sickle: sickle.xml annotate

annotate sickle.xml @ 8:505f8a806d55 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b

author	iuc
date	Tue, 11 Feb 2025 11:01:26 +0000
parents	340de8627f41
children

rev	line source
8 505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	1 <tool id="sickle" name="Sickle" version="1.33.3" profile="23.2" license="MIT">
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	2 <description>Windowed adaptive trimming of FASTQ data</description>
7 340de8627f41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7" iuc parents: 6 diff changeset	3 <xrefs>
340de8627f41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7" iuc parents: 6 diff changeset	4 <xref type="bio.tools">sickle</xref>
340de8627f41 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7" iuc parents: 6 diff changeset	5 </xrefs>
0 15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	6 <requirements>
2 2f8298ffe1ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 9cf2e1454bf23a11ca0e7eeb26b4eaa446832bf8-dirty iuc parents: 1 diff changeset	7 <requirement type="package" version="1.33">sickle-trim</requirement>
0 15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	8 </requirements>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	9 <version_command>sickle --version \| head -n 1</version_command>
5 6a4d7d95fbdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	10 <command><![CDATA[
6 73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	11 ## Link in the input files, which also determines the type of the output
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	12 #set compressed = ""
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	13 #if str($readtype.single_or_paired) == "se":
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	14 #if $readtype.input_single.is_of_type('fastq.gz'):
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	15 #set read1 = "input_1.fastq.gz"
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	16 #set compressed = "-g"
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	17 #else
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	18 #set read1 = "input_1.fastq"
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	19 #end if
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	20 ln -f -s '${readtype.input_single}' ${read1} &&
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	21 #else if str($readtype.single_or_paired) == "pe_combo":
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	22 #if $readtype.input_combo.is_of_type('fastq.gz'):
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	23 #set read1 = "input_1.fastq.gz"
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	24 #set compressed = "-g"
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	25 #else
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	26 #set read1 = "input_1.fastq"
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	27 #end if
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	28 ln -f -s '${readtype.input_combo}' ${read1} &&
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	29 #else if str($readtype.single_or_paired) == "pe_sep":
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	30 #if $readtype.input_paired1.is_of_type('fastq.gz'):
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	31 #set read1 = "input_1.fastq.gz"
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	32 #set compressed = "-g"
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	33 #else
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	34 #set read1 = "input_1.fastq"
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	35 #end if
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	36 ln -f -s '${readtype.input_paired1}' ${read1} &&
5 6a4d7d95fbdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	37
6 73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	38 #if $readtype.input_paired2.is_of_type('fastq.gz'):
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	39 #set read2 = "input_2.fastq.gz"
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	40 #else
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	41 #set read2 = "input_2.fastq"
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	42 #end if
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	43 ln -f -s '${readtype.input_paired2}' ${read2} &&
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	44 #else
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	45 #if $readtype.input_paired.forward.is_of_type('fastq.gz'):
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	46 #set read1 = "input_1.fastq.gz"
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	47 #set compressed = "-g"
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	48 #else
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	49 #set read1 = "input_1.fastq"
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	50 #end if
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	51 ln -f -s '${readtype.input_paired.forward}' ${read1} &&
5 6a4d7d95fbdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	52
6 73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	53 #if $readtype.input_paired.reverse.is_of_type('fastq.gz'):
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	54 #set read2 = "input_2.fastq.gz"
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	55 #else
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	56 #set read2 = "input_2.fastq"
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	57 #end if
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	58 ln -f -s '${readtype.input_paired.reverse}' ${read2} &&
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	59 #end if
5 6a4d7d95fbdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	60
6 73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	61 sickle
0 15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	62
6 73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	63 #if str($readtype.single_or_paired) == "se":
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	64 se -f ${read1} -o '${output_single}'
5 6a4d7d95fbdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	65
6 73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	66 #if $readtype.input_single.is_of_type('fastqillumina', 'fastqillumina.gz'):
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	67 -t illumina
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	68 #else if $readtype.input_single.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	69 -t solexa
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	70 #else:
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	71 -t sanger
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	72 #end if
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	73 #else if str($readtype.single_or_paired) == "pe_combo":
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	74 #if $readtype.output_n:
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	75 pe -c ${read1} -M '${output_combo}'
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	76 #else
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	77 pe -c ${read1} -m '${output_combo}' -s '${output_combo_single}'
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	78 #end if
0 15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	79
6 73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	80 #if $readtype.input_combo.is_of_type('fastqillumina', 'fastqillumina.gz'):
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	81 -t illumina
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	82 #else if $readtype.input_combo.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	83 -t solexa
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	84 #else:
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	85 -t sanger
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	86 #end if
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	87 #else if str($readtype.single_or_paired) == "pe_sep":
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	88 pe -f ${read1} -r ${read2} -o '${output_paired1}' -p '${output_paired2}' -s '${output_paired_single}'
5 6a4d7d95fbdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	89
6 73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	90 #if $readtype.input_paired1.is_of_type('fastqillumina', 'fastqillumina.gz'):
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	91 -t illumina
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	92 #else if $readtype.input_paired1.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	93 -t solexa
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	94 #else:
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	95 -t sanger
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	96 #end if
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	97 #else if str($readtype.single_or_paired) == "pe_collection":
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	98 pe -f ${read1} -r ${read2} -o '${output_paired_coll.forward}' -p '${output_paired_coll.reverse}' -s '${output_paired_coll_single}'
5 6a4d7d95fbdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	99
6 73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	100 #if $readtype.input_paired.forward.is_of_type('fastqillumina', 'fastqillumina.gz'):
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	101 -t illumina
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	102 #else if $readtype.input_paired.forward.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	103 -t solexa
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	104 #else:
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	105 -t sanger
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	106 #end if
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	107 #end if
0 15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	108
6 73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	109 $compressed
1 b14d0191f2c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	110
6 73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	111 #if str($qual_threshold) != "":
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	112 -q $qual_threshold
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	113 #end if
0 15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	114
6 73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	115 #if str($length_threshold) != "":
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	116 -l $length_threshold
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	117 #end if
0 15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	118
6 73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	119 #if $no_five_prime:
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	120 -x
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	121 #end if
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	122
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	123 #if $trunc_n:
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	124 -n
73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	125 #end if
8 505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	126
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	127 #if $log_out
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	128 2>&1 \| tee '${log}'
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	129 #end if
6 73d2fda8a179 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c" iuc parents: 5 diff changeset	130 ]]></command>
0 15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	131
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	132 <inputs>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	133 <conditional name="readtype">
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	134 <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.">
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	135 <option value="se" selected="true">Single-end</option>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	136 <option value="pe_combo">Paired-end (one interleaved input file)</option>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	137 <option value="pe_sep">Paired-end (two separate input files)</option>
1 b14d0191f2c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	138 <option value="pe_collection">Paired-end (as collection)</option>
0 15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	139 </param>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	140
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	141 <when value="se">
8 505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	142 <param format="fastq,fastq.gz" name="input_single" type="data" label="Single-end FASTQ reads" help="(-f)"/>
0 15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	143 </when>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	144
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	145 <when value="pe_combo">
8 505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	146 <param format="fastq,fastq.gz" name="input_combo" type="data" label="Paired-end interleaved FASTQ reads" help="(-c)"/>
0 15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	147 <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."/>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	148 </when>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	149
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	150 <when value="pe_sep">
8 505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	151 <param format="fastq,fastq.gz" name="input_paired1" type="data" label="Paired-end forward strand FASTQ reads" help="(-f)"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	152 <param format="fastq,fastq.gz" name="input_paired2" type="data" label="Paired-end reverse strand FASTQ reads" help="(-r)"/>
0 15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	153 </when>
1 b14d0191f2c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	154
b14d0191f2c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	155 <when value="pe_collection">
8 505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	156 <param format="fastq,fastq.gz" name="input_paired" type="data_collection" collection_type="paired" label="Paired-end FASTQ reads as paired collection"/>
1 b14d0191f2c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	157 </when>
0 15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	158 </conditional>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	159
8 505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	160 <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)"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	161 <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)"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	162 <param name="no_five_prime" type="boolean" label="Don't do 5' trimming" help="(-x)"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	163 <param name="trunc_n" type="boolean" label="Truncate sequences with Ns at first N position" help="(-n)"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	164 <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no"/>
0 15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	165 </inputs>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	166
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	167 <outputs>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	168 <data name="output_single" format_source="input_single" label="Single-end output of ${tool.name} on ${on_string}">
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	169 <filter>readtype['single_or_paired'] == 'se'</filter>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	170 </data>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	171
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	172 <data name="output_combo" format_source="input_combo" label="Paired-end interleaved output of ${tool.name} on ${on_string}">
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	173 <filter>readtype['single_or_paired'] == 'pe_combo'</filter>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	174 </data>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	175
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	176 <data name="output_combo_single" format_source="input_combo" label="Singletons from paired-end interleaved output of ${tool.name} on ${on_string}">
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	177 <filter>readtype['single_or_paired'] == 'pe_combo' and not readtype['output_n']</filter>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	178 </data>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	179
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	180 <data name="output_paired1" format_source="input_paired1" label="Paired-end forward strand output of ${tool.name} on ${on_string}">
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	181 <filter>readtype['single_or_paired'] == 'pe_sep'</filter>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	182 </data>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	183
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	184 <data name="output_paired2" format_source="input_paired2" label="Paired-end reverse strand output of ${tool.name} on ${on_string}">
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	185 <filter>readtype['single_or_paired'] == 'pe_sep'</filter>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	186 </data>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	187
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	188 <data name="output_paired_single" format_source="input_paired1" label="Singletons from paired-end output of ${tool.name} on ${on_string}">
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	189 <filter>readtype['single_or_paired'] == 'pe_sep'</filter>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	190 </data>
1 b14d0191f2c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	191
b14d0191f2c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	192 <collection name="output_paired_coll" type="paired" structured_like="input_paired" inherit_format="true" label="Paired-end output of ${tool.name} on ${on_string}">
b14d0191f2c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	193 <filter>readtype['single_or_paired'] == 'pe_collection'</filter>
b14d0191f2c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	194 </collection>
b14d0191f2c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	195
8 505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	196 <data name="output_paired_coll_single" format_source="input_paired['forward']" label="Singletons from paired-end collection output of ${tool.name} on ${on_string}">
1 b14d0191f2c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	197 <filter>readtype['single_or_paired'] == 'pe_collection'</filter>
b14d0191f2c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	198 </data>
8 505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	199
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	200 <data name="log" format="txt" label="${tool.name} on ${on_string}: Output Log">
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	201 <filter>log_out</filter>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	202 </data>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	203
0 15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	204 </outputs>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	205 <tests>
8 505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	206 <test expect_num_outputs="2">
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	207 <param name="single_or_paired" value="pe_combo"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	208 <param name="input_combo" ftype="fastqillumina" value="test.fastq"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	209 <param name="qual_threshold" value="3"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	210 <output name="output_combo" ftype="fastqillumina" file="output.c1.fastq"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	211 <output name="output_combo_single" ftype="fastqillumina" file="output.s.fastq"/>
0 15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	212 </test>
8 505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	213 <test expect_num_outputs="1">
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	214 <param name="single_or_paired" value="pe_combo"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	215 <param name="input_combo" ftype="fastqillumina" value="test.fastq"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	216 <param name="qual_threshold" value="3"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	217 <param name="output_n" value="true"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	218 <output name="output_combo" ftype="fastqillumina" file="output.c2.fastq"/>
0 15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	219 </test>
8 505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	220 <test expect_num_outputs="3">
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	221 <param name="single_or_paired" value="pe_sep"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	222 <param name="input_paired1" ftype="fastqillumina" value="test.f.fastq"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	223 <param name="input_paired2" ftype="fastqillumina" value="test.r.fastq"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	224 <param name="qual_threshold" value="3"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	225 <output name="output_paired1" ftype="fastqillumina" file="output.f.fastq"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	226 <output name="output_paired2" ftype="fastqillumina" file="output.r.fastq"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	227 <output name="output_paired_single" ftype="fastqillumina" file="output.s.fastq"/>
5 6a4d7d95fbdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	228 </test>
8 505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	229 <test expect_num_outputs="3"> <!-- as above, but gzipped -->
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	230 <param name="single_or_paired" value="pe_sep"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	231 <param name="input_paired1" ftype="fastqillumina.gz" value="test.f.fastq.gz"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	232 <param name="input_paired2" ftype="fastqillumina.gz" value="test.r.fastq.gz"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	233 <param name="qual_threshold" value="3"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	234 <output name="output_paired1" ftype="fastqillumina.gz" file="output.f.fastq.gz"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	235 <output name="output_paired2" ftype="fastqillumina.gz" file="output.r.fastq.gz"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	236 <output name="output_paired_single" ftype="fastqillumina.gz" file="output.s.fastq.gz"/>
1 b14d0191f2c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	237 </test>
8 505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	238 <test expect_num_outputs="4">
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	239 <param name="single_or_paired" value="pe_collection"/>
1 b14d0191f2c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	240 <param name="input_paired">
b14d0191f2c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	241 <collection type="paired">
8 505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	242 <element name="forward" ftype="fastqillumina" value="test.f.fastq"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	243 <element name="reverse" ftype="fastqillumina" value="test.r.fastq"/>
1 b14d0191f2c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	244 </collection>
b14d0191f2c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	245 </param>
8 505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	246 <param name="qual_threshold" value="3"/>
1 b14d0191f2c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	247 <output_collection name="output_paired_coll" type="paired">
8 505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	248 <element name="forward" ftype="fastqillumina" file="output.f.fastq"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	249 <element name="reverse" ftype="fastqillumina" file="output.r.fastq"/>
1 b14d0191f2c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit dc69ff0ee8c53a78d1d378cbe14c604a019bf015 iuc parents: 0 diff changeset	250 </output_collection>
8 505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	251 <output name="output_paired_coll_single" ftype="fastqillumina" file="output.s.fastq"/>
5 6a4d7d95fbdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	252 </test>
8 505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	253 <test expect_num_outputs="4"> <!-- as above, but gzipped -->
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	254 <param name="single_or_paired" value="pe_collection"/>
5 6a4d7d95fbdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	255 <param name="input_paired">
6a4d7d95fbdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	256 <collection type="paired">
8 505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	257 <element name="forward" ftype="fastqillumina.gz" value="test.f.fastq.gz"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	258 <element name="reverse" ftype="fastqillumina.gz" value="test.r.fastq.gz"/>
5 6a4d7d95fbdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	259 </collection>
6a4d7d95fbdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	260 </param>
8 505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	261 <param name="qual_threshold" value="3"/>
5 6a4d7d95fbdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	262 <output_collection name="output_paired_coll" type="paired">
8 505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	263 <element name="forward" ftype="fastqillumina.gz" file="output.f.fastq.gz"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	264 <element name="reverse" ftype="fastqillumina.gz" file="output.r.fastq.gz"/>
5 6a4d7d95fbdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit ac66c0e64af4ca48313478a69d68d0a682d4ab35 iuc parents: 4 diff changeset	265 </output_collection>
8 505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	266 <output name="output_paired_coll_single" ftype="fastqillumina.gz" file="output.s.fastq.gz"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	267 </test>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	268 <test expect_num_outputs="3">
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	269 <param name="single_or_paired" value="pe_combo"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	270 <param name="input_combo" ftype="fastqillumina" value="test.fastq"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	271 <param name="qual_threshold" value="3"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	272 <param name="log_out" value="yes"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	273 <output name="output_combo" ftype="fastqillumina" file="output.c1.fastq"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	274 <output name="output_combo_single" ftype="fastqillumina" file="output.s.fastq"/>
505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	275 <output name="log" file="sickle.log" ftype="txt"/>
0 15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	276 </test>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	277 </tests>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	278 <help>
8 505f8a806d55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit c0d7c69151c3efd66904d47757bdb6ab34c2b39b iuc parents: 7 diff changeset	279
0 15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	280 What it does
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	281
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	282 Most modern sequencing technologies produce reads that have
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	283 deteriorating quality towards the 3'-end and some towards the 5'-end
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	284 as well. Incorrectly called bases in both regions negatively impact
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	285 assembles, mapping, and downstream bioinformatics analyses.
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	286
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	287 Sickle is a tool that uses sliding windows along with quality and
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	288 length thresholds to determine when quality is sufficiently low to
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	289 trim the 3'-end of reads and also determines when the quality is
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	290 sufficiently high enough to trim the 5'-end of reads. It will also
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	291 discard reads based upon the length threshold. It takes the quality
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	292 values and slides a window across them whose length is 0.1 times the
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	293 length of the read. If this length is less than 1, then the window is
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	294 set to be equal to the length of the read. Otherwise, the window
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	295 slides along the quality values until the average quality in the
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	296 window rises above the threshold, at which point the algorithm
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	297 determines where within the window the rise occurs and cuts the read
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	298 and quality there for the 5'-end cut. Then when the average quality
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	299 in the window drops below the threshold, the algorithm determines
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	300 where in the window the drop occurs and cuts both the read and quality
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	301 strings there for the 3'-end cut. However, if the length of the
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	302 remaining sequence is less than the minimum length threshold, then the
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	303 read is discarded entirely (or replaced with an "N" record). 5'-end
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	304 trimming can be disabled. Sickle also has an option to truncate reads
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	305 with Ns at the first N position.
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	306
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	307 Sickle supports three types of quality values: Illumina, Solexa, and
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	308 Sanger. Note that the Solexa quality setting is an approximation (the
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	309 actual conversion is a non-linear transformation). The end
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	310 approximation is close. Illumina quality refers to qualities encoded
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	311 with the CASAVA pipeline between versions 1.3 and 1.7. Illumina
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	312 quality using CASAVA >= 1.8 is Sanger encoded. The quality value will
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	313 be determined from the datatype of the data, i.e. a fastqsanger datatype
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	314 is assumed to be Sanger encoded.
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	315
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	316 Note that Sickle will remove the 2nd FASTQ record header (on the "+"
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	317 line) and replace it with simply a "+". This is the default format for
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	318 CASAVA >= 1.8.
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	319
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	320 -----
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	321
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	322 Options
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	323
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	324 Single-end
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	325
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	326 This option takes one single-end input file and outputs one single-end
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	327 output file of reads that passed the filters.
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	328
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	329 Paired-End (one interleaved input file)
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	330
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	331 This option takes as input one interleaved paired-end file. If you then
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	332 check the "Output only one file with all reads" checkbox, it will output
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	333 one interleaved file where any read that did not pass filter will be replaced
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	334 with a FASTQ record where the sequence is a single "N" and the quality is the
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	335 lowest quality possible for that quality type. This will preserve the paired
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	336 nature of the data. If you leave the checkbox unchecked, it will output two files,
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	337 one interleaved file with all the passed pairs and one singletons file where only
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	338 one of the pair passed filter.
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	339
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	340 Paired-End (two separate input files)
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	341
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	342 This option takes two separate (forward and reverse) paired-end files as input.
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	343 The output is three files: Two paired-end files with pairs that passed filter and
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	344 a singletons file where only one of the pair passed filter.
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	345
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	346 Quality threshold
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	347
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	348 Input your desired quality threshold. This threshold is phred-scaled, which is typically
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	349 values between 0-41 for FASTQ data.
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	350
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	351 Length threshold
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	352
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	353 Input your desired length threshold. This is the threshold to determine if a read is kept
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	354 after all the trimming steps are done.
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	355
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	356 Disable 5-prime trimming
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	357
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	358 An option to disable trimming the read on the 5-prime end. This trimming trims the read
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	359 if the average quality values dip below the quality threshold at the 5-prime end.
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	360
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	361 Truncate sequences with Ns
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	362
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	363 This option will trim a read at the first "N" base in the read after doing quality trimming.
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	364 It is then still subject to the length threshold.
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	365
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	366 -----
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	367
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	368 Copyright: Nikhil Joshi
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	369
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	370 http://github.com/najoshi/sickle
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	371 </help>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	372 <citations>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	373 <citation type="bibtex">
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	374 @unpublished{sickle_link,
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	375 author = {Joshi, Nikhil A. and Fass, Joseph N.},
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	376 title = {Sickle: A windowed adaptive trimming tool for FASTQ files using quality},
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	377 year = 2011,
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	378 url = { https://github.com/najoshi/sickle }
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	379 }
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	380 </citation>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	381 </citations>
15cb7dc0ed41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 128d3f255f00c47fa2b16d9b7432d48a089660c1 iuc parents: diff changeset	382 </tool>

Mercurial > repos > iuc > sickle

annotate sickle.xml @ 8:505f8a806d55 draft default tip