fastp: fastp.xml annotate

annotate fastp.xml @ 20:7e30f4d7077d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a

author	iuc
date	Sun, 19 Oct 2025 07:26:44 +0000
parents	046512eda8c0
children

rev	line source
20 7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	1 <tool id="fastp" name="fastp" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1">
11 d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	2 <description>fast all-in-one preprocessing for FASTQ files</description>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	3 <macros>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	4 <import>macros.xml</import>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	5 </macros>
11 d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	6 <expand macro="biotools" />
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	7 <requirements>
11 d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	8 <requirement type="package" version="@TOOL_VERSION@">fastp</requirement>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	9 </requirements>
3 5f584c4b0f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit d4f5a03011790c36ffd0f698b1e75c80f87fd1bf iuc parents: 1 diff changeset	10 <version_command>fastp -v</version_command>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	11 <command detect_errors="exit_code"><![CDATA[
4 20c09892cfe7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	12 #import re
20c09892cfe7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	13
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	14 ## Link input files
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	15
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	16 #set ext = '.fastqsanger'
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	17
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	18 #if $single_paired.single_paired_selector == 'paired_collection'
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	19 #if $single_paired.paired_input.forward.is_of_type('fastqsanger.gz')
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	20 #set ext = '.fastqsanger.gz'
5 4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	21 #end if
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	22 #set $in1 = $single_paired.paired_input.forward
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	23 #set $in2 = $single_paired.paired_input.reverse
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	24 #set $in1_name = re.sub('[^\w\-\s]', '_', str($single_paired.paired_input.name)) + $ext
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	25 #set $in2_name = re.sub('[^\w\-\s]', '_', str("%s_%s" % ($single_paired.paired_input.name, "R2"))) + $ext
11 d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	26 ln -sf '$in1' '$in1_name' &&
d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	27 ln -sf '$in2' '$in2_name' &&
5 4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	28 #else
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	29 #if $in1.is_of_type('fastqsanger.gz')
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	30 #set ext = '.fastqsanger.gz'
5 4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	31 #end if
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	32
5 4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	33 #set $in1_name = re.sub('[^\w\-\s]', '_', str($in1.element_identifier)) + $ext
11 d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	34 ln -sf '$in1' '$in1_name' &&
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	35 #end if
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	36
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	37 ## Run fastp
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	38
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	39 fastp
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	40
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	41 --thread \${GALAXY_SLOTS:-1}
4 20c09892cfe7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	42 --report_title 'fastp report for $in1_name'
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	43
5 4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	44 -i '$in1_name'
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	45
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	46 ## Merge reads
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	47
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	48 #if str($single_paired.single_paired_selector).startswith('paired')
5 4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	49 -I '$in2_name'
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	50 #if $single_paired.merge_reads.merge
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	51 $single_paired.merge_reads.merge
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	52 --merged_out merged${ext}
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	53 #if $single_paired.merge_reads.include_unmerged
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	54 $single_paired.merge_reads.include_unmerged
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	55 #else
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	56 --out1 'unmerged_R1${ext}'
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	57 --out2 'unmerged_R2${ext}'
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	58 --unpaired1 'unpaired_R1${ext}'
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	59 --unpaired2 'unpaired_R2${ext}'
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	60 #end if
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	61 #else
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	62 -o first${ext}
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	63 -O second${ext}
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	64 #end if
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	65 #else
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	66 -o first${ext}
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	67 #end if
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	68
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	69 ## Adapter Trimming Options
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	70
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	71 $single_paired.adapter_trimming_options.disable_adapter_trimming
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	72
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	73 #if str($single_paired.adapter_trimming_options.adapter_sequence1):
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	74 --adapter_sequence '$single_paired.adapter_trimming_options.adapter_sequence1'
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	75 #end if
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	76
5 4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	77 #if str($single_paired.single_paired_selector).startswith('paired'):
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	78 #if str($single_paired.adapter_trimming_options.adapter_sequence2):
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	79 --adapter_sequence_r2 '$single_paired.adapter_trimming_options.adapter_sequence2'
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	80 #end if
11 d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	81 $single_paired.adapter_trimming_options.detect_adapter_for_pe
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	82 #end if
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	83
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	84
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	85 ## Global Trimming Options
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	86
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	87 #if str($single_paired.global_trimming_options.trim_front1):
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	88 -f $single_paired.global_trimming_options.trim_front1
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	89 #end if
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	90
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	91 #if str($single_paired.global_trimming_options.trim_tail1):
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	92 -t $single_paired.global_trimming_options.trim_tail1
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	93 #end if
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	94
5 4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	95 #if str($single_paired.single_paired_selector).startswith('paired'):
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	96 #if str($single_paired.global_trimming_options.trim_front2):
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	97 -F $single_paired.global_trimming_options.trim_front2
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	98 #end if
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	99 #if str($single_paired.global_trimming_options.trim_tail2):
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	100 -T $single_paired.global_trimming_options.trim_tail2
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	101 #end if
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	102 #end if
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	103
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	104
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	105 ## Overrepresented sequence analysis
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	106
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	107 $overrepresented_sequence_analysis.overrepresentation_analysis
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	108
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	109 #if str($overrepresented_sequence_analysis.overrepresentation_sampling):
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	110 -P $overrepresented_sequence_analysis.overrepresentation_sampling
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	111 #end if
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	112
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	113
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	114 ## Filter Options
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	115
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	116 ## Quality filtering options
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	117
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	118 $filter_options.quality_filtering_options.disable_quality_filtering
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	119
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	120 #if str($filter_options.quality_filtering_options.qualified_quality_phred):
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	121 -q $filter_options.quality_filtering_options.qualified_quality_phred
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	122 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	123 #if str($filter_options.quality_filtering_options.unqualified_percent_limit):
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	124 -u $filter_options.quality_filtering_options.unqualified_percent_limit
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	125 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	126 #if str($filter_options.quality_filtering_options.n_base_limit):
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	127 -n $filter_options.quality_filtering_options.n_base_limit
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	128 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	129
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	130
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	131 ## Length filtering options
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	132
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	133 $filter_options.length_filtering_options.disable_length_filtering
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	134
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	135 #if str($filter_options.length_filtering_options.length_required):
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	136 -l $filter_options.length_filtering_options.length_required
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	137 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	138
9 e9f30696da0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit a64eb7904f80e90a5faff04ea3fb797ee1e07d36" iuc parents: 8 diff changeset	139 #if str($filter_options.length_filtering_options.length_limit):
e9f30696da0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit a64eb7904f80e90a5faff04ea3fb797ee1e07d36" iuc parents: 8 diff changeset	140 --length_limit $filter_options.length_filtering_options.length_limit
e9f30696da0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit a64eb7904f80e90a5faff04ea3fb797ee1e07d36" iuc parents: 8 diff changeset	141 #end if
e9f30696da0e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit a64eb7904f80e90a5faff04ea3fb797ee1e07d36" iuc parents: 8 diff changeset	142
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	143 ## Low complexity filtering options
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	144
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	145 $filter_options.low_complexity_filter.enable_low_complexity_filter
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	146
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	147 #if str($filter_options.low_complexity_filter.complexity_threshold):
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	148 -Y $filter_options.low_complexity_filter.complexity_threshold
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	149 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	150
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	151
20 7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	152 ## Duplicate analysis / deduplication
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	153
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	154 $duplicated_reads.handling_options.eval_dups
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	155 #if not str($duplicated_reads.handling_options.eval_dups):
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	156 $duplicated_reads.handling_options.dedup
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	157 #end if
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	158
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	159
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	160 ## Read Modification Options
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	161
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	162 ## PolyG tail trimming, useful for NextSeq/NovaSeq data
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	163
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	164 #if $read_mod_options.polyg_tail_trimming.trimming_select in ['', '-g']:
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	165 #if str($read_mod_options.polyg_tail_trimming.poly_g_min_len):
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	166 --poly_g_min_len $read_mod_options.polyg_tail_trimming.poly_g_min_len
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	167 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	168 $read_mod_options.polyg_tail_trimming.trimming_select
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	169 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	170
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	171 ## PolyX tail trimming
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	172
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	173 #if $read_mod_options.polyx_tail_trimming.polyx_trimming_select == '-x':
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	174 $read_mod_options.polyx_tail_trimming.polyx_trimming_select
6 7c49e331a737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15 iuc parents: 5 diff changeset	175 #if str($read_mod_options.polyx_tail_trimming.poly_x_min_len):
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	176 --poly_x_min_len $read_mod_options.polyx_tail_trimming.poly_x_min_len
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	177 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	178 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	179
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	180 ## UMI processing
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	181
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	182 #if $read_mod_options.umi_processing.umi:
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	183 $read_mod_options.umi_processing.umi
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	184 #if str($read_mod_options.umi_processing.umi_loc):
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	185 --umi_loc '$read_mod_options.umi_processing.umi_loc'
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	186 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	187 #if str($read_mod_options.umi_processing.umi_len):
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	188 --umi_len $read_mod_options.umi_processing.umi_len
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	189 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	190 #if str($read_mod_options.umi_processing.umi_prefix):
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	191 --umi_prefix '$read_mod_options.umi_processing.umi_prefix'
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	192 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	193 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	194
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	195 ## Per read cutting by quality options
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	196
20 7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	197 #if str($read_mod_options.cutting_by_quality_options.cut_front_select.cut_front) == '--cut_front'
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	198 $read_mod_options.cutting_by_quality_options.cut_front_select.cut_front
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	199 --cut_front_window_size $read_mod_options.cutting_by_quality_options.cut_front_select.cut_front_window_size
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	200 --cut_front_mean_quality $read_mod_options.cutting_by_quality_options.cut_front_select.cut_front_mean_quality
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	201 #end if
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	202
20 7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	203 #if str($read_mod_options.cutting_by_quality_options.cut_tail_select.cut_tail) == '--cut_tail'
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	204 $read_mod_options.cutting_by_quality_options.cut_tail_select.cut_tail
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	205 --cut_tail_window_size $read_mod_options.cutting_by_quality_options.cut_tail_select.cut_tail_window_size
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	206 --cut_tail_mean_quality $read_mod_options.cutting_by_quality_options.cut_tail_select.cut_tail_mean_quality
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	207 #end if
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	208
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	209 #if str($read_mod_options.cutting_by_quality_options.cut_right_select.cut_right) == '--cut_right'
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	210 $read_mod_options.cutting_by_quality_options.cut_right_select.cut_right
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	211 --cut_right_window_size $read_mod_options.cutting_by_quality_options.cut_right_select.cut_right_window_size
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	212 --cut_right_mean_quality $read_mod_options.cutting_by_quality_options.cut_right_select.cut_right_mean_quality
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	213 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	214
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	215 ## Base correction by overlap analysis options
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	216
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	217 $read_mod_options.base_correction_options.correction
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	218
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	219 #if str($single_paired.single_paired_selector) == 'paired_collection'
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	220 #if $single_paired.merge_reads.merge
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	221 && mv merged${ext} '$merged_reads'
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	222 #if not $single_paired.merge_reads.include_unmerged
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	223 && mv 'unmerged_R1${ext}' '$unmerged_out_coll.forward'
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	224 && mv 'unmerged_R2${ext}' '$unmerged_out_coll.reverse'
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	225 && mv 'unpaired_R1${ext}' '$unpaired_out_coll.forward'
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	226 && mv 'unpaired_R2${ext}' '$unpaired_out_coll.reverse'
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	227 #end if
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	228 #else
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	229 && mv first${ext} '$output_paired_coll.forward'
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	230 && mv second${ext} '$output_paired_coll.reverse'
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	231 #end if
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	232 #else
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	233 && mv first${ext} '${out1}'
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	234 #end if
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	235
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	236 ]]></command>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	237 <inputs>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	238 <conditional name="single_paired">
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	239 <param name="single_paired_selector" type="select" label="Single-end or paired reads">
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	240 <option value="single" selected="true">Single-end</option>
5 4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	241 <option value="paired_collection">Paired Collection</option>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	242 </param>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	243 <when value="single">
5 4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	244 <expand macro="in" />
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	245 <expand macro="adapter_trimming_options" />
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	246 <expand macro="global_trimming_options" />
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	247 </when>
11 d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	248 <when value="paired_collection">
14 9047af1bc797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 17a0a67dfbc7541a7fe3618cfbbb71d814042889 iuc parents: 13 diff changeset	249 <param name="paired_input" type="data_collection" format="fastqsanger,fastqsanger.gz" label="Select paired collection(s)" collection_type="paired"/>
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	250 <expand macro="merge_reads" />
5 4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	251 <expand macro="adapter_trimming_options">
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	252 <expand macro="adapter_sequence" read_number="2"/>
11 d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	253 <expand macro="detect_adapter_for_pe" />
5 4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	254 </expand>
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	255 <expand macro="global_trimming_options_paired" />
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	256 </when>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	257 </conditional>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	258
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	259 <section name="overrepresented_sequence_analysis" title="Overrepresented Sequence Analysis" expanded="False">
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	260 <param name="overrepresentation_analysis" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="false" label="Enable overrepresented analysis" help="Enable overrepresented sequence analysis."/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	261 <param name="overrepresentation_sampling" argument="-P" type="integer" optional="true" label="Overrepresentation sampling" help="One in (--overrepresentation_sampling) reads will be computed for overrepresentation analysis (1~10000), smaller is slower, default is 20."/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	262 </section>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	263
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	264 <!-- Filter Options -->
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	265 <section name="filter_options" title="Filter Options">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	266 <section name="quality_filtering_options" title="Quality filtering options" expanded="True">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	267 <param name="disable_quality_filtering" argument="-Q" type="boolean" truevalue="-Q" falsevalue="" checked="false" label="Disable quality filtering" help="Quality filtering is enabled by default. If this option is specified, quality filtering is disabled."/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	268 <param name="qualified_quality_phred" argument="-q" type="integer" optional="true" label="Qualified quality phred" help="The quality value that a base is qualified. Default 15 means phred quality >=Q15 is qualified."/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	269 <param name="unqualified_percent_limit" argument="-u" type="integer" optional="true" label="Unqualified percent limit" help="How many percents of bases are allowed to be unqualified (0~100). Default 40 means 40%."/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	270 <param name="n_base_limit" argument="-n" type="integer" optional="true" label="N base limit" help="If one read's number of N base is >n_base_limit, then this read/pair is discarded. Default is 5."/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	271 </section>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	272
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	273 <section name="length_filtering_options" title="Length filtering options" expanded="True">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	274 <param name="disable_length_filtering" argument="-L" type="boolean" truevalue="-L" falsevalue="" checked="false" label="Disable length filtering" help="Length filtering is enabled by default. If this option is specified, length filtering is disabled."/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	275 <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."/>
11 d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	276 <param argument="--length_limit" type="integer" optional="true" label="Maximum length" help="Reads longer than this value will be discarded. Default is 0 and means no limitation."/>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	277 </section>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	278
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	279 <section name="low_complexity_filter" title="Low complexity filtering options" expanded="True">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	280 <param name="enable_low_complexity_filter" argument="-y" type="boolean" truevalue="-y" falsevalue="" checked="false" label="Enable low complexity filter" help="The complexity is defined as the percentage of base that is different from its next base, default is No"/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	281 <param name="complexity_threshold" argument="-Y" type="integer" optional="true" label="Complexity threshold" help="Threshold for low complexity filter (0~100). Default is 30, which means 30% complexity is required."/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	282 </section>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	283 </section>
20 7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	284 <section name="duplicated_reads" title="Duplicated Reads Options">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	285 <conditional name="handling_options">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	286 <param name="eval_dups" type="select" label="Enable duplicated reads analysis" help="If enabled, calculate and report read duplication statistics. Enabling this is also a prerequisite for optional deduplication of reads. Duplicate detection relies exclusively on exact identity between read sequences (both for SE and PE data). It also increases tool memory requirements and running time moderately. NOTE: the default (no duplication analysis) is different from the command-line tool.">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	287 <option value="">Enable</option>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	288 <option value="--dont_eval_duplication" selected="true">Disable (--dont_eval_duplication)</option>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	289 </param>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	290 <when value="--dont_eval_duplication" />
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	291 <when value="">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	292 <param argument="--dedup" type="boolean" truevalue="--dedup" falsevalue="" label="Drop duplicate reads/pairs"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	293 </when>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	294 </conditional>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	295 </section>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	296 <!-- Read Modification Options -->
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	297 <section name="read_mod_options" title="Read Modification Options">
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	298 <conditional name="polyg_tail_trimming">
6 7c49e331a737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15 iuc parents: 5 diff changeset	299 <param name="trimming_select" type="select" label="PolyG tail trimming" help="This feature is enabled for NextSeq/NovaSeq data by default. NextSeq/NovaSeq data is detected by the machine ID in the FASTQ records.">
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	300 <option value="" selected="true">Automatic trimming for Illumina NextSeq/NovaSeq data</option>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	301 <option value="-g">Force polyG tail trimming</option>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	302 <option value="-G">Disable polyG tail trimming</option>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	303 </param>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	304 <when value="-g">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	305 <expand macro="poly_g_min_len" />
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	306 </when>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	307 <when value="">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	308 <expand macro="poly_g_min_len" />
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	309 </when>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	310 <when value="-G" />
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	311 </conditional>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	312
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	313 <conditional name="polyx_tail_trimming">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	314 <param name="polyx_trimming_select" type="select" label="PolyX tail trimming" help="Similar to polyG tail trimming. When polyG tail trimming and polyX tail trimming are both enabled, fastp will perform polyG trimming first, then perform polyX trimming. Disabled by default.">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	315 <option value="" selected="true">Disable polyX trimming</option>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	316 <option value="-x">Enable polyX tail trimming</option>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	317 </param>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	318 <when value="-x">
11 d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	319 <param argument="--poly_x_min_len" type="integer" optional="true" label="PolyX minimum length"
d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	320 help="The minimum length to detect polyX in the read tail. 10 by default."/>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	321 </when>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	322 <when value="" />
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	323 </conditional>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	324
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	325 <section name="umi_processing" title="UMI processing" expanded="True">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	326 <param name="umi" argument="-U" type="boolean" truevalue="-U" falsevalue="" checked="false" label="Enable unique molecular identifer" help="Enable unique molecular identifer (UMI) preprocessing."/>
11 d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	327 <param 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."/>
d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	328 <param argument="--umi_len" type="integer" optional="true" label="UMI length" help="If the UMI is in read1/read2, its length should be provided."/>
d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	329 <param 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."/>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	330 </section>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	331
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	332 <section name="cutting_by_quality_options" title="Per read cutting by quality options" expanded="True">
20 7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	333 <conditional name="cut_front_select">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	334 <param argument="--cut_front" type="select" truevalue="--cut_front" falsevalue="" checked="false" label="Cut by quality in front (5')" help="Enable per read cutting by quality in front (5'). (WARNING: this will interfere with deduplication of both PE/SE data if performed with downstream tools.)">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	335 <option value="--cut_front">Yes</option>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	336 <option value="" selected="true">No</option>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	337 </param>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	338 <when value="--cut_front">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	339 <param argument="--cut_front_window_size" type="integer" optional="true" value="4" min="1" max="1000" label="Cutting window size for cut front" help="The size of the sliding window for sliding window trimming."/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	340 <param argument="--cut_front_mean_quality" type="integer" optional="true" value="20" min="1" max="30 " label="Cutting mean quality for cut front" help="The bases in the sliding window with mean quality below cutting_quality will be cut."/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	341 </when>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	342 <when value="">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	343 </when>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	344 </conditional>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	345 <conditional name="cut_tail_select">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	346 <param argument="--cut_tail" type="select" truevalue="--cut_tail" falsevalue="" checked="false" label="Cut by quality in tail (3')" help="Enable per read cutting by quality in tail (3'). (WARNING: this will interfere with deduplication of SE data if performed with downstream tools.)">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	347 <option value="--cut_tail">Yes</option>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	348 <option value="" selected="true">No</option>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	349 </param>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	350 <when value="--cut_tail">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	351 <param argument="--cut_tail_window_size" type="integer" optional="true" value="4" min="1" max="1000" label="Cutting window size for cut tail" help="The size of the sliding window for sliding window trimming."/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	352 <param argument="--cut_tail_mean_quality" type="integer" optional="true" value="20" min="1" max="30 " label="Cutting mean quality for cut tail" help="The bases in the sliding window with mean quality below cutting_quality will be cut."/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	353 </when>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	354 <when value="">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	355 </when>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	356 </conditional>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	357 <conditional name="cut_right_select">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	358 <param argument="--cut_right" type="select" truevalue="--cut_right" falsevalue="" checked="false" label="Cut by quality in tail (3')" help="Move a sliding window from front to tail, if meet one window with mean quality < threshold, drop the bases in the window and the right part, and then stop. (WARNING: this will interfere with deduplication of SE data if performed with downstream tools.)">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	359 <option value="--cut_right">Yes</option>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	360 <option value="" selected="true">No</option>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	361 </param>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	362 <when value="--cut_right">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	363 <param argument="--cut_right_window_size" type="integer" optional="true" value="4" min="1" max="1000" label="Cutting window size for cut right" help="The size of the sliding window for sliding window trimming."/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	364 <param argument="--cut_right_mean_quality" type="integer" optional="true" value="20" min="1" max="30 " label="Cutting mean quality for cut right" help="The bases in the sliding window with mean quality below cutting_quality will be cut."/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	365 </when>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	366 <when value="">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	367 </when>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	368 </conditional>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	369 </section>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	370
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	371 <section name="base_correction_options" title="Base correction by overlap analysis options" expanded="True">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	372 <param name="correction" argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Enable base correction" help="Enable base correction in overlapped regions (only for PE data), default is disabled."/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	373 </section>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	374 </section>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	375
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	376 <section name="output_options" title="Output Options" expanded="False">
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	377 <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"/>
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	378 <param name="report_json" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Output JSON report" help="The JSON report contains all the data visualized in the HTML report. The format of the JSON report is manually optimized to be easily readable by humans and is compatible with MultiQC"/>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	379 </section>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	380 </inputs>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	381
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	382 <outputs>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	383 <data name="out1" format_source="single_paired\|in1" label="${tool.name} on ${on_string}: Read 1 output">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	384 <filter>single_paired['single_paired_selector'] == "single"</filter>
5 4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	385 </data>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	386 <collection name="output_paired_coll" type="paired" format_source="single_paired\|paired_input['forward']" label="${tool.name} on ${on_string}: Paired-end output">
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	387 <filter>single_paired['single_paired_selector'] == "paired_collection" and not single_paired['merge_reads']['merge']</filter>
5 4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	388 </collection>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	389
8 1eb1895ab19c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6e59980ea50d84a849190460ae44c055f643355f iuc parents: 7 diff changeset	390 <data name="report_html" format="html" from_work_dir="fastp.html" label="${tool.name} on ${on_string}: HTML report">
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	391 <filter>output_options['report_html'] is True</filter>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	392 </data>
8 1eb1895ab19c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6e59980ea50d84a849190460ae44c055f643355f iuc parents: 7 diff changeset	393 <data name="report_json" format="json" from_work_dir="fastp.json" label="${tool.name} on ${on_string}: JSON report">
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	394 <filter>output_options['report_json'] is True</filter>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	395 </data>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	396 <data name="merged_reads" format_source="single_paired\|paired_input['forward']" label="${tool.name} on ${on_string}: Merged reads">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	397 <filter>single_paired['single_paired_selector'] == "paired_collection" and single_paired['merge_reads']['merge']</filter>
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	398 </data>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	399 <collection name="unmerged_out_coll" type="paired" format_source="single_paired\|paired_input['forward']" label="${tool.name} on ${on_string}: Unmerged filtered">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	400 <filter>single_paired['single_paired_selector'] == "paired_collection" and single_paired['merge_reads']['merge'] and not single_paired['merge_reads']['include_unmerged']</filter>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	401 </collection>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	402 <collection name="unpaired_out_coll" type="paired" format_source="single_paired\|paired_input['forward']" label="${tool.name} on ${on_string}: Unmerged unfiltered">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	403 <filter>single_paired['single_paired_selector'] == "paired_collection" and single_paired['merge_reads']['merge'] and not single_paired['merge_reads']['include_unmerged']</filter>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	404 </collection>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	405 </outputs>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	406
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	407 <tests>
11 d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	408 <!-- 1. Ensure default output works -->
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	409 <test expect_num_outputs="3">
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	410 <conditional name="single_paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	411 <param name="single_paired_selector" value="single"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	412 <param name="in1" ftype="fastqsanger" value="R1.fq"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	413 </conditional>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	414 <output name="out1" ftype="fastqsanger" file="out1.fq"/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	415 <output name="report_html">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	416 <assert_contents>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	417 <has_text text="fastp report"/>
20 7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	418 <not_has_text text="duplication rate:"/>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	419 </assert_contents>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	420 </output>
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	421 <output name="report_json">
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	422 <assert_contents>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	423 <has_text text="fastp report"/>
20 7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	424 <not_has_text text=""duplication":"/>
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	425 </assert_contents>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	426 </output>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	427 </test>
11 d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	428 <!-- 2. Ensure paired collection works -->
7 2fcdbf78caf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 249269561e1d3a767371c154677e5dd59147f7d7 iuc parents: 6 diff changeset	429 <test expect_num_outputs="4">
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	430 <conditional name="single_paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	431 <param name="single_paired_selector" value="paired_collection"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	432 <param name="paired_input">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	433 <collection type="paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	434 <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	435 <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	436 </collection>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	437 </param>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	438 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	439 <section name="output_options">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	440 <param name="report_json" value="False" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	441 </section>
5 4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	442 <output name="report_html">
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	443 <assert_contents>
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	444 <has_text text="fastp report"/>
20 7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	445 <not_has_text text="duplication rate:"/>
5 4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	446 </assert_contents>
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	447 </output>
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	448 <output_collection name="output_paired_coll" type="paired">
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	449 <element name="forward" value="out_bwa1.fq" ftype="fastqsanger"/>
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	450 <element name="reverse" value="out_bwa2.fq" ftype="fastqsanger"/>
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	451 </output_collection>
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	452 </test>
11 d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	453 <!-- 3. Ensure custom adapter works -->
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	454 <test expect_num_outputs="2">
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	455 <conditional name="single_paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	456 <param name="single_paired_selector" value="single"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	457 <param name="in1" ftype="fastqsanger" value="R1.fq"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	458 <section name="adapter_trimming_options">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	459 <param name="adapter_sequence1" value="ATCG"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	460 </section>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	461 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	462 <section name="output_options">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	463 <param name="report_json" value="False" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	464 </section>
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	465 <output name="out1" ftype="fastqsanger" file="out_a.fq"/>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	466 </test>
11 d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	467 <!-- 4. Ensure UMI processing works -->
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	468 <test expect_num_outputs="2">
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	469 <conditional name="single_paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	470 <param name="in1" ftype="fastqsanger" value="R1.fq"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	471 <param name="single_paired_selector" value="single"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	472 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	473 <section name="read_mod_options">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	474 <section name="umi_processing">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	475 <param name="umi" value="true"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	476 <param name="umi_loc" value="read1"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	477 <param name="umi_len" value="8"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	478 </section>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	479 </section>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	480 <section name="output_options">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	481 <param name="report_json" value="False" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	482 </section>
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	483 <output name="out1" ftype="fastqsanger" file="out2.fq"/>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	484 </test>
11 d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	485 <!-- 5. Ensure UMI processing with different lengths works -->
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	486 <test expect_num_outputs="2">
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	487 <conditional name="single_paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	488 <param name="in1" ftype="fastqsanger" value="R1.fq"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	489 <param name="single_paired_selector" value="single"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	490 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	491 <section name="read_mod_options">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	492 <section name="umi_processing">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	493 <param name="umi" value="true"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	494 <param name="umi_loc" value="read1"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	495 <param name="umi_len" value="12"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	496 </section>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	497 </section>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	498 <section name="output_options">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	499 <param name="report_json" value="False" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	500 </section>
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	501 <output name="out1" ftype="fastqsanger" file="out3.fq"/>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	502 </test>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	503 <!-- 6. Ensure paired-end UMI processing of Read 1 works -->
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	504 <test expect_num_outputs="4">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	505 <conditional name="single_paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	506 <param name="single_paired_selector" value="paired_collection"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	507 <param name="paired_input">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	508 <collection type="paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	509 <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	510 <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	511 </collection>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	512 </param>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	513 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	514 <section name="read_mod_options">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	515 <section name="umi_processing">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	516 <param name="umi" value="true"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	517 <param name="umi_loc" value="read1"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	518 <param name="umi_len" value="8"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	519 </section>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	520 </section>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	521 <section name="output_options">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	522 <param name="report_json" value="False" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	523 </section>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	524 <output_collection name="output_paired_coll" type="paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	525 <element name="forward" value="out_bwa_umi_read1_1.fq" ftype="fastqsanger"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	526 <element name="reverse" value="out_bwa_umi_read1_2.fq" ftype="fastqsanger"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	527 </output_collection>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	528 </test>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	529 <!-- 7. Ensure paired-end UMI processing of Read 2 works -->
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	530 <test expect_num_outputs="5">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	531 <conditional name="single_paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	532 <param name="single_paired_selector" value="paired_collection"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	533 <param name="paired_input">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	534 <collection type="paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	535 <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	536 <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	537 </collection>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	538 </param>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	539 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	540 <section name="read_mod_options">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	541 <section name="umi_processing">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	542 <param name="umi" value="true"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	543 <param name="umi_loc" value="read2"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	544 <param name="umi_len" value="8"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	545 </section>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	546 </section>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	547 <output_collection name="output_paired_coll" type="paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	548 <element name="forward" value="out_bwa_umi_read2_1.fq" ftype="fastqsanger"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	549 <element name="reverse" value="out_bwa_umi_read2_2.fq" ftype="fastqsanger"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	550 </output_collection>
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	551 <output name="report_json">
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	552 <assert_contents>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	553 <has_text text="fastp report"/>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	554 </assert_contents>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	555 </output>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	556 </test>
20 7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	557 <!-- 8. Ensure enabling duplicate analysis works -->
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	558 <test expect_num_outputs="3">
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	559 <conditional name="single_paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	560 <param name="single_paired_selector" value="single"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	561 <param name="in1" ftype="fastqsanger" value="R1.fq"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	562 </conditional>
20 7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	563 <section name="duplicated_reads">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	564 <conditional name="handling_options">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	565 <param name="eval_dups" value=""/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	566 </conditional>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	567 </section>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	568 <output name="out1" ftype="fastqsanger" file="out1.fq"/>
20 7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	569 <output name="report_html">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	570 <assert_contents>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	571 <has_text text="fastp report"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	572 <has_text text="duplication rate:"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	573 </assert_contents>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	574 </output>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	575 <output name="report_json">
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	576 <assert_contents>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	577 <has_text text="fastp report"/>
20 7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	578 <has_text text=""duplication":"/>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	579 </assert_contents>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	580 </output>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	581 </test>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	582 <!-- 9. Ensure polyG trimming works -->
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	583 <test expect_num_outputs="3">
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	584 <conditional name="single_paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	585 <param name="single_paired_selector" value="single"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	586 <param name="in1" ftype="fastqsanger.gz" value="R1.fq.gz"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	587 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	588 <section name="read_mod_options">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	589 <conditional name="polyg_tail_trimming">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	590 <param name="trimming_select" value="-g"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	591 <param name="poly_g_min_len" value="10"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	592 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	593 </section>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	594 <output name="out1" ftype="fastqsanger.gz" decompress="true" file="out1.fq.gz"/>
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	595 <output name="report_json">
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	596 <assert_contents>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	597 <has_text text="fastp report"/>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	598 </assert_contents>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	599 </output>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	600 </test>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	601 <!-- 10. Ensure polyX trimming works -->
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	602 <test expect_num_outputs="3">
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	603 <conditional name="single_paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	604 <param name="single_paired_selector" value="single"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	605 <param name="in1" ftype="fastqsanger.gz" value="R1.fq.gz"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	606 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	607 <section name="read_mod_options">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	608 <conditional name="polyg_tail_trimming">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	609 <param name="trimming_select" value="-G"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	610 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	611 <conditional name="polyx_tail_trimming">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	612 <param name="polyx_trimming_select" value="-x"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	613 <param name="poly_x_min_len" value="10"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	614 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	615 </section>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	616 <output name="out1" ftype="fastqsanger.gz" decompress="true" file="out1.fq.gz"/>
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	617 <output name="report_json">
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	618 <assert_contents>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	619 <has_text text="fastp report"/>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	620 </assert_contents>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	621 </output>
6 7c49e331a737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15 iuc parents: 5 diff changeset	622 </test>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	623 <!-- 11. Test fastqsanger files with different length -->
18 046512eda8c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 039359757ad615f57028cab966b2b76f8ce8a199 iuc parents: 16 diff changeset	624 <!-- Adapted for the updated version of fastp, which now ignores unmatched reads and continues filtering as expected -->
046512eda8c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 039359757ad615f57028cab966b2b76f8ce8a199 iuc parents: 16 diff changeset	625 <test expect_num_outputs="4">
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	626 <conditional name="single_paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	627 <param name="single_paired_selector" value="paired_collection"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	628 <param name="paired_input">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	629 <collection type="paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	630 <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	631 <element name="reverse" value="bwa-mem-fastq2_too_long.fq" ftype="fastqsanger" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	632 </collection>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	633 </param>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	634 </conditional>
18 046512eda8c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 039359757ad615f57028cab966b2b76f8ce8a199 iuc parents: 16 diff changeset	635 <section name="output_options">
046512eda8c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 039359757ad615f57028cab966b2b76f8ce8a199 iuc parents: 16 diff changeset	636 <param name="report_json" value="False"/>
046512eda8c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 039359757ad615f57028cab966b2b76f8ce8a199 iuc parents: 16 diff changeset	637 </section>
046512eda8c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 039359757ad615f57028cab966b2b76f8ce8a199 iuc parents: 16 diff changeset	638 <output name="report_html">
046512eda8c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 039359757ad615f57028cab966b2b76f8ce8a199 iuc parents: 16 diff changeset	639 <assert_contents>
046512eda8c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 039359757ad615f57028cab966b2b76f8ce8a199 iuc parents: 16 diff changeset	640 <has_text text="fastp report"/>
046512eda8c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 039359757ad615f57028cab966b2b76f8ce8a199 iuc parents: 16 diff changeset	641 </assert_contents>
046512eda8c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 039359757ad615f57028cab966b2b76f8ce8a199 iuc parents: 16 diff changeset	642 </output>
046512eda8c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 039359757ad615f57028cab966b2b76f8ce8a199 iuc parents: 16 diff changeset	643 <output_collection name="output_paired_coll" type="paired">
046512eda8c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 039359757ad615f57028cab966b2b76f8ce8a199 iuc parents: 16 diff changeset	644 <element name="forward" value="out_filtered_1.fq" ftype="fastqsanger"/>
046512eda8c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 039359757ad615f57028cab966b2b76f8ce8a199 iuc parents: 16 diff changeset	645 <element name="reverse" value="out_filtered_2.fq" ftype="fastqsanger"/>
046512eda8c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 039359757ad615f57028cab966b2b76f8ce8a199 iuc parents: 16 diff changeset	646 </output_collection>
11 d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	647 </test>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	648 <!-- 12. Test merge reads in combination with paired -->
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	649 <test expect_num_outputs="7">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	650 <conditional name="single_paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	651 <param name="single_paired_selector" value="paired_collection"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	652 <param name="paired_input">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	653 <collection type="paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	654 <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	655 <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	656 </collection>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	657 </param>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	658 <conditional name="merge_reads">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	659 <param name="merge" value="--merge" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	660 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	661 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	662 <section name="output_options">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	663 <param name="report_json" value="False" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	664 <param name="report_html" value="False" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	665 </section>
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	666 <output name="merged_reads" ftype="fastqsanger" file="bwa-mem-merged-reads.fastqsanger" />
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	667 <output_collection name="unmerged_out_coll" type="paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	668 <element name="forward" value="bwa-mem-unmerged-filtered-reads1.fastqsanger" ftype="fastqsanger"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	669 <element name="reverse" value="bwa-mem-unmerged-filtered-reads2.fastqsanger" ftype="fastqsanger"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	670 </output_collection>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	671 <output_collection name="unpaired_out_coll" type="paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	672 <element name="forward" value="bwa-mem-unmerged-unfiltered-reads1.fastqsanger" ftype="fastqsanger"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	673 <element name="reverse" ftype="fastqsanger">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	674 <assert_contents>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	675 <has_size size="0" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	676 </assert_contents>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	677 </element>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	678 </output_collection>
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	679 </test>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	680 <!-- 13. Test merge and include_unmerged in combination with paired collection -->
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	681 <test expect_num_outputs="2">
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	682 <conditional name="single_paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	683 <param name="single_paired_selector" value="paired_collection"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	684 <param name="paired_input">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	685 <collection type="paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	686 <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	687 <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	688 </collection>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	689 </param>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	690 <conditional name="merge_reads">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	691 <param name="merge" value="--merge" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	692 <param name="include_unmerged" value="true" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	693 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	694 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	695 <section name="output_options">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	696 <param name="report_html" value="False" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	697 </section>
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	698 <output name="merged_reads" ftype="fastqsanger" file="bwa-mem-merged-read-include-unmerged.fastqsanger" />
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	699 <output name="report_json">
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	700 <assert_contents>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	701 <has_text text="fastp report"/>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	702 </assert_contents>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	703 </output>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	704 </test>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	705 <!-- 14. Test merge reads in combination with paired -->
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	706 <test expect_num_outputs="7">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	707 <conditional name="single_paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	708 <param name="single_paired_selector" value="paired_collection"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	709 <param name="paired_input">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	710 <collection type="paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	711 <element name="forward" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	712 <element name="reverse" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	713 </collection>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	714 </param>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	715 <conditional name="merge_reads">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	716 <param name="merge" value="--merge" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	717 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	718 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	719 <section name="output_options">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	720 <param name="report_html" value="False" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	721 <param name="report_json" value="False" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	722 </section>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	723 <output name="merged_reads" ftype="fastqsanger.gz" decompress="true" file="bwa-mem-merged-reads.fastqsanger.gz" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	724 <output_collection name="unmerged_out_coll" type="paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	725 <element name="forward" value="bwa-mem-unmerged-filtered-reads1.fastqsanger.gz" decompress="true" ftype="fastqsanger.gz"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	726 <element name="reverse" value="bwa-mem-unmerged-filtered-reads2.fastqsanger.gz" decompress="true" ftype="fastqsanger.gz"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	727 </output_collection>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	728 <output_collection name="unpaired_out_coll" type="paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	729 <element name="forward" value="bwa-mem-unmerged-unfiltered-reads1.fastqsanger.gz" decompress="true" ftype="fastqsanger.gz"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	730 <element name="reverse" ftype="fastqsanger.gz">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	731 <assert_contents>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	732 <has_size size="0" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	733 </assert_contents>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	734 </element>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	735 </output_collection>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	736 </test>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	737 <!-- 15. Test merge and include_unmerged in combination with paired collection -->
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	738 <test expect_num_outputs="2">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	739 <conditional name="single_paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	740 <param name="single_paired_selector" value="paired_collection"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	741 <param name="paired_input">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	742 <collection type="paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	743 <element name="forward" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	744 <element name="reverse" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	745 </collection>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	746 </param>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	747 <conditional name="merge_reads">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	748 <param name="merge" value="--merge" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	749 <param name="include_unmerged" value="true" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	750 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	751 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	752 <section name="output_options">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	753 <param name="report_html" value="False" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	754 </section>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	755 <output name="merged_reads" ftype="fastqsanger.gz" decompress="true" file="bwa-mem-merged-read-include-unmerged.fastqsanger.gz" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	756 <output name="report_json">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	757 <assert_contents>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	758 <has_text text="fastp report"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	759 </assert_contents>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	760 </output>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	761 </test>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	762 <!--16. Test paired collection in combination with compressed input-->
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	763 <test expect_num_outputs="4">
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	764 <conditional name="single_paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	765 <param name="single_paired_selector" value="paired_collection"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	766 <param name="paired_input">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	767 <collection type="paired">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	768 <element name="forward" value="bwa-mem-fastq-paired-collection/input_forward.fastqsanger.gz" ftype="fastqsanger.gz" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	769 <element name="reverse" value="bwa-mem-fastq-paired-collection/input_reverse.fastqsanger.gz" ftype="fastqsanger.gz" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	770 </collection>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	771 </param>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	772 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	773 <section name="output_options">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	774 <param name="report_json" value="False" />
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	775 </section>
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	776 <output name="report_html">
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	777 <assert_contents>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	778 <has_text text="fastp report"/>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	779 </assert_contents>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	780 </output>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	781 <output_collection name="output_paired_coll" type="paired">
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	782 <element name="forward" value="bwa-mem-fastq-paired-collection/output_forward.fastqsanger.gz" decompress="true" ftype="fastqsanger.gz"/>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	783 <element name="reverse" value="bwa-mem-fastq-paired-collection/output_reverse.fastqsanger.gz" decompress="true" ftype="fastqsanger.gz"/>
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	784 </output_collection>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	785 </test>
20 7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	786 <!-- 17. Ensure quality cutting work -->
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	787 <test expect_num_outputs="3">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	788 <conditional name="single_paired">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	789 <param name="single_paired_selector" value="single"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	790 <param name="in1" ftype="fastqsanger.gz" value="R1.fq.gz"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	791 </conditional>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	792 <section name="read_mod_options">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	793 <section name="cutting_by_quality_options">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	794 <conditional name="cut_front_select">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	795 <param name="cut_front" value="--cut_front"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	796 <param name="cut_front_window_size" value="2"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	797 <param name="cut_front_mean_quality" value="3"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	798 </conditional>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	799 <conditional name="cut_tail_select">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	800 <param name="cut_tail" value="--cut_tail"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	801 <param name="cut_tail_window_size" value="4"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	802 <param name="cut_tail_mean_quality" value="5"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	803 </conditional>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	804 <conditional name="cut_right_select">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	805 <param name="cut_right" value="--cut_right"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	806 <param name="cut_right_window_size" value="6"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	807 <param name="cut_right_mean_quality" value="7"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	808 </conditional>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	809 </section>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	810 </section>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	811 <output name="out1" ftype="fastqsanger.gz" decompress="true" file="quality_cutting_output.fq.gz"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	812 <output name="report_json">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	813 <assert_contents>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	814 <has_text text="--cut_front"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	815 <has_text text="--cut_tail"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	816 <has_text text="--cut_right"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	817 <has_text text="--cut_front_window_size 2"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	818 <has_text text="--cut_front_mean_quality 3"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	819 <has_text text="--cut_tail_window_size 4"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	820 <has_text text="--cut_tail_mean_quality 5"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	821 <has_text text="--cut_right_window_size 6"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	822 <has_text text="--cut_right_mean_quality 7"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	823 </assert_contents>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	824 </output>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	825 </test>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	826 <!-- 18. Ensure deduplication works -->
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	827 <test expect_num_outputs="2">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	828 <conditional name="single_paired">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	829 <param name="single_paired_selector" value="single"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	830 <param name="in1" ftype="fastqsanger" value="R1_with_dup.fq"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	831 </conditional>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	832 <section name="duplicated_reads">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	833 <conditional name="handling_options">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	834 <param name="eval_dups" value=""/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	835 <param name="dedup" value="true"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	836 </conditional>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	837 </section>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	838 <section name="output_options">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	839 <param name="report_html" value="false"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	840 </section>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	841 <output name="out1" ftype="fastqsanger" file="out1.fq"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	842 <output name="report_json">
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	843 <assert_contents>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	844 <has_text text="fastp report"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	845 <has_text text=""duplication":"/>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	846 </assert_contents>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	847 </output>
7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	848 </test>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	849 </tests>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	850 <help><![CDATA[
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	851 .. class:: infomark
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	852
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	853 What it does
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	854
11 d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	855 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
d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	856 afford high performance.
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	857
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	858 Features
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	859
20 7e30f4d7077d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp commit 3214ce465671de3c15da94f71f2c3558f332d39a iuc parents: 18 diff changeset	860 1. Filter out bad (too low quality, too short, or too many N...) and/or duplicate reads
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	861
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	862 2. Cut low quality bases for per read in its 5' and 3' by evaluating the mean quality from a sliding window (like Trimmomatic but faster)
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	863
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	864 3. Trim all reads in front and tail
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	865
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	866 4. Cut adapters. Adapter sequences can be automatically detected, which means you don't have to input the adapter sequences to trim them.
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	867
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	868 5. Correct mismatched base pairs in overlapped regions of paired end reads, if one base is with high quality while the other is with ultra-low quality
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	869
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	870 6. Trim polyG in 3' ends, which is commonly seen in NovaSeq/NextSeq data. Trim polyX in 3' ends to remove unwanted polyX tailing (i.e. polyA tailing for mRNA-Seq data)
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	871
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	872 7. Preprocess unique molecular identifier (UMI) enabled data, shift UMI to sequence name
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	873
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	874 8. Report JSON format result for further interpreting
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	875
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	876 9. Visualize quality control and filtering results on a single HTML page (like FASTQC but faster and more informative)
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	877
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	878 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 limiting the lines of each split file (Not enabled in this Galaxy tool)
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	879
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	880 11. Support long reads (data from PacBio / Nanopore devices)
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	881
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	882 -----
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	883
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	884 Inputs
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	885
14 9047af1bc797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 17a0a67dfbc7541a7fe3618cfbbb71d814042889 iuc parents: 13 diff changeset	886 Single-end or Paired-end (compressed) fastqsanger files
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	887
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	888 -----
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	889
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	890 Outputs
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	891
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	892 * Processed reads
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	893 * Merged reads
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	894 * Unmerged filtered reads, reads that cannot be merged successfully, but both pass all the filters.
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	895 * Unmerged unfiltered reads, reads that cannot be merged, i.e. forward passes filters but reverse doesn't.
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	896
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	897 Optionally, under Output Options you can choose to output
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	898
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	899 * HTML report (default is Yes)
4 20c09892cfe7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984 iuc parents: 3 diff changeset	900 * JSON report (compatible with MultiQC)
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	901
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	902 .. _fastp: https://github.com/OpenGene/fastp
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	903
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	904 ]]></help>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	905 <citations>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	906 <citation type="doi">10.1101/274100</citation>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	907 </citations>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	908 </tool>

Mercurial > repos > iuc > fastp

annotate fastp.xml @ 20:7e30f4d7077d draft default tip