fastp: fastp.xml annotate

annotate fastp.xml @ 16:d6c9f863a9db draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 68607e04ba077a9a2b0549ec7b8b9fceedd19d86

author	iuc
date	Mon, 21 Apr 2025 18:16:11 +0000
parents	515315f1a8a0
children	046512eda8c0

rev	line source
16 d6c9f863a9db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 68607e04ba077a9a2b0549ec7b8b9fceedd19d86 iuc parents: 15 diff changeset	1 <tool id="fastp" name="fastp" version="@TOOL_VERSION@+galaxy0" 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
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	152 ## 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	153
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	154 ## 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	155
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	156 #if $read_mod_options.polyg_tail_trimming.trimming_select in ['', '-g']:
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	157 #if str($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	158 --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	159 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	160 $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	161 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	162
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	163 ## 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	164
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	165 #if $read_mod_options.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	166 $read_mod_options.polyx_tail_trimming.polyx_trimming_select
6 7c49e331a737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15 iuc parents: 5 diff changeset	167 #if str($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	168 --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	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 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	171
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	172 ## UMI processing
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	173
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	174 #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	175 $read_mod_options.umi_processing.umi
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	176 #if str($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	177 --umi_loc '$read_mod_options.umi_processing.umi_loc'
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	178 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	179 #if str($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	180 --umi_len $read_mod_options.umi_processing.umi_len
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	181 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	182 #if str($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	183 --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	184 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	185 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	186
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	187 ## 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	188
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	189 #if $read_mod_options.cutting_by_quality_options.cut_by_quality5 or $read_mod_options.cutting_by_quality_options.cut_by_quality3:
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	190
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	191 $read_mod_options.cutting_by_quality_options.cut_by_quality5
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	192
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	193 $read_mod_options.cutting_by_quality_options.cut_by_quality3
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	194
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	195 #if str($read_mod_options.cutting_by_quality_options.cut_window_size):
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	196 -W $read_mod_options.cutting_by_quality_options.cut_window_size
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	197 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	198 #if str($read_mod_options.cutting_by_quality_options.cut_mean_quality):
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	199 -M $read_mod_options.cutting_by_quality_options.cut_mean_quality
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	200 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	201 #end if
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	202
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	203 ## 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	204
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	205 $read_mod_options.base_correction_options.correction
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	206
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	207 #if str($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	208 #if $single_paired.merge_reads.merge
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	209 && mv merged${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	210 #if not $single_paired.merge_reads.include_unmerged
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	211 && mv 'unmerged_R1${ext}' '$unmerged_out_coll.forward'
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	212 && mv 'unmerged_R2${ext}' '$unmerged_out_coll.reverse'
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	213 && mv 'unpaired_R1${ext}' '$unpaired_out_coll.forward'
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	214 && mv 'unpaired_R2${ext}' '$unpaired_out_coll.reverse'
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	215 #end if
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	216 #else
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	217 && mv first${ext} '$output_paired_coll.forward'
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	218 && mv second${ext} '$output_paired_coll.reverse'
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	219 #end if
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	220 #else
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	221 && mv first${ext} '${out1}'
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	222 #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	223
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	224 ]]></command>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	225 <inputs>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	226 <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	227 <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	228 <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	229 <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	230 </param>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	231 <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	232 <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	233 <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	234 <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	235 </when>
11 d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	236 <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	237 <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	238 <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	239 <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	240 <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	241 <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	242 </expand>
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	243 <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	244 </when>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	245 </conditional>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	246
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	247 <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	248 <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	249 <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	250 </section>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	251
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	252 <!-- Filter Options -->
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	253 <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	254 <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	255 <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	256 <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	257 <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	258 <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	259 </section>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	260
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	261 <section name="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	262 <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	263 <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	264 <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	265 </section>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	266
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	267 <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	268 <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	269 <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	270 </section>
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 <!-- 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	274 <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	275 <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	276 <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	277 <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	278 <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	279 <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	280 </param>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	281 <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	282 <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	283 </when>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	284 <when value="">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	285 <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	286 </when>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	287 <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	288 </conditional>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	289
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	290 <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	291 <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	292 <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	293 <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	294 </param>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	295 <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	296 <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	297 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	298 </when>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	299 <when value="" />
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	300 </conditional>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	301
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	302 <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	303 <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	304 <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	305 <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	306 <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	307 </section>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	308
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	309 <section name="cutting_by_quality_options" title="Per read cutting by quality options" expanded="True">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	310 <param name="cut_by_quality5" argument="-5" type="boolean" truevalue="-5" falsevalue="" checked="false" label="Cut by quality in front (5')" help="Enable per read cutting by quality in front (5'), default is disabled (WARNING: this will interfere deduplication for both PE/SE data)."/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	311 <param name="cut_by_quality3" argument="-3" type="boolean" truevalue="-3" falsevalue="" checked="false" label="Cut by quality in tail (3')" help="Enable per read cutting by quality in tail (3'), default is disabled (WARNING: this will interfere deduplication for SE data)."/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	312 <param name="cut_window_size" argument="-W" type="integer" optional="true" label="Cutting window size" help="The size of the sliding window for sliding window trimming, default is 4."/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	313 <param name="cut_mean_quality" argument="-M" type="integer" optional="true" label="Cutting mean quality" help="The bases in the sliding window with mean quality below cutting_quality will be cut, default is Q20."/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	314 </section>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	315
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	316 <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	317 <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	318 </section>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	319 </section>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	320
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	321 <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	322 <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	323 <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	324 </section>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	325 </inputs>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	326
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	327 <outputs>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	328 <data name="out1" format_source="single_paired\|in1" label="${tool.name} on ${on_string}: Read 1 output">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	329 <filter>single_paired['single_paired_selector'] == "single"</filter>
5 4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	330 </data>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	331 <collection name="output_paired_coll" type="paired" format_source="single_paired\|paired_input['forward']" label="${tool.name} on ${on_string}: Paired-end output">
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	332 <filter>single_paired['single_paired_selector'] == "paired_collection" and not single_paired['merge_reads']['merge']</filter>
5 4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	333 </collection>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	334
8 1eb1895ab19c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6e59980ea50d84a849190460ae44c055f643355f iuc parents: 7 diff changeset	335 <data name="report_html" format="html" from_work_dir="fastp.html" label="${tool.name} on ${on_string}: HTML report">
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	336 <filter>output_options['report_html'] is True</filter>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	337 </data>
8 1eb1895ab19c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6e59980ea50d84a849190460ae44c055f643355f iuc parents: 7 diff changeset	338 <data name="report_json" format="json" from_work_dir="fastp.json" label="${tool.name} on ${on_string}: JSON report">
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	339 <filter>output_options['report_json'] is True</filter>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	340 </data>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	341 <data name="merged_reads" format_source="single_paired\|paired_input['forward']" label="${tool.name} on ${on_string}: Merged reads">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	342 <filter>single_paired['single_paired_selector'] == "paired_collection" and single_paired['merge_reads']['merge']</filter>
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	343 </data>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	344 <collection name="unmerged_out_coll" type="paired" format_source="single_paired\|paired_input['forward']" label="${tool.name} on ${on_string}: Unmerged filtered">
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	345 <filter>single_paired['single_paired_selector'] == "paired_collection" and single_paired['merge_reads']['merge'] and not single_paired['merge_reads']['include_unmerged']</filter>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	346 </collection>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	347 <collection name="unpaired_out_coll" type="paired" format_source="single_paired\|paired_input['forward']" label="${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	348 <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	349 </collection>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	350 </outputs>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	351
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	352 <tests>
11 d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	353 <!-- 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	354 <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	355 <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	356 <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	357 <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	358 </conditional>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	359 <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	360 <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	361 <assert_contents>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	362 <has_text text="fastp report"/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	363 </assert_contents>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	364 </output>
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	365 <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	366 <assert_contents>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	367 <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	368 </assert_contents>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	369 </output>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	370 </test>
11 d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	371 <!-- 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	372 <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	373 <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	374 <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	375 <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	376 <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	377 <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	378 <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	379 </collection>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	380 </param>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	381 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	382 <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	383 <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	384 </section>
5 4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	385 <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	386 <assert_contents>
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	387 <has_text text="fastp report"/>
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	388 </assert_contents>
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	389 </output>
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	390 <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	391 <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	392 <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	393 </output_collection>
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498 iuc parents: 4 diff changeset	394 </test>
11 d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	395 <!-- 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	396 <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	397 <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	398 <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	399 <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	400 <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	401 <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	402 </section>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	403 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	404 <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	405 <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	406 </section>
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	407 <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	408 </test>
11 d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	409 <!-- 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	410 <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	411 <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	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 <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	414 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	415 <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	416 <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	417 <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	418 <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	419 <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	420 </section>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	421 </section>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	422 <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	423 <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	424 </section>
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	425 <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	426 </test>
11 d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	427 <!-- 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	428 <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	429 <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	430 <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	431 <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	432 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	433 <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	434 <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	435 <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	436 <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	437 <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	438 </section>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	439 </section>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	440 <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	441 <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	442 </section>
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	443 <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	444 </test>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	445 <!-- 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	446 <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	447 <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	448 <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	449 <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	450 <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	451 <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	452 <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	453 </collection>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	454 </param>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	455 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	456 <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	457 <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	458 <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	459 <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	460 <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	461 </section>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	462 </section>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	463 <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	464 <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	465 </section>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	466 <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	467 <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	468 <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	469 </output_collection>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	470 </test>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	471 <!-- 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	472 <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	473 <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	474 <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	475 <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	476 <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	477 <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	478 <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	479 </collection>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	480 </param>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	481 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	482 <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	483 <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	484 <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	485 <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	486 <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	487 </section>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	488 </section>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	489 <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	490 <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	491 <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	492 </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	493 <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	494 <assert_contents>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	495 <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	496 </assert_contents>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	497 </output>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	498 </test>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	499 <!-- 8. Ensure JSON report output works -->
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	500 <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	501 <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	502 <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	503 <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	504 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	505 <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	506 <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	507 </section>
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	508 <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	509 <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	510 <assert_contents>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	511 <has_text text="fastp report"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	512 </assert_contents>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	513 </output>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	514 </test>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	515 <!-- 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	516 <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	517 <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	518 <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	519 <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	520 </conditional>
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="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	522 <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	523 <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	524 <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	525 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	526 </section>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	527 <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	528 <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	529 <assert_contents>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	530 <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	531 </assert_contents>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	532 </output>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	533 </test>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	534 <!-- 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	535 <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	536 <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	537 <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	538 <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	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 <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	542 <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	543 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	544 <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	545 <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	546 <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	547 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	548 </section>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	549 <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	550 <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	551 <assert_contents>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	552 <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	553 </assert_contents>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	554 </output>
6 7c49e331a737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15 iuc parents: 5 diff changeset	555 </test>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	556 <!-- 11. Test fastqsanger files with different length -->
11 d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	557 <test expect_exit_code="255" expect_failure="true">
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	558 <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	559 <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	560 <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	561 <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	562 <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	563 <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	564 </collection>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	565 </param>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	566 </conditional>
11 d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	567 </test>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	568 <!-- 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	569 <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	570 <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	571 <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	572 <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	573 <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	574 <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	575 <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	576 </collection>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	577 </param>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	578 <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	579 <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	580 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	581 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	582 <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	583 <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	584 <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	585 </section>
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	586 <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	587 <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	588 <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	589 <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	590 </output_collection>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	591 <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	592 <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	593 <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	594 <assert_contents>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	595 <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	596 </assert_contents>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	597 </element>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	598 </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	599 </test>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	600 <!-- 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	601 <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	602 <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	603 <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	604 <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	605 <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	606 <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	607 <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	608 </collection>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	609 </param>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	610 <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	611 <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	612 <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	613 </conditional>
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 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	616 <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	617 </section>
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	618 <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	619 <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	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 <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	622 </assert_contents>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	623 </output>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	624 </test>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	625 <!-- 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	626 <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	627 <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	628 <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	629 <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	630 <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	631 <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	632 <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	633 </collection>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	634 </param>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	635 <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	636 <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	637 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	638 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	639 <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	640 <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	641 <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	642 </section>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	643 <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	644 <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	645 <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	646 <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	647 </output_collection>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	648 <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	649 <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	650 <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	651 <assert_contents>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	652 <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	653 </assert_contents>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	654 </element>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	655 </output_collection>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	656 </test>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	657 <!-- 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	658 <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	659 <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	660 <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	661 <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	662 <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	663 <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	664 <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	665 </collection>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	666 </param>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	667 <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	668 <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	669 <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	670 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	671 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	672 <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	673 <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	674 </section>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	675 <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	676 <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	677 <assert_contents>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	678 <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	679 </assert_contents>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	680 </output>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	681 </test>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	682 <!--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	683 <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	684 <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	685 <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	686 <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	687 <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	688 <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	689 <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	690 </collection>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	691 </param>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	692 </conditional>
515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	693 <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	694 <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	695 </section>
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	696 <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	697 <assert_contents>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	698 <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	699 </assert_contents>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	700 </output>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	701 <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	702 <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	703 <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	704 </output_collection>
6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	705 </test>
0 cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	706 </tests>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	707 <help><![CDATA[
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	708 .. class:: infomark
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	709
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	710 What it does
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	711
11 d5ae828d1c3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6b8fbd9db12329e2f49eee672b185015c3e35d4f iuc parents: 9 diff changeset	712 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	713 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	714
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	715 Features
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	716
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	717 1. Filter out bad reads (too low quality, too short, or too many N...)
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	718
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	719 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	720
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	721 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	722
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	723 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	724
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	725 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	726
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	727 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	728
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	729 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	730
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	731 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	732
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	733 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	734
12 6292d4ff1ddd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d iuc parents: 11 diff changeset	735 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	736
1 adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28 iuc parents: 0 diff changeset	737 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	738
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	739 -----
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	740
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	741 Inputs
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	742
14 9047af1bc797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 17a0a67dfbc7541a7fe3618cfbbb71d814042889 iuc parents: 13 diff changeset	743 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	744
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	745 -----
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	746
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	747 Outputs
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	748
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	749 * 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	750 * 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	751 * 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	752 * 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	753
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	754 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	755
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	756 * 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	757 * 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	758
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	759 .. _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	760
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	761 ]]></help>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	762 <citations>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304 iuc parents: diff changeset	763 <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	764 </citations>
15 515315f1a8a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4 iuc parents: 14 diff changeset	765 </tool>

Mercurial > repos > iuc > fastp

annotate fastp.xml @ 16:d6c9f863a9db draft