Mercurial > repos > iuc > fastp

annotate fastp.xml @ 6:a935cbdf1c0e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15
author iuc
date Thu, 23 Aug 2018 02:53:34 -0400
parents 3e2551a37201
children 6c2351178f8d
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6
a935cbdf1c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15
iuc
parents: 5
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1 <tool id="fastp" name="fastp" version="@WRAPPER_VERSION@.3">
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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2 <description>- fast all-in-one preprocessing for FASTQ files</description>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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3 <macros>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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4 <import>macros.xml</import>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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5 </macros>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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6 <requirements>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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7 <requirement type="package" version="@WRAPPER_VERSION@">fastp</requirement>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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8 </requirements>
3
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9 <version_command>fastp -v</version_command>
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10 <command detect_errors="exit_code"><![CDATA[
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11 #import re
7c82cb2a90c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984
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12
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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13 ## Link input files
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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15 #set ext = '.fastq'
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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5
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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17 #if $single_paired.single_paired_selector == 'paired_collection':
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
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18 #if $single_paired.paired_input.forward.is_of_type('fastq.gz'):
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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19 #set ext = '.fastq.gz'
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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20 #end if
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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21 #set $in1 = $single_paired.paired_input.forward
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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22 #set $in2 = $single_paired.paired_input.reverse
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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23 #set $in1_name = re.sub('[^\w\-\s]', '_', str($single_paired.paired_input.name)) + $ext
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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24 #set $in2_name = re.sub('[^\w\-\s]', '_', str("%s_%s" % ($single_paired.paired_input.name, "R2"))) + $ext
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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25 #set out1 = $output_paired_coll.forward
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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26 #set out2 = $output_paired_coll.reverse
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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27 ln -s '$in1' '$in1_name' &&
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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28 ln -s '$in2' '$in2_name' &&
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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29 #else
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
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30 #if $in1.is_of_type('fastq.gz')
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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31 #set ext = '.fastq.gz'
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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32 #end if
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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33
5
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34 #set $in1_name = re.sub('[^\w\-\s]', '_', str($in1.element_identifier)) + $ext
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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35 ln -s '$in1' '$in1_name' &&
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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36
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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37 #if str($single_paired.single_paired_selector) == 'paired':
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
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38 #set $in2_name = re.sub('[^\w\-\s]', '_', str("%s_R2" % $in2.element_identifier)) + $ext
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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39 ln -s '$in2' '$in2_name' &&
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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40 #end if
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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41 #end if
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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44 ## Run fastp
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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46 fastp
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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47
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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48 --thread \${GALAXY_SLOTS:-1}
4
7c82cb2a90c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984
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49 --report_title 'fastp report for $in1_name'
1
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50
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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51 #if $in1.is_of_type('fastqillumina', 'fastqsolexa', 'fastqillumina.gz', 'fastqsolexa.gz'):
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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52 --phred64
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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53 #end if
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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54
5
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55 -i '$in1_name'
4
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56 -o first${ext}
0
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57
5
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58 #if str($single_paired.single_paired_selector).startswith('paired'):
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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59 -I '$in2_name'
4
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60 -O second${ext}
0
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61 #end if
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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62
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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63
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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64 ## Adapter Trimming Options
0
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65
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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66 $single_paired.adapter_trimming_options.disable_adapter_trimming
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67
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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68 #if str($single_paired.adapter_trimming_options.adapter_sequence1):
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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69 --adapter_sequence '$single_paired.adapter_trimming_options.adapter_sequence1'
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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70 #end if
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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71
5
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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72 #if str($single_paired.single_paired_selector).startswith('paired'):
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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73 #if str($single_paired.adapter_trimming_options.adapter_sequence2):
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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74 --adapter_sequence_r2 '$single_paired.adapter_trimming_options.adapter_sequence2'
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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75 #end if
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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76 #end if
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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78
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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79 ## Global Trimming Options
0
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988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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81 #if str($single_paired.global_trimming_options.trim_front1):
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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82 -f $single_paired.global_trimming_options.trim_front1
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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83 #end if
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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84
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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85 #if str($single_paired.global_trimming_options.trim_tail1):
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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86 -t $single_paired.global_trimming_options.trim_tail1
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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87 #end if
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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88
5
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89 #if str($single_paired.single_paired_selector).startswith('paired'):
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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90 #if str($single_paired.global_trimming_options.trim_front2):
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91 -F $single_paired.global_trimming_options.trim_front2
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92 #end if
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93 #if str($single_paired.global_trimming_options.trim_tail2):
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94 -T $single_paired.global_trimming_options.trim_tail2
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95 #end if
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96 #end if
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97
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98
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99 ## Overrepresented sequence analysis
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100
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101 $overrepresented_sequence_analysis.overrepresentation_analysis
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102
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103 #if str($overrepresented_sequence_analysis.overrepresentation_sampling):
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104 -P $overrepresented_sequence_analysis.overrepresentation_sampling
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105 #end if
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106
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107
1
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108 ## Filter Options
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109
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110 ## Quality filtering options
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111
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112 $filter_options.quality_filtering_options.disable_quality_filtering
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113
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114 #if str($filter_options.quality_filtering_options.qualified_quality_phred):
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115 -q $filter_options.quality_filtering_options.qualified_quality_phred
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116 #end if
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117 #if str($filter_options.quality_filtering_options.unqualified_percent_limit):
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118 -u $filter_options.quality_filtering_options.unqualified_percent_limit
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119 #end if
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120 #if str($filter_options.quality_filtering_options.n_base_limit):
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121 -n $filter_options.quality_filtering_options.n_base_limit
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122 #end if
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123
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124
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125 ## Length filtering options
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126
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127 $filter_options.length_filtering_options.disable_length_filtering
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128
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129 #if str($filter_options.length_filtering_options.length_required):
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130 -l $filter_options.length_filtering_options.length_required
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131 #end if
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132
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133 ## Low complexity filtering options
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134
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135 $filter_options.low_complexity_filter.enable_low_complexity_filter
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136
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137 #if str($filter_options.low_complexity_filter.complexity_threshold):
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138 -Y $filter_options.low_complexity_filter.complexity_threshold
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139 #end if
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140
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141
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142 ## Read Modification Options
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143
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144 ## PolyG tail trimming, useful for NextSeq/NovaSeq data
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145
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146 #if $read_mod_options.polyg_tail_trimming.trimming_select in ['', '-g']:
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147 #if str($read_mod_options.polyg_tail_trimming.poly_g_min_len):
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148 --poly_g_min_len $read_mod_options.polyg_tail_trimming.poly_g_min_len
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149 #end if
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150 $read_mod_options.polyg_tail_trimming.trimming_select
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151 #end if
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152
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153 ## PolyX tail trimming
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154
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155 #if $read_mod_options.polyx_tail_trimming.polyx_trimming_select == '-x':
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156 $read_mod_options.polyx_tail_trimming.polyx_trimming_select
6
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157 #if str($read_mod_options.polyx_tail_trimming.poly_x_min_len):
1
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158 --poly_x_min_len $read_mod_options.polyx_tail_trimming.poly_x_min_len
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159 #end if
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160 #end if
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161
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162 ## UMI processing
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163
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164 #if $read_mod_options.umi_processing.umi:
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165 $read_mod_options.umi_processing.umi
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166 #if str($read_mod_options.umi_processing.umi_loc):
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167 --umi_loc '$read_mod_options.umi_processing.umi_loc'
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168 #end if
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169 #if str($read_mod_options.umi_processing.umi_len):
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170 --umi_len $read_mod_options.umi_processing.umi_len
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171 #end if
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172 #if str($read_mod_options.umi_processing.umi_prefix):
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173 --umi_prefix '$read_mod_options.umi_processing.umi_prefix'
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174 #end if
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175 #end if
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176
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177 ## Per read cutting by quality options
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178
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179 #if $read_mod_options.cutting_by_quality_options.cut_by_quality5 or $read_mod_options.cutting_by_quality_options.cut_by_quality3:
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180
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181 $read_mod_options.cutting_by_quality_options.cut_by_quality5
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182
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183 $read_mod_options.cutting_by_quality_options.cut_by_quality3
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184
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185 #if str($read_mod_options.cutting_by_quality_options.cut_window_size):
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186 -W $read_mod_options.cutting_by_quality_options.cut_window_size
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187 #end if
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188 #if str($read_mod_options.cutting_by_quality_options.cut_mean_quality):
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189 -M $read_mod_options.cutting_by_quality_options.cut_mean_quality
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190 #end if
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191 #end if
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192
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193 ## Base correction by overlap analysis options
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194
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195 $read_mod_options.base_correction_options.correction
0
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196
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197 &&
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198
4
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199 mv first${ext} '${out1}'
5
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200 #if str($single_paired.single_paired_selector).startswith('paired'):
0
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201 &&
4
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202 mv second${ext} '${out2}'
0
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203 #end if
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204 ]]></command>
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205 <inputs>
1
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206
0
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207 <conditional name="single_paired">
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208 <param name="single_paired_selector" type="select" label="Single-end or paired reads">
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209 <option value="single" selected="true">Single-end</option>
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210 <option value="paired">Paired</option>
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211 <option value="paired_collection">Paired Collection</option>
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212 </param>
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213 <when value="single">
5
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214 <expand macro="in" />
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215 <expand macro="adapter_trimming_options" />
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216 <expand macro="global_trimming_options" />
0
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217 </when>
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218 <when value="paired">
5
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219 <expand macro="in" read_number="1" argument="-i"/>
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220 <expand macro="in" read_number="2" argument="-I"/>
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221 <expand macro="adapter_trimming_options">
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222 <expand macro="adapter_sequence" read_number="2"/>
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223 </expand>
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224 <expand macro="global_trimming_options_paired" />
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225 </when>
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226 <when value="paired_collection">
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227 <param name="paired_input" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Select paired collection(s)"/>
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228 <expand macro="adapter_trimming_options">
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229 <expand macro="adapter_sequence" read_number="2"/>
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230 </expand>
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231 <expand macro="global_trimming_options_paired" />
0
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232 </when>
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233 </conditional>
1
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234
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235 <section name="overrepresented_sequence_analysis" title="Overrepresented Sequence Analysis" expanded="False">
0
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236 <param name="overrepresentation_analysis" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="false" label="Enable overrepresented analysis" help="Enable overrepresented sequence analysis."/>
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237 <param name="overrepresentation_sampling" argument="-P" type="integer" optional="true" label="Overrepresentation sampling" help="One in (--overrepresentation_sampling) reads will be computed for overrepresentation analysis (1~10000), smaller is slower, default is 20."/>
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238 </section>
1
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239
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240 <!-- Filter Options -->
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241 <section name="filter_options" title="Filter Options">
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242 <section name="quality_filtering_options" title="Quality filtering options" expanded="True">
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243 <param name="disable_quality_filtering" argument="-Q" type="boolean" truevalue="-Q" falsevalue="" checked="false" label="Disable quality filtering" help="Quality filtering is enabled by default. If this option is specified, quality filtering is disabled."/>
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244 <param name="qualified_quality_phred" argument="-q" type="integer" optional="true" label="Qualified quality phred" help="The quality value that a base is qualified. Default 15 means phred quality >=Q15 is qualified."/>
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245 <param name="unqualified_percent_limit" argument="-u" type="integer" optional="true" label="Unqualified percent limit" help="How many percents of bases are allowed to be unqualified (0~100). Default 40 means 40%."/>
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246 <param name="n_base_limit" argument="-n" type="integer" optional="true" label="N base limit" help="If one read's number of N base is >n_base_limit, then this read/pair is discarded. Default is 5."/>
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247 </section>
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248
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249 <section name="length_filtering_options" title="Length filtering options" expanded="True">
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250 <param name="disable_length_filtering" argument="-L" type="boolean" truevalue="-L" falsevalue="" checked="false" label="Disable length filtering" help="Length filtering is enabled by default. If this option is specified, length filtering is disabled."/>
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251 <param name="length_required" argument="-l" type="integer" optional="true" label="Length required" help="Reads shorter than this value will be discarded. Default is 15."/>
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252 </section>
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253
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254 <section name="low_complexity_filter" title="Low complexity filtering options" expanded="True">
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255 <param name="enable_low_complexity_filter" argument="-y" type="boolean" truevalue="-y" falsevalue="" checked="false" label="Enable low complexity filter" help="The complexity is defined as the percentage of base that is different from its next base, default is No"/>
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256 <param name="complexity_threshold" argument="-Y" type="integer" optional="true" label="Complexity threshold" help="Threshold for low complexity filter (0~100). Default is 30, which means 30% complexity is required."/>
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257 </section>
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258 </section>
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259
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260 <!-- Read Modification Options -->
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261 <section name="read_mod_options" title="Read Modification Options">
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262 <conditional name="polyg_tail_trimming">
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263 <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
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264 <option value="" selected="true">Automatic trimming for Illumina NextSeq/NovaSeq data</option>
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265 <option value="-g">Force polyG tail trimming</option>
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266 <option value="-G">Disable polyG tail trimming</option>
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267 </param>
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268 <when value="-g">
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269 <expand macro="poly_g_min_len" />
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270 </when>
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271 <when value="">
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272 <expand macro="poly_g_min_len" />
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273 </when>
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274 <when value="-G" />
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275 </conditional>
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276
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277 <conditional name="polyx_tail_trimming">
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278 <param name="polyx_trimming_select" type="select" label="PolyX tail trimming" help="Similar to polyG tail trimming. When polyG tail trimming and polyX tail trimming are both enabled, fastp will perform polyG trimming first, then perform polyX trimming. Disabled by default.">
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279 <option value="" selected="true">Disable polyX trimming</option>
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280 <option value="-x">Enable polyX tail trimming</option>
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281 </param>
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282 <when value="-x">
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283 <param name="poly_x_min_len" argument="--poly_x_min_len" type="integer" optional="true" label="PolyX minimum length"
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284 help="The minimum length to detect polyX in the read tail. 10 by default."/>
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285 </when>
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286 <when value="" />
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287 </conditional>
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288
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289 <section name="umi_processing" title="UMI processing" expanded="True">
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290 <param name="umi" argument="-U" type="boolean" truevalue="-U" falsevalue="" checked="false" label="Enable unique molecular identifer" help="Enable unique molecular identifer (UMI) preprocessing."/>
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291 <param name="umi_loc" argument="--umi_loc" type="text" optional="true" label="UMI location" help="Specify the location of UMI, can be (index1/index2/read1/read2/per_index/per_read, default is none."/>
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292 <param name="umi_len" argument="--umi_len" type="integer" optional="true" label="UMI length" help="If the UMI is in read1/read2, its length should be provided."/>
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293 <param name="umi_prefix" argument="--umi_prefix" type="text" optional="true" label="UMI prefix" help="If specified, an underline will be used to connect prefix and UMI (i.e. prefix=UMI, UMI=AATTCG, final=UMI_AATTCG). No prefix by default."/>
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294 </section>
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295
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296 <section name="cutting_by_quality_options" title="Per read cutting by quality options" expanded="True">
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297 <param name="cut_by_quality5" argument="-5" type="boolean" truevalue="-5" falsevalue="" checked="false" label="Cut by quality in front (5')" help="Enable per read cutting by quality in front (5'), default is disabled (WARNING: this will interfere deduplication for both PE/SE data)."/>
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298 <param name="cut_by_quality3" argument="-3" type="boolean" truevalue="-3" falsevalue="" checked="false" label="Cut by quality in tail (3')" help="Enable per read cutting by quality in tail (3'), default is disabled (WARNING: this will interfere deduplication for SE data)."/>
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299 <param name="cut_window_size" argument="-W" type="integer" optional="true" label="Cutting window size" help="The size of the sliding window for sliding window trimming, default is 4."/>
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300 <param name="cut_mean_quality" argument="-M" type="integer" optional="true" label="Cutting mean quality" help="The bases in the sliding window with mean quality below cutting_quality will be cut, default is Q20."/>
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301 </section>
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302
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303 <section name="base_correction_options" title="Base correction by overlap analysis options" expanded="True">
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304 <param name="correction" argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Enable base correction" help="Enable base correction in overlapped regions (only for PE data), default is disabled."/>
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305 </section>
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306 </section>
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307
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308 <section name="output_options" title="Output Options" expanded="False">
0
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309 <param name="report_html" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Output HTML report" help="fastp provides a QC report for the data Before and After filtering within a single HTML page, which enables comparison of the quality statistics changed by the preprocessing step directly"/>
4
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310 <param name="report_json" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output JSON report" help="The JSON report contains all the data visualized in the HTML report. The format of the JSON report is manually optimized to be easily readable by humans and is compatible with MultiQC"/>
0
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311 </section>
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312 </inputs>
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313
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314 <outputs>
5
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315 <data name="out1" format_source="in1" label="${tool.name} on ${on_string}: Read 1 Output">
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316 <filter>single_paired['single_paired_selector'] in ["single", "paired"]</filter>
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317 </data>
0
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318 <data name="out2" format_source="in2" label="${tool.name} on ${on_string}: Read 2 Output">
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319 <filter>single_paired['single_paired_selector'] == "paired"</filter>
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320 </data>
5
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321 <collection name="output_paired_coll" type="paired" structured_like="paired_input" inherit_format="true" label="Paired-end output of ${tool.name} on ${on_string}">
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322 <filter>single_paired['single_paired_selector'] == "paired_collection"</filter>
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323 </collection>
0
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324 <data name="report_html" format="html" from_work_dir="fastp.html" label="${tool.name} on ${on_string}: HTML Report">
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325 <filter>output_options['report_html'] is True</filter>
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326 </data>
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327 <data name="report_json" format="json" from_work_dir="fastp.json" label="${tool.name} on ${on_string}: JSON Report">
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328 <filter>output_options['report_json'] is True</filter>
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329 </data>
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330 </outputs>
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331
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332 <tests>
1
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333 <!-- Ensure default output works -->
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334 <test expect_num_outputs="2">
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335 <param name="in1" ftype="fastqsanger" value="R1.fq"/>
0
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336 <param name="single_paired_selector" value="single"/>
1
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337 <output name="out1" ftype="fastqsanger" file="out1.fq"/>
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338 <output name="report_html">
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339 <assert_contents>
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340 <has_text text="fastp report"/>
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341 </assert_contents>
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342 </output>
0
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343 </test>
5
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344 <!-- Ensure paired collection works -->
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345 <test expect_num_outputs="3">
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346 <param name="single_paired_selector" value="paired_collection"/>
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347 <param name="paired_input">
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348 <collection type="paired">
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349 <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
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350 <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
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351 </collection>
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352 </param>
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353 <output name="report_html">
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354 <assert_contents>
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355 <has_text text="fastp report"/>
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356 </assert_contents>
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357 </output>
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358 <output_collection name="output_paired_coll" type="paired">
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parents: 4
diff changeset
359 <element name="forward" value="out_bwa1.fq" ftype="fastqsanger"/>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 4
diff changeset
360 <element name="reverse" value="out_bwa2.fq" ftype="fastqsanger"/>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 4
diff changeset
361 </output_collection>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 4
diff changeset
362 </test>
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
363 <!-- Ensure custom adapter works -->
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
364 <test expect_num_outputs="2">
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
365 <param name="in1" ftype="fastq" value="R1.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
366 <param name="single_paired_selector" value="single"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
367 <param name="adapter_sequence1" value="ATCG"/>
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
368 <output name="out1" ftype="fastq" file="out_a.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
369 </test>
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
370 <!-- Ensure UMI processing works -->
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
371 <test expect_num_outputs="2">
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
372 <param name="in1" ftype="fastq" value="R1.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
373 <param name="single_paired_selector" value="single"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
374 <section name="umi_processing">
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
375 <param name="umi" value="true"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
376 <param name="umi_loc" value="read1"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
377 <param name="umi_len" value="8"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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diff changeset
378 </section>
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
379 <output name="out1" ftype="fastq" file="out2.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
380 </test>
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
381 <!-- Ensure UMI processing with different lengths works -->
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
382 <test expect_num_outputs="2">
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
383 <param name="in1" ftype="fastq" value="R1.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
384 <param name="single_paired_selector" value="single"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
385 <section name="umi_processing">
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
386 <param name="umi" value="true"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
387 <param name="umi_loc" value="read1"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
388 <param name="umi_len" value="12"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
389 </section>
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
390 <output name="out1" ftype="fastq" file="out3.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
391 </test>
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
392 <!-- Ensure paired-end fastq works -->
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
393 <test expect_num_outputs="3">
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
394 <param name="in1" ftype="fastq" value="bwa-mem-fastq1.fq"/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
395 <param name="in2" ftype="fastq" value="bwa-mem-fastq2.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
396 <param name="single_paired_selector" value="paired"/>
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
397 <output name="out1" ftype="fastq" file="out_bwa1.fq"/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
398 <output name="out2" ftype="fastq" file="out_bwa2.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
399 </test>
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
400 <!-- Ensure paired-end UMI processing of Read 1 works -->
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
401 <test expect_num_outputs="3">
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
402 <param name="in1" ftype="fastq" value="bwa-mem-fastq1.fq"/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
403 <param name="in2" ftype="fastq" value="bwa-mem-fastq2.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
404 <param name="single_paired_selector" value="paired"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
405 <section name="umi_processing">
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
406 <param name="umi" value="true"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
407 <param name="umi_loc" value="read1"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
408 <param name="umi_len" value="8"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
409 </section>
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
410 <output name="out1" ftype="fastq" file="out_bwa_umi_read1_1.fq"/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
411 <output name="out2" ftype="fastq" file="out_bwa_umi_read1_2.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
412 </test>
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
413 <!-- Ensure paired-end UMI processing of Read 2 works -->
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
414 <test expect_num_outputs="3">
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
415 <param name="in1" ftype="fastq" value="bwa-mem-fastq1.fq"/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
416 <param name="in2" ftype="fastq" value="bwa-mem-fastq2.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
417 <param name="single_paired_selector" value="paired"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
418 <section name="umi_processing">
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
419 <param name="umi" value="true"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
420 <param name="umi_loc" value="read2"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
421 <param name="umi_len" value="8"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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diff changeset
422 </section>
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
423 <output name="out1" ftype="fastq" file="out_bwa_umi_read2_1.fq"/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
424 <output name="out2" ftype="fastq" file="out_bwa_umi_read2_2.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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diff changeset
425 </test>
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
426 <!-- Ensure JSON report output works -->
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
427 <test expect_num_outputs="2">
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
428 <param name="in1" ftype="fastqsanger" value="R1.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
429 <param name="single_paired_selector" value="single"/>
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
430 <param name="report_html" value="False"/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
431 <param name="report_json" value="True"/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
432 <output name="out1" ftype="fastqsanger" file="out1.fq"/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
433 <output name="report_json">
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
434 <assert_contents>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
435 <has_text text="fastp report"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
436 </assert_contents>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
437 </output>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
438 </test>
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
439 <!-- Ensure polyG trimming works -->
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
440 <test expect_num_outputs="2">
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
441 <param name="in1" ftype="fastq.gz" value="R1.fq.gz"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
442 <param name="single_paired_selector" value="single"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
443 <param name="trimming_select" value="-g"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
444 <param name="poly_g_min_len" value="10"/>
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
445 <output name="out1" ftype="fastq.gz" decompress="True" file="out1.fq.gz"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
446 </test>
6
a935cbdf1c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15
iuc
parents: 5
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447 <!-- Ensure polyX trimming works -->
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448 <test expect_num_outputs="2">
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449 <param name="in1" ftype="fastq.gz" value="R1.fq.gz"/>
a935cbdf1c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15
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450 <param name="single_paired_selector" value="single"/>
a935cbdf1c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15
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451 <param name="trimming_select" value="-G"/>
a935cbdf1c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15
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452 <param name="polyx_trimming_select" value="-x"/>
a935cbdf1c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15
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453 <param name="poly_x_min_len" value="10"/>
a935cbdf1c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15
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454 <output name="out1" ftype="fastq.gz" decompress="True" file="out1.fq.gz"/>
a935cbdf1c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15
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455 </test>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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456 </tests>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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457 <help><![CDATA[
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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458 .. class:: infomark
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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459
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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460 **What it does**
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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461
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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462 fastp_ is a tool designed to provide fast all-in-one preprocessing for FASTQ files. This tool is developed in C++ with multithreading supported to afford high performance.
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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463
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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464 *Features*
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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465
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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466 1. Filter out bad reads (too low quality, too short, or too many N...)
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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467
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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468 2. Cut low quality bases for per read in its 5' and 3' by evaluating the mean quality from a sliding window (like Trimmomatic but faster)
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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469
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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470 3. Trim all reads in front and tail
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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471
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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472 4. Cut adapters. Adapter sequences can be automatically detected, which means you don't have to input the adapter sequences to trim them.
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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473
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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474 5. Correct mismatched base pairs in overlapped regions of paired end reads, if one base is with high quality while the other is with ultra-low quality
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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475
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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476 6. Trim polyG in 3' ends, which is commonly seen in NovaSeq/NextSeq data. Trim polyX in 3' ends to remove unwanted polyX tailing (i.e. polyA tailing for mRNA-Seq data)
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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477
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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478 7. Preprocess unique molecular identifer (UMI) enabled data, shift UMI to sequence name
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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479
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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480 8. Report JSON format result for further interpreting
0
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481
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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482 9. Visualize quality control and filtering results on a single HTML page (like FASTQC but faster and more informative)
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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483
1
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484 10. Split the output to multiple files (0001.R1.gz, 0002.R1.gz...) to support parallel processing. Two modes can be used, limiting the total split file number, or limitting the lines of each split file (*Not enabled in this Galaxy tool*)
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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485
1
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486 11. Support long reads (data from PacBio / Nanopore devices)
0
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487
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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488 -----
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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489
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490 **Inputs**
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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491
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492 Single-end or Paired-end FASTQ or FASTQ.GZ reads
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493
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494 -----
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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495
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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496 **Outputs**
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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497
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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498 * Processed reads
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499
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500 Optionally, under **Output Options** you can choose to output
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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501
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502 * HTML report (default is Yes)
4
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503 * JSON report (compatible with MultiQC)
0
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504
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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505 .. _fastp: https://github.com/OpenGene/fastp
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506
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507 ]]></help>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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508 <citations>
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509 <citation type="doi">10.1101/274100</citation>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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510 </citations>
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511 </tool>