fastp: fastp.xml annotate

annotate fastp.xml @ 4:7c82cb2a90c4 draft

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

author	iuc
date	Wed, 08 Aug 2018 08:49:26 -0400
parents	e0b44bf2543e
children	3e2551a37201

rev	line source
4 7c82cb2a90c4 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 988729b728f0 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>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	3 <macros>
988729b728f0 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>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	5 </macros>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	6 <requirements>
988729b728f0 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>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	8 </requirements>
3 e0b44bf2543e 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 988729b728f0 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 7c82cb2a90c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	11 #import re
7c82cb2a90c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	12
0 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	13 ## Link input files
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	14
988729b728f0 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 7c82cb2a90c4 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 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	17 #else
4 7c82cb2a90c4 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 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	19 #end if
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	20
4 7c82cb2a90c4 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)) + $ext
7c82cb2a90c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	22 ln -s '$in1' $in1_name &&
0 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	23
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	24 #if str($single_paired.single_paired_selector) == 'paired':
4 7c82cb2a90c4 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)) + $ext
7c82cb2a90c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	26 ln -s '$in2' $in2_name &&
0 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	27 #end if
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	28
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	29
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	30 ## Run fastp
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	31
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	32 fastp
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	33
1 f44e93b4529c 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 7c82cb2a90c4 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 f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	36
0 988729b728f0 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'):
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	38 --phred64
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	39 #end if
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	40
4 7c82cb2a90c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	41 -i $in1_name
7c82cb2a90c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	42 -o first${ext}
0 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	43
988729b728f0 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 7c82cb2a90c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	45 -I $in2_name
7c82cb2a90c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	46 -O second${ext}
0 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	47 #end if
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	48
1 f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	49
f44e93b4529c 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 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	51
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	52 $single_paired.adapter_trimming_options.disable_adapter_trimming
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	53
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	54 #if str($single_paired.adapter_trimming_options.adapter_sequence1):
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	55 --adapter_sequence '$single_paired.adapter_trimming_options.adapter_sequence1'
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	56 #end if
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	57
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	58 #if str($single_paired.single_paired_selector) == 'paired':
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	59 #if str($single_paired.adapter_trimming_options.adapter_sequence2):
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	60 --adapter_sequence_r2 '$single_paired.adapter_trimming_options.adapter_sequence2'
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	61 #end if
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	62 #end if
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	63
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	64
1 f44e93b4529c 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 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	66
988729b728f0 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):
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	68 -f $single_paired.global_trimming_options.trim_front1
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	69 #end if
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	70
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	71 #if str($single_paired.global_trimming_options.trim_tail1):
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	72 -t $single_paired.global_trimming_options.trim_tail1
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	73 #end if
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	74
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	75 #if str($single_paired.single_paired_selector) == 'paired':
988729b728f0 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):
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	77 -F $single_paired.global_trimming_options.trim_front2
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	78 #end if
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	79 #if str($single_paired.global_trimming_options.trim_tail2):
988729b728f0 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
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	81 #end if
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	82 #end if
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	83
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	84
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	85 ## Overrepresented sequence analysis
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	86
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	87 $overrepresented_sequence_analysis.overrepresentation_analysis
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	88
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	89 #if str($overrepresented_sequence_analysis.overrepresentation_sampling):
988729b728f0 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
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	91 #end if
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	92
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	93
1 f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	94 ## Filter Options
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	95
f44e93b4529c 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
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	97
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	98 $filter_options.quality_filtering_options.disable_quality_filtering
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	99
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	100 #if str($filter_options.quality_filtering_options.qualified_quality_phred):
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	101 -q $filter_options.quality_filtering_options.qualified_quality_phred
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	102 #end if
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	103 #if str($filter_options.quality_filtering_options.unqualified_percent_limit):
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	104 -u $filter_options.quality_filtering_options.unqualified_percent_limit
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	105 #end if
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	106 #if str($filter_options.quality_filtering_options.n_base_limit):
f44e93b4529c 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
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	108 #end if
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	109
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	110
f44e93b4529c 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
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	112
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	113 $filter_options.length_filtering_options.disable_length_filtering
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	114
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	115 #if str($filter_options.length_filtering_options.length_required):
f44e93b4529c 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
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	117 #end if
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	118
f44e93b4529c 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
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	120
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	121 $filter_options.low_complexity_filter.enable_low_complexity_filter
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	122
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	123 #if str($filter_options.low_complexity_filter.complexity_threshold):
f44e93b4529c 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
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	125 #end if
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	126
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	127
f44e93b4529c 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
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	129
f44e93b4529c 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
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	131
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	132 #if $read_mod_options.polyg_tail_trimming.trimming_select in ['', '-g']:
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	133 #if str($read_mod_options.polyg_tail_trimming.poly_g_min_len):
f44e93b4529c 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
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	135 #end if
f44e93b4529c 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
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	137 #end if
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	138
f44e93b4529c 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
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	140
f44e93b4529c 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':
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	142 $read_mod_options.polyx_tail_trimming.polyx_trimming_select
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	143 #if str($read_mod_options.polyg_tail_trimming.poly_g_min_len):
f44e93b4529c 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
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	145 #end if
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	146 #end if
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	147
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	148 ## UMI processing
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	149
f44e93b4529c 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:
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	151 $read_mod_options.umi_processing.umi
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	152 #if str($read_mod_options.umi_processing.umi_loc):
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	153 --umi_loc '$read_mod_options.umi_processing.umi_loc'
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	154 #end if
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	155 #if str($read_mod_options.umi_processing.umi_len):
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	156 --umi_len $read_mod_options.umi_processing.umi_len
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	157 #end if
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	158 #if str($read_mod_options.umi_processing.umi_prefix):
f44e93b4529c 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'
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	160 #end if
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	161 #end if
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	162
f44e93b4529c 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
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	164
f44e93b4529c 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:
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	166
f44e93b4529c 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
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	168
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	169 $read_mod_options.cutting_by_quality_options.cut_by_quality3
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	170
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	171 #if str($read_mod_options.cutting_by_quality_options.cut_window_size):
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	172 -W $read_mod_options.cutting_by_quality_options.cut_window_size
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	173 #end if
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	174 #if str($read_mod_options.cutting_by_quality_options.cut_mean_quality):
f44e93b4529c 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
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	176 #end if
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	177 #end if
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	178
f44e93b4529c 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
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	180
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	181 $read_mod_options.base_correction_options.correction
0 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	182
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	183 &&
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	184
4 7c82cb2a90c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	185 mv first${ext} '${out1}'
0 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	186 #if str($single_paired.single_paired_selector) == 'paired':
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	187 &&
4 7c82cb2a90c4 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 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	189 #end if
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	190 ]]></command>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	191 <inputs>
1 f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	192
0 988729b728f0 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">
988729b728f0 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">
988729b728f0 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>
988729b728f0 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>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	197 </param>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	198 <when value="single">
988729b728f0 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 f44e93b4529c 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 988729b728f0 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."/>
988729b728f0 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" />
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	203 </section>
1 f44e93b4529c 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 988729b728f0 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."/>
988729b728f0 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."/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	207 </section>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	208 </when>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	209 <when value="paired">
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	210 <expand macro="in1" />
988729b728f0 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."/>
988729b728f0 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">
988729b728f0 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."/>
988729b728f0 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" />
988729b728f0 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.">
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	216 <sanitizer>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	217 <valid>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	218 <add value="A"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	219 <add value="T"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	220 <add value="C"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	221 <add value="G"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	222 </valid>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	223 </sanitizer>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	224 </param>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	225 </section>
988729b728f0 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">
988729b728f0 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."/>
988729b728f0 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."/>
988729b728f0 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."/>
988729b728f0 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."/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	231 </section>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	232 </when>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	233 </conditional>
1 f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	234
f44e93b4529c 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 988729b728f0 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."/>
988729b728f0 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."/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	238 </section>
1 f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	239
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	240 <!-- Filter Options -->
f44e93b4529c 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">
f44e93b4529c 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">
f44e93b4529c 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."/>
f44e93b4529c 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."/>
f44e93b4529c 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%."/>
f44e93b4529c 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."/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	247 </section>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	248
f44e93b4529c 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">
f44e93b4529c 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."/>
f44e93b4529c 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."/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	252 </section>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	253
f44e93b4529c 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">
f44e93b4529c 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"/>
f44e93b4529c 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."/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	257 </section>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	258 </section>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	259
f44e93b4529c 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 -->
f44e93b4529c 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">
f44e93b4529c 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">
f44e93b4529c 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">
f44e93b4529c 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>
f44e93b4529c 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>
f44e93b4529c 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>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	267 </param>
f44e93b4529c 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">
f44e93b4529c 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" />
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	270 </when>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	271 <when value="">
f44e93b4529c 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" />
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	273 </when>
f44e93b4529c 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" />
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	275 </conditional>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	276
f44e93b4529c 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">
f44e93b4529c 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.">
f44e93b4529c 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>
f44e93b4529c 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>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	281 </param>
f44e93b4529c 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">
f44e93b4529c 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"
f44e93b4529c 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."/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	285 </when>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	286 <when value="" />
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	287 </conditional>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	288
f44e93b4529c 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">
f44e93b4529c 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."/>
f44e93b4529c 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."/>
f44e93b4529c 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."/>
f44e93b4529c 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."/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	294 </section>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	295
f44e93b4529c 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">
f44e93b4529c 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)."/>
f44e93b4529c 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)."/>
f44e93b4529c 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."/>
f44e93b4529c 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."/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	301 </section>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	302
f44e93b4529c 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">
f44e93b4529c 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."/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	305 </section>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	306 </section>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	307
f44e93b4529c 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 988729b728f0 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 7c82cb2a90c4 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 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	311 </section>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	312 </inputs>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	313
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	314 <outputs>
988729b728f0 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 ${on_string}: Read 1 Output"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	316 <data name="out2" format_source="in2" label="${tool.name} on ${on_string}: Read 2 Output">
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	317 <filter>single_paired['single_paired_selector'] == "paired"</filter>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	318 </data>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	319 <data name="report_html" format="html" from_work_dir="fastp.html" label="${tool.name} on ${on_string}: HTML Report">
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	320 <filter>output_options['report_html'] is True</filter>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	321 </data>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	322 <data name="report_json" format="json" from_work_dir="fastp.json" label="${tool.name} on ${on_string}: JSON Report">
988729b728f0 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>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	324 </data>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	325 </outputs>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	326
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	327 <tests>
1 f44e93b4529c 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 -->
f44e93b4529c 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">
f44e93b4529c 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 988729b728f0 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 f44e93b4529c 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"/>
f44e93b4529c 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">
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	334 <assert_contents>
f44e93b4529c 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"/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	336 </assert_contents>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	337 </output>
0 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	338 </test>
1 f44e93b4529c 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 -->
f44e93b4529c 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">
f44e93b4529c 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 988729b728f0 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"/>
988729b728f0 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 f44e93b4529c 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 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	345 </test>
1 f44e93b4529c 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 -->
f44e93b4529c 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">
f44e93b4529c 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 988729b728f0 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"/>
988729b728f0 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">
988729b728f0 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"/>
988729b728f0 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"/>
988729b728f0 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"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	354 </section>
1 f44e93b4529c 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 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	356 </test>
1 f44e93b4529c 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 -->
f44e93b4529c 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">
f44e93b4529c 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 988729b728f0 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"/>
988729b728f0 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">
988729b728f0 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"/>
988729b728f0 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"/>
988729b728f0 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"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	365 </section>
1 f44e93b4529c 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 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	367 </test>
1 f44e93b4529c 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 -->
f44e93b4529c 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">
f44e93b4529c 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"/>
f44e93b4529c 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 988729b728f0 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 f44e93b4529c 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"/>
f44e93b4529c 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 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	375 </test>
1 f44e93b4529c 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 -->
f44e93b4529c 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">
f44e93b4529c 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"/>
f44e93b4529c 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 988729b728f0 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"/>
988729b728f0 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">
988729b728f0 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"/>
988729b728f0 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"/>
988729b728f0 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"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	385 </section>
1 f44e93b4529c 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"/>
f44e93b4529c 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 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	388 </test>
1 f44e93b4529c 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 -->
f44e93b4529c 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">
f44e93b4529c 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"/>
f44e93b4529c 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 988729b728f0 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"/>
988729b728f0 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">
988729b728f0 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"/>
988729b728f0 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"/>
988729b728f0 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"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	398 </section>
1 f44e93b4529c 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"/>
f44e93b4529c 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 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	401 </test>
1 f44e93b4529c 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 -->
f44e93b4529c 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">
f44e93b4529c 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 988729b728f0 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 f44e93b4529c 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"/>
f44e93b4529c 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"/>
f44e93b4529c 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"/>
f44e93b4529c 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 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	410 <assert_contents>
988729b728f0 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"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	412 </assert_contents>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	413 </output>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	414 </test>
1 f44e93b4529c 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 -->
f44e93b4529c 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">
f44e93b4529c 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 988729b728f0 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"/>
988729b728f0 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"/>
988729b728f0 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 f44e93b4529c 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 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	422 </test>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	423 </tests>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	424 <help><![CDATA[
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	425 .. class:: infomark
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	426
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	427 What it does
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	428
988729b728f0 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.
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	430
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	431 Features
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	432
988729b728f0 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...)
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	434
1 f44e93b4529c 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 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	436
988729b728f0 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
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	438
1 f44e93b4529c 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.
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	440
f44e93b4529c 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 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	442
1 f44e93b4529c 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 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	444
1 f44e93b4529c 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 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	446
1 f44e93b4529c 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 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	448
1 f44e93b4529c 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 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	450
1 f44e93b4529c 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 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	452
1 f44e93b4529c 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 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	454
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	455 -----
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	456
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	457 Inputs
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	458
988729b728f0 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
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	460
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	461 -----
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	462
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	463 Outputs
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	464
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	465 * Processed reads
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	466
988729b728f0 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
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	468
988729b728f0 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 7c82cb2a90c4 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 988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	471
988729b728f0 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
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	473
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	474 ]]></help>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	475 <citations>
988729b728f0 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>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	477 </citations>
988729b728f0 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 @ 4:7c82cb2a90c4 draft