output is three files: Two paired-end files with pairs that passed filter and
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	324 a singletons file where only one of the pair passed filter.
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	325
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	326 Quality threshold
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	327
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	328 Input your desired quality threshold. This threshold is phred-scaled, which is typically
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	329 values between 0-41 for FASTQ data.
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	330
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	331 Length threshold
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	332
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	333 Input your desired length threshold. This is the threshold to determine if a read is kept
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	334 after all the trimming steps are done.
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	335
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	336 Disable 5-prime trimming
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	337
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	338 An option to disable trimming the read on the 5-prime end. This trimming trims the read
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	339 if the average quality values dip below the quality threshold at the 5-prime end.
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	340
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	341 Truncate sequences with Ns
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	342
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	343 This option will trim a read at the first "N" base in the read after doing quality trimming.
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	344 It is then still subject to the length threshold.
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	345
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	346 -----
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	347
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	348 Copyright: Nikhil Joshi
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	349
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	350 http://github.com/najoshi/sickle
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	351 </help>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	352 <citations>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	353 <citation type="bibtex">
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	354 @unpublished{sickle_link,
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	355 author = {Joshi, Nikhil A. and Fass, Joseph N.},
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	356 title = {Sickle: A windowed adaptive trimming tool for FASTQ files using quality},
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	357 year = 2011,
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	358 url = { https://github.com/najoshi/sickle }
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	359 }
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	360 </citation>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	361 </citations>
a5f56370e870 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	362 </tool>

Mercurial > repos > iuc > sickle

annotate sickle.xml @ 6:6756c87dc2d4 draft default tip