fastp: fastp.xml annotate

annotate fastp.xml @ 4:20c09892cfe7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984

author	iuc
date	Wed, 08 Aug 2018 08:48:49 -0400
parents	5f584c4b0f7e
children	4c14c2f8f4fb

rev	line source
4 20c09892cfe7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	1 <tool id="fastp" name="fastp" version="@WRAPPER_VERSION@.1">
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	2 <description>- fast all-in-one preprocessing for FASTQ files</description>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	3 <macros>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	4 <import>macros.xml</import>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	5 </macros>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	6 <requirements>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	7 <requirement type="package" version="@WRAPPER_VERSION@">fastp</requirement>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	8 </requirements>
3 5f584c4b0f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit d4f5a03011790c36ffd0f698b1e75c80f87fd1bf iuc parents: 1 diff changeset	9 <version_command>fastp -v</version_command>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	10 <command detect_errors="exit_code"><![CDATA[
4 20c09892cfe7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	11 #import re
20c09892cfe7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	12
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	13 ## Link input files
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	14
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	15 #if $in1.is_of_type('fastq.gz')
4 20c09892cfe7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	16 #set ext = '.fastq.gz'
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	17 #else
4 20c09892cfe7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	18 #set ext = '.fastq'
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	19 #end if
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	20
4 20c09892cfe7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	21 #set $in1_name = re.sub('[^\w\-\s]', '_', str($in1.element_identifier)) + $ext
20c09892cfe7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	22 ln -s '$in1' $in1_name &&
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	23
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	24 #if str($single_paired.single_paired_selector) == 'paired':
4 20c09892cfe7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	25 #set $in2_name = re.sub('[^\w\-\s]', '_', str($in2.element_identifier)) + $ext
20c09892cfe7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	26 ln -s '$in2' $in2_name &&
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	27 #end if
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	28
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	29
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	30 ## Run fastp
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	31
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	32 fastp
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	33
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	34 --thread \${GALAXY_SLOTS:-1}
4 20c09892cfe7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	35 --report_title 'fastp report for $in1_name'
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	36
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	37 #if $in1.is_of_type('fastqillumina', 'fastqsolexa', 'fastqillumina.gz', 'fastqsolexa.gz'):
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	38 --phred64
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	39 #end if
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	40
4 20c09892cfe7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	41 -i $in1_name
20c09892cfe7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	42 -o first${ext}
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	43
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	44 #if str($single_paired.single_paired_selector) == 'paired':
4 20c09892cfe7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	45 -I $in2_name
20c09892cfe7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	46 -O second${ext}
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	47 #end if
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	48
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	49
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	50 ## Adapter Trimming Options
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	51
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	52 $single_paired.adapter_trimming_options.disable_adapter_trimming
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	53
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	54 #if str($single_paired.adapter_trimming_options.adapter_sequence1):
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	55 --adapter_sequence '$single_paired.adapter_trimming_options.adapter_sequence1'
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	56 #end if
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	57
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	58 #if str($single_paired.single_paired_selector) == 'paired':
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	59 #if str($single_paired.adapter_trimming_options.adapter_sequence2):
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	60 --adapter_sequence_r2 '$single_paired.adapter_trimming_options.adapter_sequence2'
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	61 #end if
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	62 #end if
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	63
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	64
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	65 ## Global Trimming Options
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	66
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	67 #if str($single_paired.global_trimming_options.trim_front1):
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	68 -f $single_paired.global_trimming_options.trim_front1
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	69 #end if
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	70
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	71 #if str($single_paired.global_trimming_options.trim_tail1):
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	72 -t $single_paired.global_trimming_options.trim_tail1
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	73 #end if
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	74
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	75 #if str($single_paired.single_paired_selector) == 'paired':
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	76 #if str($single_paired.global_trimming_options.trim_front2):
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	77 -F $single_paired.global_trimming_options.trim_front2
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	78 #end if
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	79 #if str($single_paired.global_trimming_options.trim_tail2):
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	80 -T $single_paired.global_trimming_options.trim_tail2
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	81 #end if
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	82 #end if
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	83
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	84
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	85 ## Overrepresented sequence analysis
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	86
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	87 $overrepresented_sequence_analysis.overrepresentation_analysis
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	88
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	89 #if str($overrepresented_sequence_analysis.overrepresentation_sampling):
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	90 -P $overrepresented_sequence_analysis.overrepresentation_sampling
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	91 #end if
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	92
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	93
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	94 ## Filter Options
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	95
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	96 ## Quality filtering options
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	97
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	98 $filter_options.quality_filtering_options.disable_quality_filtering
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	99
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	100 #if str($filter_options.quality_filtering_options.qualified_quality_phred):
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	101 -q $filter_options.quality_filtering_options.qualified_quality_phred
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	102 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	103 #if str($filter_options.quality_filtering_options.unqualified_percent_limit):
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	104 -u $filter_options.quality_filtering_options.unqualified_percent_limit
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	105 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	106 #if str($filter_options.quality_filtering_options.n_base_limit):
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	107 -n $filter_options.quality_filtering_options.n_base_limit
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	108 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	109
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	110
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	111 ## Length filtering options
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	112
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	113 $filter_options.length_filtering_options.disable_length_filtering
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	114
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	115 #if str($filter_options.length_filtering_options.length_required):
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	116 -l $filter_options.length_filtering_options.length_required
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	117 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	118
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	119 ## Low complexity filtering options
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	120
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	121 $filter_options.low_complexity_filter.enable_low_complexity_filter
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	122
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	123 #if str($filter_options.low_complexity_filter.complexity_threshold):
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	124 -Y $filter_options.low_complexity_filter.complexity_threshold
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	125 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	126
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	127
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	128 ## Read Modification Options
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	129
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	130 ## PolyG tail trimming, useful for NextSeq/NovaSeq data
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	131
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	132 #if $read_mod_options.polyg_tail_trimming.trimming_select in ['', '-g']:
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	133 #if str($read_mod_options.polyg_tail_trimming.poly_g_min_len):
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	134 --poly_g_min_len $read_mod_options.polyg_tail_trimming.poly_g_min_len
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	135 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	136 $read_mod_options.polyg_tail_trimming.trimming_select
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	137 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	138
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	139 ## PolyX tail trimming
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	140
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	141 #if $read_mod_options.polyx_tail_trimming.polyx_trimming_select == '-x':
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	142 $read_mod_options.polyx_tail_trimming.polyx_trimming_select
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	143 #if str($read_mod_options.polyg_tail_trimming.poly_g_min_len):
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	144 --poly_x_min_len $read_mod_options.polyx_tail_trimming.poly_x_min_len
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	145 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	146 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	147
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	148 ## UMI processing
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	149
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	150 #if $read_mod_options.umi_processing.umi:
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	151 $read_mod_options.umi_processing.umi
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	152 #if str($read_mod_options.umi_processing.umi_loc):
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	153 --umi_loc '$read_mod_options.umi_processing.umi_loc'
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	154 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	155 #if str($read_mod_options.umi_processing.umi_len):
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	156 --umi_len $read_mod_options.umi_processing.umi_len
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	157 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	158 #if str($read_mod_options.umi_processing.umi_prefix):
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	159 --umi_prefix '$read_mod_options.umi_processing.umi_prefix'
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	160 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	161 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	162
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	163 ## Per read cutting by quality options
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	164
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	165 #if $read_mod_options.cutting_by_quality_options.cut_by_quality5 or $read_mod_options.cutting_by_quality_options.cut_by_quality3:
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	166
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	167 $read_mod_options.cutting_by_quality_options.cut_by_quality5
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	168
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	169 $read_mod_options.cutting_by_quality_options.cut_by_quality3
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	170
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	171 #if str($read_mod_options.cutting_by_quality_options.cut_window_size):
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	172 -W $read_mod_options.cutting_by_quality_options.cut_window_size
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	173 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	174 #if str($read_mod_options.cutting_by_quality_options.cut_mean_quality):
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	175 -M $read_mod_options.cutting_by_quality_options.cut_mean_quality
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	176 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	177 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	178
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	179 ## Base correction by overlap analysis options
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	180
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	181 $read_mod_options.base_correction_options.correction
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	182
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	183 &&
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	184
4 20c09892cfe7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	185 mv first${ext} '${out1}'
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	186 #if str($single_paired.single_paired_selector) == 'paired':
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	187 &&
4 20c09892cfe7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	188 mv second${ext} '${out2}'
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	189 #end if
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	190 ]]></command>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	191 <inputs>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	192
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	193 <conditional name="single_paired">
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	194 <param name="single_paired_selector" type="select" label="Single-end or paired reads">
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	195 <option value="single" selected="true">Single-end</option>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	196 <option value="paired">Paired</option>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	197 </param>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	198 <when value="single">
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	199 <expand macro="in1" />
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	200 <section name="adapter_trimming_options" title="Adapter Trimming Options" expanded="False">
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	201 <param name="disable_adapter_trimming" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false" label="Disable adapter trimming" help="Adapter trimming is enabled by default. If this option is specified, adapter trimming is disabled."/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	202 <expand macro="adapter_sequence1" />
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	203 </section>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	204 <section name="global_trimming_options" title="Global Trimming Options" expanded="False">
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	205 <param name="trim_front1" argument="-f" type="integer" optional="true" label="Trim front for input 1" help="Trimming how many bases in front for read1, default is 0."/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	206 <param name="trim_tail1" argument="-t" type="integer" optional="true" label="Trim tail for input 1" help="Trimming how many bases in tail for read1, default is 0."/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	207 </section>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	208 </when>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	209 <when value="paired">
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	210 <expand macro="in1" />
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	211 <param name="in2" argument="-I" type="data" format="fastq,fastq.gz" optional="true" label="Input 2" help="Input FASTQ file #2."/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	212 <section name="adapter_trimming_options" title="Adapter trimming options" expanded="False">
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	213 <param name="disable_adapter_trimming" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false" label="Disable adapter trimming" help="Adapter trimming is enabled by default. If this option is specified, adapter trimming is disabled."/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	214 <expand macro="adapter_sequence1" />
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	215 <param name="adapter_sequence2" argument="--adapter_sequence_r2" type="text" optional="true" label="Adapter sequence for input 2" help="The adapter for read2 (PE data only). This is used if R1/R2 are found not overlapped. If not specified, it will be the same as adapter sequence value for input 1.">
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	216 <sanitizer>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	217 <valid>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	218 <add value="A"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	219 <add value="T"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	220 <add value="C"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	221 <add value="G"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	222 </valid>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	223 </sanitizer>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	224 </param>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	225 </section>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	226 <section name="global_trimming_options" title="Global trimming options" expanded="False">
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	227 <param name="trim_front1" argument="-f" type="integer" optional="true" label="Trim front for input 1" help="Trimming how many bases in front for read1, default is 0."/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	228 <param name="trim_tail1" argument="-t" type="integer" optional="true" label="Trim tail for input 1" help="Trimming how many bases in tail for read1, default is 0."/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	229 <param name="trim_front2" argument="-F" type="integer" optional="true" label="Trim front for input 2" help="Trimming how many bases in front for read2. If it's not specified, it will follow read1's settings."/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	230 <param name="trim_tail2" argument="-T" type="integer" optional="true" label="Trim tail for input 2" help="Trimming how many bases in tail for read2. If it's not specified, it will follow read1's settings."/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	231 </section>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	232 </when>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	233 </conditional>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	234
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	235 <section name="overrepresented_sequence_analysis" title="Overrepresented Sequence Analysis" expanded="False">
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	236 <param name="overrepresentation_analysis" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="false" label="Enable overrepresented analysis" help="Enable overrepresented sequence analysis."/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	237 <param name="overrepresentation_sampling" argument="-P" type="integer" optional="true" label="Overrepresentation sampling" help="One in (--overrepresentation_sampling) reads will be computed for overrepresentation analysis (1~10000), smaller is slower, default is 20."/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	238 </section>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	239
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	240 <!-- Filter Options -->
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	241 <section name="filter_options" title="Filter Options">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	242 <section name="quality_filtering_options" title="Quality filtering options" expanded="True">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	243 <param name="disable_quality_filtering" argument="-Q" type="boolean" truevalue="-Q" falsevalue="" checked="false" label="Disable quality filtering" help="Quality filtering is enabled by default. If this option is specified, quality filtering is disabled."/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	244 <param name="qualified_quality_phred" argument="-q" type="integer" optional="true" label="Qualified quality phred" help="The quality value that a base is qualified. Default 15 means phred quality >=Q15 is qualified."/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	245 <param name="unqualified_percent_limit" argument="-u" type="integer" optional="true" label="Unqualified percent limit" help="How many percents of bases are allowed to be unqualified (0~100). Default 40 means 40%."/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	246 <param name="n_base_limit" argument="-n" type="integer" optional="true" label="N base limit" help="If one read's number of N base is >n_base_limit, then this read/pair is discarded. Default is 5."/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	247 </section>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	248
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	249 <section name="length_filtering_options" title="Length filtering options" expanded="True">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	250 <param name="disable_length_filtering" argument="-L" type="boolean" truevalue="-L" falsevalue="" checked="false" label="Disable length filtering" help="Length filtering is enabled by default. If this option is specified, length filtering is disabled."/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	251 <param name="length_required" argument="-l" type="integer" optional="true" label="Length required" help="Reads shorter than this value will be discarded. Default is 15."/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	252 </section>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	253
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	254 <section name="low_complexity_filter" title="Low complexity filtering options" expanded="True">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	255 <param name="enable_low_complexity_filter" argument="-y" type="boolean" truevalue="-y" falsevalue="" checked="false" label="Enable low complexity filter" help="The complexity is defined as the percentage of base that is different from its next base, default is No"/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	256 <param name="complexity_threshold" argument="-Y" type="integer" optional="true" label="Complexity threshold" help="Threshold for low complexity filter (0~100). Default is 30, which means 30% complexity is required."/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	257 </section>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	258 </section>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	259
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	260 <!-- Read Modification Options -->
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	261 <section name="read_mod_options" title="Read Modification Options">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	262 <conditional name="polyg_tail_trimming">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	263 <param name="trimming_select" type="select" label="PolyG tail trimming" help="Useful for NextSeq/NovaSeq data">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	264 <option value="" selected="true">Automatic trimming for Illumina NextSeq/NovaSeq data</option>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	265 <option value="-g">Force polyG tail trimming</option>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	266 <option value="-G">Disable polyG tail trimming</option>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	267 </param>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	268 <when value="-g">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	269 <expand macro="poly_g_min_len" />
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	270 </when>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	271 <when value="">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	272 <expand macro="poly_g_min_len" />
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	273 </when>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	274 <when value="-G" />
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	275 </conditional>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	276
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	277 <conditional name="polyx_tail_trimming">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	278 <param name="polyx_trimming_select" type="select" label="PolyX tail trimming" help="Similar to polyG tail trimming. When polyG tail trimming and polyX tail trimming are both enabled, fastp will perform polyG trimming first, then perform polyX trimming. Disabled by default.">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	279 <option value="" selected="true">Disable polyX trimming</option>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	280 <option value="-x">Enable polyX tail trimming</option>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	281 </param>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	282 <when value="-x">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	283 <param name="poly_x_min_len" argument="--poly_x_min_len" type="integer" optional="true" label="PolyX minimum length"
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	284 help="The minimum length to detect polyX in the read tail. 10 by default."/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	285 </when>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	286 <when value="" />
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	287 </conditional>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	288
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	289 <section name="umi_processing" title="UMI processing" expanded="True">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	290 <param name="umi" argument="-U" type="boolean" truevalue="-U" falsevalue="" checked="false" label="Enable unique molecular identifer" help="Enable unique molecular identifer (UMI) preprocessing."/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	291 <param name="umi_loc" argument="--umi_loc" type="text" optional="true" label="UMI location" help="Specify the location of UMI, can be (index1/index2/read1/read2/per_index/per_read, default is none."/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	292 <param name="umi_len" argument="--umi_len" type="integer" optional="true" label="UMI length" help="If the UMI is in read1/read2, its length should be provided."/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	293 <param name="umi_prefix" argument="--umi_prefix" type="text" optional="true" label="UMI prefix" help="If specified, an underline will be used to connect prefix and UMI (i.e. prefix=UMI, UMI=AATTCG, final=UMI_AATTCG). No prefix by default."/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	294 </section>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	295
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	296 <section name="cutting_by_quality_options" title="Per read cutting by quality options" expanded="True">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	297 <param name="cut_by_quality5" argument="-5" type="boolean" truevalue="-5" falsevalue="" checked="false" label="Cut by quality in front (5')" help="Enable per read cutting by quality in front (5'), default is disabled (WARNING: this will interfere deduplication for both PE/SE data)."/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	298 <param name="cut_by_quality3" argument="-3" type="boolean" truevalue="-3" falsevalue="" checked="false" label="Cut by quality in tail (3')" help="Enable per read cutting by quality in tail (3'), default is disabled (WARNING: this will interfere deduplication for SE data)."/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	299 <param name="cut_window_size" argument="-W" type="integer" optional="true" label="Cutting window size" help="The size of the sliding window for sliding window trimming, default is 4."/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	300 <param name="cut_mean_quality" argument="-M" type="integer" optional="true" label="Cutting mean quality" help="The bases in the sliding window with mean quality below cutting_quality will be cut, default is Q20."/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	301 </section>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	302
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	303 <section name="base_correction_options" title="Base correction by overlap analysis options" expanded="True">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	304 <param name="correction" argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Enable base correction" help="Enable base correction in overlapped regions (only for PE data), default is disabled."/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	305 </section>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	306 </section>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	307
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	308 <section name="output_options" title="Output Options" expanded="False">
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	309 <param name="report_html" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Output HTML report" help="fastp provides a QC report for the data Before and After filtering within a single HTML page, which enables comparison of the quality statistics changed by the preprocessing step directly"/>
4 20c09892cfe7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	310 <param name="report_json" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output JSON report" help="The JSON report contains all the data visualized in the HTML report. The format of the JSON report is manually optimized to be easily readable by humans and is compatible with MultiQC"/>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	311 </section>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	312 </inputs>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	313
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	314 <outputs>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	315 <data name="out1" format_source="in1" label="${tool.name} on ${on_string}: Read 1 Output"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	316 <data name="out2" format_source="in2" label="${tool.name} on ${on_string}: Read 2 Output">
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	317 <filter>single_paired['single_paired_selector'] == "paired"</filter>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	318 </data>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	319 <data name="report_html" format="html" from_work_dir="fastp.html" label="${tool.name} on ${on_string}: HTML Report">
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	320 <filter>output_options['report_html'] is True</filter>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	321 </data>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	322 <data name="report_json" format="json" from_work_dir="fastp.json" label="${tool.name} on ${on_string}: JSON Report">
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	323 <filter>output_options['report_json'] is True</filter>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	324 </data>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	325 </outputs>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	326
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	327 <tests>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	328 <!-- Ensure default output works -->
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	329 <test expect_num_outputs="2">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	330 <param name="in1" ftype="fastqsanger" value="R1.fq"/>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	331 <param name="single_paired_selector" value="single"/>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	332 <output name="out1" ftype="fastqsanger" file="out1.fq"/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	333 <output name="report_html">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	334 <assert_contents>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	335 <has_text text="fastp report"/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	336 </assert_contents>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	337 </output>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	338 </test>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	339 <!-- Ensure custom adapter works -->
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	340 <test expect_num_outputs="2">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	341 <param name="in1" ftype="fastq" value="R1.fq"/>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	342 <param name="single_paired_selector" value="single"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	343 <param name="adapter_sequence1" value="ATCG"/>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	344 <output name="out1" ftype="fastq" file="out_a.fq"/>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	345 </test>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	346 <!-- Ensure UMI processing works -->
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	347 <test expect_num_outputs="2">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	348 <param name="in1" ftype="fastq" value="R1.fq"/>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	349 <param name="single_paired_selector" value="single"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	350 <section name="umi_processing">
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	351 <param name="umi" value="true"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	352 <param name="umi_loc" value="read1"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	353 <param name="umi_len" value="8"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	354 </section>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	355 <output name="out1" ftype="fastq" file="out2.fq"/>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	356 </test>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	357 <!-- Ensure UMI processing with different lengths works -->
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	358 <test expect_num_outputs="2">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	359 <param name="in1" ftype="fastq" value="R1.fq"/>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	360 <param name="single_paired_selector" value="single"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	361 <section name="umi_processing">
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	362 <param name="umi" value="true"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	363 <param name="umi_loc" value="read1"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	364 <param name="umi_len" value="12"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	365 </section>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	366 <output name="out1" ftype="fastq" file="out3.fq"/>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	367 </test>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	368 <!-- Ensure paired-end fastq works -->
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	369 <test expect_num_outputs="3">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	370 <param name="in1" ftype="fastq" value="bwa-mem-fastq1.fq"/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	371 <param name="in2" ftype="fastq" value="bwa-mem-fastq2.fq"/>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	372 <param name="single_paired_selector" value="paired"/>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	373 <output name="out1" ftype="fastq" file="out_bwa1.fq"/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	374 <output name="out2" ftype="fastq" file="out_bwa2.fq"/>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	375 </test>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	376 <!-- Ensure paired-end UMI processing of Read 1 works -->
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	377 <test expect_num_outputs="3">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	378 <param name="in1" ftype="fastq" value="bwa-mem-fastq1.fq"/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	379 <param name="in2" ftype="fastq" value="bwa-mem-fastq2.fq"/>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	380 <param name="single_paired_selector" value="paired"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	381 <section name="umi_processing">
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	382 <param name="umi" value="true"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	383 <param name="umi_loc" value="read1"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	384 <param name="umi_len" value="8"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	385 </section>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	386 <output name="out1" ftype="fastq" file="out_bwa_umi_read1_1.fq"/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	387 <output name="out2" ftype="fastq" file="out_bwa_umi_read1_2.fq"/>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	388 </test>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	389 <!-- Ensure paired-end UMI processing of Read 2 works -->
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	390 <test expect_num_outputs="3">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	391 <param name="in1" ftype="fastq" value="bwa-mem-fastq1.fq"/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	392 <param name="in2" ftype="fastq" value="bwa-mem-fastq2.fq"/>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	393 <param name="single_paired_selector" value="paired"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	394 <section name="umi_processing">
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	395 <param name="umi" value="true"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	396 <param name="umi_loc" value="read2"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	397 <param name="umi_len" value="8"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	398 </section>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	399 <output name="out1" ftype="fastq" file="out_bwa_umi_read2_1.fq"/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	400 <output name="out2" ftype="fastq" file="out_bwa_umi_read2_2.fq"/>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	401 </test>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	402 <!-- Ensure JSON report output works -->
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	403 <test expect_num_outputs="2">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	404 <param name="in1" ftype="fastqsanger" value="R1.fq"/>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	405 <param name="single_paired_selector" value="single"/>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	406 <param name="report_html" value="False"/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	407 <param name="report_json" value="True"/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	408 <output name="out1" ftype="fastqsanger" file="out1.fq"/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	409 <output name="report_json">
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	410 <assert_contents>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	411 <has_text text="fastp report"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	412 </assert_contents>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	413 </output>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	414 </test>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	415 <!-- Ensure polyG trimming works -->
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	416 <test expect_num_outputs="2">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	417 <param name="in1" ftype="fastq.gz" value="R1.fq.gz"/>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	418 <param name="single_paired_selector" value="single"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	419 <param name="trimming_select" value="-g"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	420 <param name="poly_g_min_len" value="10"/>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	421 <output name="out1" ftype="fastq.gz" decompress="True" file="out1.fq.gz"/>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	422 </test>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	423 </tests>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	424 <help><![CDATA[
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	425 .. class:: infomark
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	426
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	427 What it does
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	428
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	429 fastp_ is a tool designed to provide fast all-in-one preprocessing for FASTQ files. This tool is developed in C++ with multithreading supported to afford high performance.
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	430
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	431 Features
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	432
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	433 1. Filter out bad reads (too low quality, too short, or too many N...)
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	434
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	435 2. Cut low quality bases for per read in its 5' and 3' by evaluating the mean quality from a sliding window (like Trimmomatic but faster)
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	436
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	437 3. Trim all reads in front and tail
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	438
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	439 4. Cut adapters. Adapter sequences can be automatically detected, which means you don't have to input the adapter sequences to trim them.
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	440
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	441 5. Correct mismatched base pairs in overlapped regions of paired end reads, if one base is with high quality while the other is with ultra-low quality
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	442
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	443 6. Trim polyG in 3' ends, which is commonly seen in NovaSeq/NextSeq data. Trim polyX in 3' ends to remove unwanted polyX tailing (i.e. polyA tailing for mRNA-Seq data)
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	444
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	445 7. Preprocess unique molecular identifer (UMI) enabled data, shift UMI to sequence name
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	446
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	447 8. Report JSON format result for further interpreting
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	448
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	449 9. Visualize quality control and filtering results on a single HTML page (like FASTQC but faster and more informative)
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	450
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	451 10. Split the output to multiple files (0001.R1.gz, 0002.R1.gz...) to support parallel processing. Two modes can be used, limiting the total split file number, or limitting the lines of each split file (Not enabled in this Galaxy tool)
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	452
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	453 11. Support long reads (data from PacBio / Nanopore devices)
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	454
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	455 -----
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	456
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	457 Inputs
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	458
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	459 Single-end or Paired-end FASTQ or FASTQ.GZ reads
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	460
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	461 -----
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	462
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	463 Outputs
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	464
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	465 * Processed reads
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	466
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	467 Optionally, under Output Options you can choose to output
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	468
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	469 * HTML report (default is Yes)
4 20c09892cfe7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	470 * JSON report (compatible with MultiQC)
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	471
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	472 .. _fastp: https://github.com/OpenGene/fastp
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	473
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	474 ]]></help>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	475 <citations>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	476 <citation type="doi">10.1101/274100</citation>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	477 </citations>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	478 </tool>

Mercurial > repos > iuc > fastp

annotate fastp.xml @ 4:20c09892cfe7 draft