Mercurial > repos > lparsons > cutadapt

annotate cutadapt.xml @ 25:4e5056fefd88 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
author iuc
date Fri, 02 Jul 2021 21:20:57 +0000
parents 288f97432497
children 44e2cc14f75b
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288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
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1 <tool id="cutadapt" name="Cutadapt" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@" profile="20.01">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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2 <description>Remove adapter sequences from FASTQ/FASTA</description>
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3 <macros>
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iuc
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4 <import>macros.xml</import>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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5 </macros>
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288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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6 <expand macro='edam_ontology' />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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7 <expand macro='requirements' />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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8 <expand macro='xrefs'/>
8
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation)
lparsons
parents: 5
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9 <version_command>cutadapt --version</version_command>
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
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10
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11 <command detect_errors="exit_code"><![CDATA[
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12 ## Link in the input and output files, so Cutadapt can tell their type
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f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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14 #import re
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
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15 #set read1 = "input_f"
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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16 #set read2 = "input_r"
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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17 #set paired = False
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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18 #set library_type = str($library.type)
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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19 #if $library_type == 'paired':
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iuc
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20 #set paired = True
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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21 #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.element_identifier))
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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22 #set read2 = re.sub('[^\w\-\s]', '_', str($library.input_2.element_identifier))
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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23 #set input_1 = $library.input_1
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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24 #set input_2 = $library.input_2
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25 #else if $library_type == 'paired_collection'
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288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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26 #set paired = True
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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27 #set input_1 = $library.input_1.forward
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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28 #set input_2 = $library.input_1.reverse
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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29 #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.name)) + "_1"
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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30 #set read2 = re.sub('[^\w\-\s]', '_', str($library.input_1.name)) + "_2"
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31 #else
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288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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32 #set input_1 = $library.input_1
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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33 #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.element_identifier))
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34 #end if
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36 #if $input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
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37 #set ext = ".fq.gz"
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f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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38 #else if $input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
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39 #set ext = ".fq.bz2"
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f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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40 #else if $input_1.is_of_type('fasta'):
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41 #set ext = ".fa"
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42 #else:
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43 #set ext = ".fq"
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44 #end if
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45 #set read1 = $read1 + $ext
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iuc
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46 #set out1 = "out1" + $ext
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iuc
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47 #set rest_output = "rest_output" + $ext
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iuc
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48 #set wild_output = "wild_output" + $ext
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iuc
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49 #set too_short_output = "too_short_output" + $ext
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50 #set too_long_output = "too_long_output" + $ext
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51 #set untrimmed_output = "untrimmed_output" + $ext
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52 ln -f -s '${input_1}' '$read1' &&
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53
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54 #if $paired:
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
iuc
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55 #if $input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
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e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
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56 #set ext2 = ".fq.gz"
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57 #else if $input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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58 #set ext2 = ".fq.gz"
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59 #else if $input_2.is_of_type('fasta'):
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60 #set ext2 = ".fa"
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61 #else:
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62 #set ext2 = ".fq"
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63 #end if
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64 #set read2 = $read2 + $ext2
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65 #set out2 = "out2" + $ext2
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66 #set too_short_paired_output = "too_short_paired_output" + $ext2
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67 #set too_long_paired_output = "too_long_paired_output" + $ext2
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68 #set untrimmed_paired_output = "untrimmed_paired_output" + $ext2
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69 ln -f -s '${input_2}' '$read2' &&
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70 #end if
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71
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72 ## Run Cutadapt
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
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73
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74 #if 'multiple_output' in $output_selector:
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75 mkdir split &&
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76 #end if
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77
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78 cutadapt
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79
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80 -j=\${GALAXY_SLOTS:-4}
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81
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82 #if str( $library.type ) == "single":
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83 @read1_options@
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84 #if 'multiple_output' in $output_selector:
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85 --output='split/{name}.${input_1.ext}'
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86 #else:
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87 --output='$out1'
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88 #end if
13
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89 #else:
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90 @read1_options@
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91 @read2_options@
23
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92 #if $library.type == "paired"
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93 --output='$out1'
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94 --paired-output='$out2'
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
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95 #else
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96 --output='$out_pairs.forward'
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
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97 --paired-output='$out_pairs.reverse'
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98 #end if
13
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99 #end if
8
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lparsons
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100
13
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101 --error-rate=$adapter_options.error_rate
24
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102 --times=$adapter_options.times
13
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103 --overlap=$adapter_options.overlap
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104 $adapter_options.no_indels
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105 $adapter_options.match_read_wildcards
24
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106 --action=$adapter_options.action
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107 $adapter_options.revcomp
11
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108
24
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109 $filter_options.discard_trimmed
13
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110 $filter_options.discard_untrimmed
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111
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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112 #if str($filter_options.minimum_length) and str($filter_options.length_R2_options.length_R2_status) == 'True':
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113 --minimum-length=$filter_options.minimum_length:$filter_options.length_R2_options.R2_minimum
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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114 #else if str($filter_options.minimum_length):
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115 --minimum-length=$filter_options.minimum_length
13
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116 #end if
24
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117 #if str($filter_options.maximum_length) and str($filter_options.length_R2_options.length_R2_status) == 'True':
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118 --maximum-length=$filter_options.maximum_length:$filter_options.length_R2_options.R2_maximum
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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119 #else if str($filter_options.maximum_length):
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120 --maximum-length=$filter_options.maximum_length
13
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121 #end if
22
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122 #if str($filter_options.max_n):
13
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123 --max-n=$filter_options.max_n
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124 #end if
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125 #if str( $library.type ) != "single":
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126 #if $filter_options.pair_filter:
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127 --pair-filter=$filter_options.pair_filter
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128 #end if
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129 #end if
24
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130 #if str($filter_options.max_expected_errors):
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131 --max-expected-errors=$filter_options.max_expected_errors
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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132 #end if
9
93d58ffe39f1 Updated to version 1.6
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133
93d58ffe39f1 Updated to version 1.6
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134
13
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135 #if str($read_mod_options.quality_cutoff) != '0':
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136 --quality-cutoff=$read_mod_options.quality_cutoff
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137 #end if
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138 #if str($read_mod_options.nextseq_trim) != '0':
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
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139 --nextseq-trim=$read_mod_options.nextseq_trim
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140 #end if
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141 $read_mod_options.trim_n
24
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142 #if str($read_mod_options.shorten_options.shorten_values) == 'True':
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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143 #if str($read_mod_options.shorten_options.shorten_end) == '3prime'
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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144 --length=$read_mod_options.shorten_options.length
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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145 #else
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146 --length=-$read_mod_options.shorten_options.length
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
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147 #end if
13
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148 #end if
24
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149 #if str($read_mod_options.length_tag) != '':
22
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150 --length-tag='$read_mod_options.length_tag'
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151 #end if
24
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152 #if str($read_mod_options.rename) != '':
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153 --rename='$read_mod_options.rename'
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154 #end if
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155 $read_mod_options.zero_cap
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156
8
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lparsons
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diff changeset
157
13
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158 '${read1}'
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159 #if $paired:
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160 '${read2}'
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161 #end if
0
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162
24
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163 #if 'report' in $output_selector:
13
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164 > report.txt
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165 #end if
11
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166 ]]></command>
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167 <inputs>
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168
11
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169 <!-- Reads -->
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170 <conditional name="library">
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171 <param name="type" type="select" label="Single-end or Paired-end reads?">
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172 <option value="single">Single-end</option>
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173 <option value="paired">Paired-end</option>
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174 <option value="paired_collection">Paired-end Collection</option>
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175 </param>
0
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176
11
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177 <when value="single">
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178 <param name="input_1" format="fastq.gz,fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTQ/A file" help="Should be of datatype &quot;fastq.gz&quot; or &quot;fasta&quot;" />
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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179 <expand macro="single_end_options" />
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180 </when>
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181
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182 <when value="paired">
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183 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTQ/A file #1" help="Should be of datatype &quot;fastq.gz&quot;or &quot;fasta&quot;" />
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184 <param name="input_2" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTQ/A file #2" help="Should be of datatype &quot;fastq.gz&quot;or &quot;fasta&quot;" />
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185 <expand macro="paired_end_options" />
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186 </when>
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187
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188 <when value="paired_collection">
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189 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data_collection" collection_type="paired" label="Paired Collection" help="Should be of datatype &quot;fastq.gz&quot; or &quot;fasta&quot;" />
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190 <expand macro="paired_end_options" />
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191 </when>
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192
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193 </conditional>
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194
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195 <!-- Adapter Options -->
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196 <section name="adapter_options" title="Adapter Options">
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197 <param name="action" type="select" label="What to do if a match is found">
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198 <option value="trim" selected="True">Trim: trim adapter and upstream or downstream sequence</option>
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199 <option value="retain">Retain: the read is trimmed, but the adapter sequence is not removed</option>
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200 <option value="mask">Mask: mask adapters with 'N' characters instead of trimming them</option>
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201 <option value="lowercase">Lowercase: convert to lowercase</option>
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202 <option value="none">None: leave unchanged</option>
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203 </param>
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204 <param name="internal" type="select" label="Disallow internal adaptor ocurrences" help="The non-internal 5’ and 3’ adapter types disallow internal occurrences of the adapter sequence. The adapter must always be at one of the ends of the read, but partial occurrences are also ok.">
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205 <option value="X">Enabled</option>
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206 <option value="" selected="True">Disabled</option>
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207 </param>
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208 <param argument="--error-rate" type="float" min="0" max="1" value="0.1" label="Maximum error rate" help="Maximum allowed error rate (no. of errors divided by the length of the matching region)." />
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209 <param argument="--no-indels" type="boolean" value="False" truevalue="--no-indels" falsevalue="" label="Do not allow indels (Use ONLY with anchored 5' (front) adapters)." help="Do not allow indels in the alignments. That is, allow only mismatches. This option is currently only supported for anchored 5' adapters ('^ADAPTER') (default: both mismatches and indels are allowed)." />
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210 <param argument="--times" type="integer" min="1" value="1" label="Match times" help="Try to remove adapters at most COUNT times. Useful when an adapter gets appended multiple times." />
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211 <param argument="--overlap" type="integer" min="1" value="3" label="Minimum overlap length" help="Minimum overlap length. If the overlap between the adapter and the sequence is shorter than LENGTH, the read is not modified. This reduces the number of bases trimmed purely due to short random adapter matches." />
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212 <param name="match_read_wildcards" type="select" label="Match wildcards" help="Allow 'N's as matches. Default: in the adapters but not in the reads">
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213 <option value=" " selected="True">In the adapters but not in the reads</option>
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214 <option value="--match-read-wildcards">In the adapters and in the reads</option>
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215 <option value="--no-match-adapter-wildcards">Nowhere</option>
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216 </param>
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217 <param argument="--revcomp" type="boolean" value="False" truevalue="--revcomp" falsevalue="" label="Look for adapters in the reverse complement" help="Check both the read and its reverse complement for adapter matches. If match is on reverse-complemented version, output that one. Default: check only read." />
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218 </section>
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219
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220 <!-- Filter Options -->
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221 <section name="filter_options" title="Filter Options">
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222 <param argument="--discard-trimmed" type="boolean" value="False" truevalue="--discard-trimmed" falsevalue="" label="Discard Trimmed Reads" help="Discard reads that contain the adapter instead of trimming them. Use the 'Minimum overlap length' option in order to avoid throwing away too many randomly matching reads!" />
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223 <param argument="--discard_untrimmed" type="boolean" value="False" truevalue="--discard-untrimmed" falsevalue="" label="Discard Untrimmed Reads" help="Discard reads that do not contain the adapter." />
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224 <param argument="--minimum-length" type="integer" min="0" optional="True" value="" label="Minimum length (R1)" help="Discard trimmed reads that are shorter than LENGTH. Reads that are too short even before adapter removal are also discarded." />
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225 <param argument="--maximum-length" type="integer" min="0" optional="True" value="" label="Maximum length (R1)" help="Discard trimmed reads that are longer than LENGTH. Reads that are too long even before adapter removal are also discarded." />
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226 <conditional name="length_R2_options">
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227 <param name="length_R2_status" type="select" label="Specify a minimum/maximum length for reverse reads (R2)" help="When trimming paired-end reads, the minimum/maximum lengths for R1 and R2 can be specified separately. If not provided, the same minimum length applies to both reads.">
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228 <option value="True">Enabled</option>
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229 <option value="False" selected="True">Disabled</option>
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230 </param>
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231 <when value="True">
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232 <param name="R2_minimum" type="integer" min="0" value="" optional="True" label="Minimum length (R2)" />
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233 <param name="R2_maximum" type="integer" min="0" value="" optional="True" label="Maximum length (R2)" />
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234 </when>
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235 <when value="False">
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236 </when>
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237 </conditional>
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238 <param argument="--max-n" type="float" min="0" optional="True" label="Max N" help="Discard reads with more than this number of 'N' bases. A number between 0 and 1 is interpreted as a fraction of the read length." />
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239 <param argument="--pair-filter" type="select" optional="True" label="Pair filter" help="Which of the reads in a paired-end read have to match the filtering criterion in order for the pair to be filtered. Default: any">
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240 <option value="any" selected="True">Any: a read pair is discarded (or redirected) if one of the reads (R1 or R2) fulfills the filtering criterion. </option>
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241 <option value="both">Both: filtering criteria must apply to both reads in order for a read pair to be discarded. </option>
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242 <option value="first">First: will make a decision about the read pair by inspecting whether the filtering criterion applies to the first read, ignoring the second read.</option>
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243
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244 </param>
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245 <param argument="--max-expected-errors" type="integer" min="0" optional="True" value="" label="Max expected errors" help="Discard reads whose expected number of errors (computed from quality values) exceeds this value." />
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246 <param argument="--discard-cassava" type="boolean" truevalue="--discard-cassava" falsevalue="" checked="False" label="Discard CASAVA filtering" help="Discard reads that did not pass CASAVA filtering (header has :Y:)." />
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247 </section>
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248
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249 <!-- Read Modification Options -->
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250 <section name="read_mod_options" title="Read Modification Options">
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251 <param argument="--quality-cutoff" type="text" value="0" label="Quality cutoff" help=" Trim low-quality bases from 5' and/or 3' ends of each read before adapter removal. Applied to both reads if data is paired. If one value is given, only the 3' end is trimmed. If two comma-separated cutoffs are given, the 5' end is trimmed with the first cutoff, the 3' end with the second.">
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252 <sanitizer>
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253 <valid initial="string.digits"><add value="," /></valid>
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254 </sanitizer>
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255 <validator type="regex">[0-9,]+</validator>
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256 </param>
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257 <param argument="--nextseq-trim" type="integer" value="0" label="NextSeq trimming" help="Experimental option for quality trimming of NextSeq data. This is necessary because that machine cannot distinguish between G and reaching the end of the fragment (it encodes G as ‘black’). This option works like regular quality trimming (where one would use -q 20 instead), except that the qualities of G bases are ignored." />
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258 <param argument="--trim-n" type="boolean" truevalue="--trim-n" falsevalue="" checked="False" label="Trim Ns" help="Trim N's on ends of reads." />
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259 <param argument="--strip-suffix" label="Strip suffix" type="text" help="Remove this suffix from read names if present." />
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260 <conditional name="shorten_options">
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261 <param name="shorten_values" type="select" label="Shortening reads to a fixed length" help="If you want to remove a fixed number of bases from each read, use the –cut option instead.">
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262 <option value="True">Enabled</option>
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263 <option value="False" selected="True">Disabled</option>
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264 </param>
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265 <when value="True">
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266 <param argument="--length" type="integer" value="0" label="Length" help="Shorten reads to this length. This modification is applied after adapter trimming." />
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267 <param name="shorten_end" type="select" label="End at which to apply the slice">
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268 <option value="3prime">3' ends</option>
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269 <option value="5prime">5' ends</option>
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270 </param>
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271 </when>
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272 <when value="False">
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273 </when>
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274 </conditional>
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275 <param argument="--length-tag" label="Length tag" type="text" optional="True" help="Search for TAG followed by a decimal number in the name of the read (description/comment field of the FASTA or FASTQ file). Replace the decimal number with the correct length of the trimmed read. For example, use --length-tag 'length=' to search for fields like 'length=123'." >
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276 <sanitizer invalid_char="">
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277 <valid initial="string.letters,string.digits">
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278 <add value="/" />
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279 <add value="+" />
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280 <add value="-" />
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281 <add value="=" />
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282 <add value=" " />
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283 <add value="_" />
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284 </valid>
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285 </sanitizer>
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286 <validator type="regex">[A-Za-z0-9 =-_/+]+</validator>
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287 </param>
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288 <param argument="--rename" label="Rename reads" type="text" optional="True" help="This option can be used to rename both single-end and paired-end reads. ">
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289 <sanitizer invalid_char="">
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290 <valid initial="string.letters,string.digits">
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291 <add value="{" />
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292 <add value="}" />
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293 <add value="_" />
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294 <add value="=" />
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295 <add value=" " />
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296 </valid>
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297 </sanitizer>
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298 <validator type="regex">[A-Za-z0-9 {}=_]+</validator>
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299 </param>
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300 <param argument="--zero-cap" type="boolean" truevalue="--zero-cap" falsevalue="" checked="False" label="Change negative quality values to zero" />
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301 </section>
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302
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303 <!-- Output Options -->
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304 <param name="output_selector" type="select" multiple="True" display="checkboxes" label="Outputs selector">
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305 <option value="report">Report: Cutadapt's per-adapter statistics. You can use this file with MultiQC.</option>
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306 <option value="info_file">Info file: write information about each read and its adapter matches.</option>
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307 <option value="rest_file">Rest of read: when the adapter matches in the middle of a read, write the rest (after the adapter).</option>
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308 <option value="wildcard_file">Wildcard file: when the adapter has wildcard bases (Ns) write adapter bases matching wildcard positions.</option>
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309 <option value="too_short_file">Too short reads: write reads that are too short according to minimum length specified (default: discard reads).</option>
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310 <option value="too_long_file">Too long reads: write reads that are too long (according to maximum length specified)</option>
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311 <option value="untrimmed_file">Untrimmed reads: write reads that do not contain the adapter to a separate file, instead of writing them to the regular output file (default: output to same file as trimmed)</option>
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312 <option value="multiple_output">Multiple output: create a separate file for each adapter trimmed (default: all trimmed reads are in a single file)</option>
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313 </param>
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314 </inputs>
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315
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316 <outputs>
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317 <data name="out1" format="fastqsanger" metadata_source="input_1" from_work_dir="out1*" label="${tool.name} on ${on_string}: Read 1 Output">
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318 <filter>library['type'] != 'paired_collection' and 'multiple_output' not in output_selector</filter>
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319 <expand macro="inherit_format_1" />
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320 </data>
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321
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322 <data name="out2" format="fastqsanger" metadata_source="input_2" from_work_dir="out2*" label="${tool.name} on ${on_string}: Read 2 Output" >
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323 <filter>library['type'] == 'paired' and 'multiple_output' not in output_selector</filter>
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324 <expand macro="inherit_format_2" />
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325 </data>
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326
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327 <collection name="out_pairs" type="paired" format_source="input_1" label="${tool.name} on ${on_string}: Reads">
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328 <filter>library['type'] == 'paired_collection' and 'multiple_output' not in output_selector</filter>
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329 </collection>
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330
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331 <data name="report" format="txt" from_work_dir="report.txt" label="${tool.name} on ${on_string}: Report">
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332 <filter>output_selector and 'report' in output_selector</filter>
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333 </data>
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334 <data name="info_file" format="txt" metadata_source="input_1" label="${tool.name} on ${on_string}: Info File" >
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335 <filter>output_selector and 'info_file' in output_selector</filter>
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336 </data>
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337
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338 <data name="rest_output" format="fastqsanger" metadata_source="input_1" from_work_dir="rest_output*" label="${tool.name} on ${on_string}: Rest of Reads (R1 only)" >
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339 <filter>output_selector and 'rest_file' in output_selector</filter>
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340 <expand macro="inherit_format_1" />
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341 </data>
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342
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343 <data name="wild_output" format="txt" metadata_source="input_1" from_work_dir="wild_output*" label="${tool.name} on ${on_string}: Wildcard File" >
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344 <filter>output_selector and 'wildcard_file' in output_selector</filter>
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345 </data>
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346
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347 <data name="untrimmed_output" format="fastqsanger" metadata_source="input_1" from_work_dir="untrimmed_output*" label="${tool.name} on ${on_string}: Untrimmed Read 1" >
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348 <filter>output_selector and 'untrimmed_file' in output_selector</filter>
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349 <expand macro="inherit_format_1" />
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lparsons
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350 </data>
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351 <data name="untrimmed_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="untrimmed_paired_output*" label="${tool.name} on ${on_string}: Untrimmed Read 2" >
24
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352 <filter>library['type'] == 'paired' or library['type'] == 'paired_collection'</filter>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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353 <filter>output_selector and 'untrimmed_file' in output_selector </filter>
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354 <expand macro="inherit_format_2" />
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355 </data>
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356
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diff changeset
357 <data name="too_short_output" format="fastqsanger" metadata_source="input_1" from_work_dir="too_short_output*" label="${tool.name} on ${on_string}: Too Short Read 1" >
24
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iuc
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358 <filter>output_selector and 'too_short_file' in output_selector</filter>
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iuc
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359 <expand macro="inherit_format_1" />
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lparsons
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360 </data>
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diff changeset
361 <data name="too_short_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="too_short_paired_output*" label="${tool.name} on ${on_string}: Too Short Read 2" >
24
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iuc
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362 <filter>library['type'] == 'paired' or library['type'] == 'paired_collection'</filter>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
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363 <filter>output_selector and 'too_short_file' in output_selector</filter>
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iuc
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364 <expand macro="inherit_format_2" />
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lparsons
parents: 8
diff changeset
365 </data>
20
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diff changeset
366 <data name="too_long_output" format="fastqsanger" metadata_source="input_1" from_work_dir="too_long_output*" label="${tool.name} on ${on_string}: Too Long Read 1" >
24
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iuc
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diff changeset
367 <filter>output_selector and 'too_long_file' in output_selector</filter>
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diff changeset
368 <expand macro="inherit_format_1" />
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369 </data>
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diff changeset
370 <data name="too_long_paired_output" format="fastqsanger" metadata_source="input_2" from_work_dir="too_long_paired_output*" label="${tool.name} on ${on_string}: Too Long Read 2" >
24
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iuc
parents: 23
diff changeset
371 <filter>library['type'] == 'paired' or library['type'] == 'paired_collection'</filter>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
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diff changeset
372 <filter>output_selector and 'too_long_file' in output_selector</filter>
12
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iuc
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diff changeset
373 <expand macro="inherit_format_2" />
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lparsons
parents: 8
diff changeset
374 </data>
16
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parents: 15
diff changeset
375
18
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iuc
parents: 17
diff changeset
376 <collection name="split_output" type="list" label="${tool.name} on ${on_string}: Split outputs" >
5c7e7d905b33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b58d6ff959a1d920fd0d9b02e43d2482667d61e8
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diff changeset
377 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;fastq.*)" directory="split" />
24
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iuc
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diff changeset
378 <filter>output_selector and 'multiple_output' in output_selector</filter>
16
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iuc
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diff changeset
379 </collection>
9
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lparsons
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diff changeset
380 </outputs>
93d58ffe39f1 Updated to version 1.6
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diff changeset
381
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lparsons
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diff changeset
382 <tests>
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diff changeset
383 <!-- Ensure fastq works -->
23
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iuc
parents: 22
diff changeset
384 <test expect_num_outputs="1">
11
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iuc
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diff changeset
385 <param name="type" value="single" />
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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diff changeset
386 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
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iuc
parents: 24
diff changeset
387 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
388 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
389 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
390 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
391 <param name="adapter" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
392 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
393 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
394 </section>
12
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iuc
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diff changeset
395 <output name="out1" file="cutadapt_small.out" ftype="fastq"/>
11
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iuc
parents: 10
diff changeset
396 </test>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
397 <!-- Ensure single end fastq.gz works -->
23
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iuc
parents: 22
diff changeset
398 <test expect_num_outputs="1">
11
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iuc
parents: 10
diff changeset
399 <param name="type" value="single" />
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
400 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
25
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iuc
parents: 24
diff changeset
401 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
402 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
403 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
404 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
405 <param name="adapter" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
406 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
407 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
408 </section>
12
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diff changeset
409 <output name="out1" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/>
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lparsons
parents: 8
diff changeset
410 </test>
11
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iuc
parents: 10
diff changeset
411 <!-- Ensure paired end fastq.gz works -->
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
412 <test expect_num_outputs="2">
11
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iuc
parents: 10
diff changeset
413 <param name="type" value="paired" />
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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diff changeset
414 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
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iuc
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diff changeset
415 <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />
25
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iuc
parents: 24
diff changeset
416 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
417 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
418 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
419 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
420 <param name="adapter" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
421 </conditional>
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iuc
parents: 24
diff changeset
422 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
423 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
424 <section name="r2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
425 <repeat name="adapters2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
426 <conditional name="adapter_source2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
427 <param name="adapter_source_list2" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
428 <param name="adapter2" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
429 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
430 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
431 </section>
12
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iuc
parents: 11
diff changeset
432 <output name="out1" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/>
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iuc
parents: 11
diff changeset
433 <output name="out2" decompress="True" file="cutadapt_out2.fq.gz" ftype="fastq.gz"/>
21
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
434 <assert_command>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
435 <not_has_text text="--discard-trimmed"/>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
436 <not_has_text text="--discard-untrimmed"/>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
437 <not_has_text text="--minimum-length"/>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
438 <not_has_text text="--maximum-length"/>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
439 <not_has_text text="--max-n"/>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
440 <has_text text="--pair-filter=any"/>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
441 </assert_command>
12
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iuc
parents: 11
diff changeset
442 </test>
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
443 <!-- Ensure paired collection works -->
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
444 <test expect_num_outputs="3">
12
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
445 <param name="type" value="paired_collection" />
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
446 <param name="input_1">
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
447 <collection type="paired">
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
448 <element name="forward" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
449 <element name="reverse" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
450 </collection>
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
451 </param>
25
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iuc
parents: 24
diff changeset
452 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
453 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
454 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
455 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
456 <param name="adapter" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
457 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
458 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
459 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
460 <section name="r2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
461 <repeat name="adapters2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
462 <conditional name="adapter_source2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
463 <param name="adapter_source_list2" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
464 <param name="adapter2" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
465 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
466 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
467 </section>
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
468 <output_collection name="out_pairs" type="paired">
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
469 <element name="forward" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz" />
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
470 <element name="reverse" decompress="True" file="cutadapt_out2.fq.gz" ftype="fastq.gz" />
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
471 </output_collection>
11
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iuc
parents: 10
diff changeset
472 </test>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
473 <!-- Ensure built-in adapters work -->
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
474 <test expect_num_outputs="1">
11
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iuc
parents: 10
diff changeset
475 <param name="type" value="single" />
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
476 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
477 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
478 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
479 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
480 <param name="adapter_source_list" value="builtin"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
481 <param name="adapter" value="TGTAGGCC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
482 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
483 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
484 </section>
12
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
485 <output name="out1" file="cutadapt_builtin.out" ftype="fastq"/>
11
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iuc
parents: 10
diff changeset
486 </test>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
487 <!-- Ensure discard file output works -->
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
488 <test expect_num_outputs="1">
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
489 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
490 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
491 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
492 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
493 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
494 <param name="adapter" value="TTAGACATATCTCCGTCG"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
495 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
496 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
497 </section>
9
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
498 <param name="output_filtering" value="filter"/>
21
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iuc
parents: 20
diff changeset
499 <section name="filter_options">
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
500 <param name="discard_trimmed" value="True"/>
21
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
501 </section>
9
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
502 <param name="read_modification" value="none"/>
12
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
503 <output name="out1" file="cutadapt_discard.out" ftype="fastq"/>
21
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
504 <assert_command>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
505 <has_text text="--discard-trimmed"/>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
506 </assert_command>
9
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
507 </test>
11
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iuc
parents: 10
diff changeset
508 <!-- Ensure rest file output works -->
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
509 <test expect_num_outputs="2">
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
510 <param name="input_1" ftype="fasta" value="cutadapt_rest.fa" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
511 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
512 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
513 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
514 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
515 <param name="adapter" value="AAAGATG"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
516 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
517 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
518 </section>
9
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
519 <param name="output_filtering" value="default"/>
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
520 <param name="read_modification" value="none"/>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
521 <param name="output_selector" value="rest_file"/>
12
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iuc
parents: 11
diff changeset
522 <output name="out1" file="cutadapt_rest.out" ftype="fasta"/>
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
523 <output name="rest_output" file="cutadapt_rest2.out" ftype="fasta"/>
9
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
524 </test>
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
525 <!-- Ensure nextseq-trim option works -->
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
526 <test expect_num_outputs="1">
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
527 <param name="type" value="single" />
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
528 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
529 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
530 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
531 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
532 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
533 <param name="adapter" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
534 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
535 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
536 </section>
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
537 <param name="read_modification" value="modify"/>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
538 <param name="nextseq_trim" value="20" />
12
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
539 <output name="out1" decompress="True" file="cutadapt_nextseq_out.fq.gz" ftype="fastq.gz"/>
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
540 </test>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
541 <!-- Ensure Report and Info file output work -->
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
542 <test expect_num_outputs="3">
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
543 <param name="type" value="single" />
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
544 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
545 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
546 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
547 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
548 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
549 <param name="adapter" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
550 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
551 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
552 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
553 <param name="output_selector" value="report,info_file" />
12
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
554 <output name="out1" value="cutadapt_small.out" ftype="fastq"/>
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
555 <output name="report">
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
556 <assert_contents>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
557 <has_text text="Summary"/>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
558 </assert_contents>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
559 </output>
12
78e1cf88d133 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
iuc
parents: 11
diff changeset
560 <output name="info_file" value="cutadapt_info_out.txt" ftype="txt"/>
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
561 </test>
16
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
562
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
563
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
564 <test expect_num_outputs="1">
16
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
565 <conditional name="library">
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
566 <param name="type" value="single" />
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
567 <param name="input_1" ftype="fastq" value="cutadapt_in_split.fastq" />
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
568 <section name="r1" >
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
569 <repeat name="front_adapters">
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
570 <conditional name="front_adapter_source">
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
571 <param name="front_adapter_source_list" value="user"/>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
572 <param name="front_adapter_name" value="A1" />
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
573 <param name="front_adapter" value="^GTCGGTAA" />
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
574 </conditional>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
575 </repeat>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
576 <repeat name="front_adapters">
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
577 <conditional name="front_adapter_source">
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
578 <param name="front_adapter_source_list" value="user"/>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
579 <param name="front_adapter_name" value="A2" />
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
580 <param name="front_adapter" value="^AGGTCACT" />
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
581 </conditional>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
582 </repeat>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
583 </section>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
584 </conditional>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
585 <param name="output_selector" value="multiple_output" />
16
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
586 <output_collection name="split_output" type="list" count="3">
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
587 <element name="A1" value="A1.fastq" ftype="fastq">
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
588 </element>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
589 <element name="A2" value="A2.fastq" ftype="fastq">
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
590 </element>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
591 <element name="unknown" value="unknown.fastq" ftype="fastq">
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
592 </element>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
593 </output_collection>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
594 </test>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
595
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
596 <test expect_num_outputs="1">
21
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
597 <conditional name="library">
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
598 <param name="type" value="single" />
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
599 <param name="input_1" ftype="fastq.gz" value="cutadapt_in_split.fastq.gz" />
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
600 <section name="r1" >
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
601 <repeat name="front_adapters">
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
602 <conditional name="front_adapter_source">
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
603 <param name="front_adapter_source_list" value="file"/>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
604 <param name="front_adapter_file" ftype="fasta" value="barcodes.fasta" />
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
605 </conditional>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
606 </repeat>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
607 </section>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
608 </conditional>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
609 <param name="output_selector" value="multiple_output" />
21
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
610 <output_collection name="split_output" type="list" count="3">
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
611 <element name="A1" decompress="True" file="A1.fastq.gz" ftype="fastq.gz">
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
612 </element>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
613 <element name="A2" decompress="True" file="A2.fastq.gz" ftype="fastq.gz">
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
614 </element>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
615 <element name="unknown" decompress="True" file="unknown.fastq.gz" ftype="fastq.gz">
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
616 </element>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
617 </output_collection>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
618 </test>
18
5c7e7d905b33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b58d6ff959a1d920fd0d9b02e43d2482667d61e8
iuc
parents: 17
diff changeset
619
20
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
620 <!-- Ensure untrimmed file output works -->
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
621 <test expect_num_outputs="2">
20
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
622 <param name="type" value="single" />
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
623 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
624 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
625 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
626 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
627 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
628 <param name="adapter" value="AAAT"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
629 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
630 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
631 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
632 <param name="output_selector" value="untrimmed_file" />
20
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
633 <output name="out1" file="cutadapt_trimmed.out" ftype="fastq"/>
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
634 <output name="untrimmed_output" file="cutadapt_untrimmed.out" ftype="fastq"/>
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
635 </test>
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
636 <!-- Ensure untrimmed gzip file output works -->
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
637 <test expect_num_outputs="2">
20
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
638 <param name="type" value="single" />
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
639 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
640 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
641 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
642 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
643 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
644 <param name="adapter" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
645 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
646 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
647 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
648 <param name="output_selector" value="untrimmed_file" />
20
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
649 <output name="out1" decompress="True" file="cutadapt_trimmed.out.gz" ftype="fastq.gz"/>
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
650 <!--
20
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
651 Do not use the decompress option for this assertion, since it does NOT test that the file is compressed
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
652 See discussion at https://github.com/galaxyproject/galaxy/issues/7671
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
653 `delta="4000" is more than the difference between gzip level 1 and gzip level 9, but much less than the
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
654 difference between level 1 compression and no compression
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
655 -->
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
656 <output name="untrimmed_output" file="cutadapt_untrimmed.out.gz" compare="sim_size" delta="4000" ftype="fastq.gz"/>
e4691e1589d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
iuc
parents: 19
diff changeset
657 </test>
21
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
658 <!-- same as 1st test with paired data + filter options (because of discard_untrimmed no comparison is done) -->
23
c4b82dce8335 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit d1e907795fa943b505723dd6f7bf0a61723d8818"
iuc
parents: 22
diff changeset
659 <test expect_num_outputs="2">
21
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
660 <param name="type" value="paired" />
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
661 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
662 <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
663 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
664 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
665 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
666 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
667 <param name="adapter" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
668 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
669 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
670 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
671 <section name="r2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
672 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
673 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
674 <param name="adapter_source_list2" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
675 <param name="adapter2" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
676 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
677 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
678 </section>
21
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
679 <section name="filter_options">
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
680 <param name="discard_untrimmed" value="true"/>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
681 <param name="minimun_length" value="1"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
682 <param name="maximum_length" value="1000"/>
22
093678460093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
iuc
parents: 21
diff changeset
683 <param name="max_n" value="0"/>
21
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
684 <param name="pair_filter" value="both"/>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
685 </section>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
686 <assert_command>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
687 <has_text text="--discard-untrimmed"/>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
688 <has_text text="--maximum-length=1000"/>
22
093678460093 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
iuc
parents: 21
diff changeset
689 <has_text text="--max-n=0"/>
21
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
690 <has_text text="--pair-filter=both"/>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
691 </assert_command>
104d86c98776 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1e4c2d05b7f1052a16101cb4fc0d9ca4393e9e96"
iuc
parents: 20
diff changeset
692 </test>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
693 <!-- Test cut option -->
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
694 <test expect_num_outputs="1">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
695 <param name="type" value="single" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
696 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
697 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
698 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
699 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
700 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
701 <param name="adapter" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
702 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
703 </repeat>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
704 <param name="cut" value="5"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
705 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
706 <output name="out1" file="cutadapt_small_cut.out" ftype="fastq"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
707 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
708 <!-- Test rename options -->
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
709 <test expect_num_outputs="1">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
710 <param name="type" value="single" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
711 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
712 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
713 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
714 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
715 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
716 <param name="adapter" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
717 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
718 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
719 <param name="cut" value="5"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
720 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
721 <section name="read_mod_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
722 <param name="rename" value="{id} barcode={cut_prefix}"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
723 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
724 <output name="out1" file="cutadapt_small_rename.out" ftype="fastq">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
725 <assert_contents>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
726 <has_text text="@prefix:1_13_1259/1 barcode=AGCCG"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
727 </assert_contents>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
728 </output>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
729 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
730 <!-- Test action options -->
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
731 <test expect_num_outputs="1">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
732 <param name="type" value="single" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
733 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
734 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
735 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
736 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
737 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
738 <param name="adapter" value="CGTCCGAANTAG"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
739 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
740 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
741 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
742 <section name="adapter_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
743 <param name="action" value="retain"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
744 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
745 <output name="out1" file="cutadapt_action_retain.out" ftype="fastq"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
746 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
747 <test expect_num_outputs="1">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
748 <param name="type" value="single" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
749 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
750 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
751 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
752 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
753 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
754 <param name="adapter" value="CGTCCGAANTAG"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
755 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
756 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
757 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
758 <section name="adapter_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
759 <param name="action" value="mask"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
760 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
761 <output name="out1" file="cutadapt_action_mask.out" ftype="fastq"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
762 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
763 <test expect_num_outputs="1">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
764 <param name="type" value="single" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
765 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
766 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
767 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
768 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
769 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
770 <param name="adapter" value="CGTCCGAANTAG"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
771 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
772 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
773 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
774 <section name="adapter_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
775 <param name="action" value="lowercase"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
776 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
777 <output name="out1" file="cutadapt_action_lowercase.out" ftype="fastq"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
778 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
779 <test expect_num_outputs="1">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
780 <param name="type" value="single" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
781 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
782 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
783 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
784 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
785 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
786 <param name="adapter" value="CGTCCGAANTAG"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
787 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
788 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
789 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
790 <section name="adapter_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
791 <param name="action" value="none"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
792 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
793 <output name="out1" file="cutadapt_action_none.out" ftype="fastq"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
794 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
795 <!-- Test revcomp options -->
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
796 <test expect_num_outputs="1">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
797 <param name="type" value="single" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
798 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
799 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
800 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
801 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
802 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
803 <param name="adapter" value="TAAACAGATTAGT"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
804 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
805 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
806 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
807 <section name="adapter_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
808 <param name="revcomp" value="true"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
809 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
810 <output name="out1" file="cutadapt_revcomp.out" ftype="fastq"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
811 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
812 <!-- Test minimum lenghth paired-reads -->
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
813 <test expect_num_outputs="2">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
814 <param name="type" value="paired" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
815 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
816 <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
817 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
818 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
819 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
820 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
821 <param name="adapter" value="ATCTGGTTCC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
822 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
823 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
824 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
825 <section name="r2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
826 <repeat name="adapters2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
827 <conditional name="adapter_source2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
828 <param name="adapter_source_list2" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
829 <param name="adapter2" value="CTACAAG"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
830 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
831 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
832 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
833 <section name="filter_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
834 <param name="minimum_length" value="30"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
835 <param name="pair_filter" value="both"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
836 <conditional name="length_R2_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
837 <param name="length_R2_status" value="True"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
838 <param name="R2_minimum" value="10"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
839 </conditional>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
840 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
841 <output name="out1" decompress="True" file="cutadapt_out1_min_length.fq.gz" ftype="fastq.gz"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
842 <output name="out2" decompress="True" file="cutadapt_out2_min_length.fq.gz" ftype="fastq.gz"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
843 <assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
844 <has_text text="--minimum-length=30:10"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
845 <has_text text="--pair-filter=both"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
846 </assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
847 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
848 <!-- Test maximum lenghth paired-reads -->
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
849 <test expect_num_outputs="2">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
850 <param name="type" value="paired" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
851 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
852 <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
853 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
854 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
855 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
856 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
857 <param name="adapter" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
858 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
859 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
860 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
861 <section name="r2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
862 <repeat name="adapters2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
863 <conditional name="adapter_source2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
864 <param name="adapter_source_list2" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
865 <param name="adapter2" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
866 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
867 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
868 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
869 <section name="filter_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
870 <param name="pair_filter" value="both"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
871 <param name="maximum_length" value="50"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
872 <conditional name="length_R2_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
873 <param name="length_R2_status" value="True"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
874 <param name="R2_maximum" value="30"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
875 </conditional>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
876 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
877 <output name="out1" decompress="True" file="cutadapt_out1_max_length.fq.gz" ftype="fastq.gz"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
878 <output name="out2" decompress="True" file="cutadapt_out2_max_length.fq.gz" ftype="fastq.gz"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
879 <assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
880 <has_text text="--maximum-length=50:30"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
881 <has_text text="--pair-filter=both"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
882 </assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
883 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
884 <!-- Test combination maximum and minimum length paired reads -->
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
885 <test expect_num_outputs="2">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
886 <param name="type" value="paired" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
887 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
888 <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
889 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
890 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
891 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
892 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
893 <param name="adapter" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
894 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
895 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
896 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
897 <section name="r2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
898 <repeat name="adapters2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
899 <conditional name="adapter_source2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
900 <param name="adapter_source_list2" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
901 <param name="adapter2" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
902 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
903 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
904 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
905 <section name="filter_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
906 <param name="pair_filter" value="both"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
907 <param name="minimum_length" value="10"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
908 <param name="maximum_length" value="50"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
909 <conditional name="length_R2_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
910 <param name="length_R2_status" value="True"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
911 <param name="R2_maximum" value="30"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
912 </conditional>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
913 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
914 <output name="out1" decompress="True" file="cutadapt_out1_max_min_01.fq.gz" ftype="fastq.gz"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
915 <output name="out2" decompress="True" file="cutadapt_out2_max_min_01.fq.gz" ftype="fastq.gz"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
916 <assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
917 <has_text text="--minimum-length=10:"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
918 <has_text text="--maximum-length=50:30"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
919 <has_text text="--pair-filter=both"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
920 </assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
921 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
922 <test expect_num_outputs="2">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
923 <param name="type" value="paired" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
924 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
925 <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
926 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
927 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
928 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
929 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
930 <param name="adapter" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
931 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
932 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
933 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
934 <section name="r2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
935 <repeat name="adapters2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
936 <conditional name="adapter_source2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
937 <param name="adapter_source_list2" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
938 <param name="adapter2" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
939 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
940 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
941 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
942 <section name="filter_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
943 <param name="pair_filter" value="both"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
944 <param name="minimum_length" value="10"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
945 <param name="maximum_length" value="50"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
946 <conditional name="length_R2_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
947 <param name="length_R2_status" value="True"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
948 <param name="R2_minimum" value="10"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
949 </conditional>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
950 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
951 <output name="out1" decompress="True" file="cutadapt_out1_max_min_02.fq.gz" ftype="fastq.gz"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
952 <output name="out2" decompress="True" file="cutadapt_out2_max_min_02.fq.gz" ftype="fastq.gz"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
953 <assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
954 <has_text text="--minimum-length=10:10"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
955 <has_text text="--maximum-length=50:"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
956 <has_text text="--pair-filter=both"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
957 </assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
958 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
959 <!-- Test length options -->
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
960 <test expect_num_outputs="1">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
961 <param name="type" value="single" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
962 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
963 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
964 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
965 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
966 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
967 <param name="adapter" value="AGCCGCTANGACG"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
968 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
969 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
970 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
971 <section name="read_mod_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
972 <conditional name="shorten_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
973 <param name="shorten_values" value="True"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
974 <param name="shorten_end" value="3prime"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
975 <param name="length" value="10"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
976 </conditional>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
977 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
978 <output name="out1" file="cutadapt_shorten_3prime.out" ftype="fastq"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
979 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
980 <test expect_num_outputs="1">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
981 <param name="type" value="single" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
982 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
983 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
984 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
985 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
986 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
987 <param name="adapter" value="AGCCGCTANGACG"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
988 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
989 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
990 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
991 <section name="read_mod_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
992 <conditional name="shorten_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
993 <param name="shorten_values" value="True"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
994 <param name="shorten_end" value="5prime"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
995 <param name="length" value="10"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
996 </conditional>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
997 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
998 <output name="out1" file="cutadapt_shorten_5prime.out" ftype="fastq"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
999 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1000 <!-- Test max expected errors options -->
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1001 <test expect_num_outputs="1">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1002 <param name="type" value="single" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1003 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1004 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1005 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1006 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1007 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1008 <param name="adapter" value="AGCGGCTTAGACG"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1009 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1010 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1011 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1012 <section name="filter_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1013 <param name="max_expected_errors" value="10"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1014 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1015 <output name="out1" file="cutadapt_shorten_expected_errors.out" ftype="fastq"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1016 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1017 <!-- Test disallow internal adaptors option -->
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1018 <test expect_num_outputs="1">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1019 <param name="type" value="single" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1020 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1021 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1022 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1023 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1024 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1025 <param name="adapter" value="GAANTAGCTACCAC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1026 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1027 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1028 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1029 <section name="adapter_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1030 <param name="internal" value="X"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1031 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1032 <output name="out1" file="cutadapt_shorten_internal_adapters.out" ftype="fastq"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1033 <assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1034 <has_text text="GAANTAGCTACCACX"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1035 </assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1036 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1037 <test expect_num_outputs="2">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1038 <param name="type" value="paired" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1039 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1_assimetric.fq.gz" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1040 <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2_assimetric.fq.gz" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1041 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1042 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1043 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1044 <param name="adapter_source_list" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1045 <param name="adapter" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1046 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1047 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1048 </section>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1049 <section name="r2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1050 <repeat name="adapters2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1051 <conditional name="adapter_source2">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1052 <param name="adapter_source_list2" value="user"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1053 <param name="adapter2" value="AGATCGGAAGAGC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1054 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1055 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1056 </section>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1057 <section name="adapter_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1058 <param name="internal" value="X"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1059 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1060 <output name="out1" decompress="True" file="cutadapt_out1_internal_adapter.fq.gz" ftype="fastq.gz"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1061 <output name="out2" decompress="True" file="cutadapt_out2_internal_adapter.fq.gz" ftype="fastq.gz"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1062 <assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1063 <has_text text="AGATCGGAAGAGCX"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1064 </assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1065 </test>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1066 <test expect_num_outputs="1">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1067 <param name="type" value="single" />
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1068 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
25
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1069 <section name="r1">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1070 <repeat name="adapters">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1071 <conditional name="adapter_source">
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1072 <param name="adapter_source_list" value="builtin"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1073 <param name="adapter" value="TGTAGGCC"/>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1074 </conditional>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1075 </repeat>
4e5056fefd88 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit cf6548ab28f5f6b2bdce8b1159cfc7ee472f0af6"
iuc
parents: 24
diff changeset
1076 </section>
24
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iuc
parents: 23
diff changeset
1077 <section name="adapter_options">
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1078 <param name="internal" value="X"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1079 </section>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1080 <output name="out1" file="cutadapt_builtin_internal_adapter.out" ftype="fastq"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1081 <assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1082 <has_text text="TGTAGGCCX"/>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1083 </assert_command>
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1084 </test>
9
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
1085 </tests>
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1086
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1087 <help><![CDATA[
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1088
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1089 .. class:: infomark
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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parents: 10
diff changeset
1090
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1091 **What it does**
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1092
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1093 -------------------
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1094
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1095 **Cutadapt** finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1096
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1097 Cleaning your data in this way is often required: Reads from small-RNA sequencing contain the 3’ sequencing adapter because the read is longer than the molecule that is sequenced, such as in microRNA, or CRISPR data, or Poly-A tails that are useful for pulling out RNA from your sample but often you don’t want them to be in your reads.
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1098
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1099 Cutadapt_ helps with these trimming tasks by finding the adapter or primer sequences in an error-tolerant way. It can also modify and filter reads in various ways. Cutadapt searches for the adapter in all reads and removes it when it finds it. Unless you use a filtering option, all reads that were present in the input file will also be present in the output file, some of them trimmed, some of them not. Even reads that were trimmed entirely (because the adapter was found in the very beginning) are output. All of this can be changed with options in the tool form above.
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1100
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1101 The tool is based on the **Open Source** Cutadapt_ tool. See the complete `Cutadapt documentation`_ for additional details. If you use Cutadapt, please cite *Marcel, 2011* under **Citations** below.
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1102
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1103 -------------------
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1104
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1105 **Inputs**
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1106
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1107 -------------------
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1108
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1109 Input files for Cutadapt need to be:
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1110
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1111 - FASTQ.GZ, FASTQ.BZ2, FASTQ or FASTA
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1112
19
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diff changeset
1113 To trim an adapter, input the ADAPTER sequence in plain text or in a FASTA file e.g. AACCGGTT (with the characters: **$**, **^**, **...**, if anchored or linked).
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1114
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1115 ============================================= ===================
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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parents: 10
diff changeset
1116 **Option** **Sequence**
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1117 --------------------------------------------- -------------------
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1118 3’ (End) Adapter ADAPTER
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1119 Anchored 3’ Adapter ADAPTER$
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1120
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1121 5’ (Front) Adapter ADAPTER
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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diff changeset
1122 Anchored 5’ Adapter ^ADAPTER
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1123
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1124 5’ or 3’ (Both possible) ADAPTER
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1125
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1126 Linked Adapter - 3' (End) only ADAPTER1...ADAPTER2
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1127 Non-anchored Linked Adapter - 5' (Front) only ADAPTER1...ADAPTER2
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1128 ============================================= ===================
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1129
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1130 Below is an illustration of the allowed adapter locations relative to the read and depending on the adapter type:
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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diff changeset
1131
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1132 .. image:: $PATH_TO_IMAGES/adapters.svg
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1133
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1134
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1135 -------------------
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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parents: 10
diff changeset
1136
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1137 *Example: Illumina TruSeq Adapters*
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1138
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1139 -------------------
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1140
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1141 If you have reads containing Illumina TruSeq adapters, for example, follow these steps.
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1142
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1143
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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diff changeset
1144 For Single-end reads as well as the first reads of Paired-end data:
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1145
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1146 **Read 1**
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1147
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1148 In the **3' (End) Adapters** option above, insert A + the “TruSeq Indexed Adapter” prefix that is common to all Indexed Adapter sequences, e.g insert:
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1149
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1150 AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1151
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1152
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1153 For the second reads of Paired-end data:
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1154
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1155 **Read 2**
8
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation)
lparsons
parents: 5
diff changeset
1156
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1157 In the **3' (End) Adapters** option above, insert the reverse complement of the “TruSeq Universal Adapter”:
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1158
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1159 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1160
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1161 The adapter sequences can be found in the document `Illumina TruSeq Adapters De-Mystified`_.
8
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation)
lparsons
parents: 5
diff changeset
1162
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1163 -----------
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1164
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1165 **Outputs**
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1166
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1167 -----------
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1168
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1169 - Trimmed reads
8
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation)
lparsons
parents: 5
diff changeset
1170
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1171 Optionally, under **Output Options** you can choose to output
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1172
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1173 * Report
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1174 * Info file
8
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation)
lparsons
parents: 5
diff changeset
1175
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation)
lparsons
parents: 5
diff changeset
1176
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1177 **Report**
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1178
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1179 Cutadapt can output per-adapter statistics if you select to output the report above.
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1180
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1181 Example:
8
2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation)
lparsons
parents: 5
diff changeset
1182
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1183 ::
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1184
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1185 This is cutadapt 3.4 with Python 3.9.2
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1186
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1187 Command line parameters: -j=1 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --output=out1.fq.gz --paired-output=out2.fq.gz --error-rate=0.1 --times=1
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1188 --overlap=3 --action=trim --minimum-length=30:40 --pair-filter=both --cut=0 bwa-mem-fastq1_assimetric_fq_gz.fq.gz bwa-mem-fastq2_assimetric_fq_gz.fq.gz
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1189
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1190 Processing reads on 1 core in paired-end mode ...
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1191 Finished in 0.01 s (129 µs/read; 0.46 M reads/minute).
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1192
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1193 === Summary ===
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1194
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1195 Total read pairs processed: 99
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1196 Read 1 with adapter: 2 (2.0%)
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1197 Read 2 with adapter: 4 (4.0%)
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1198 Pairs that were too short: 3 (3.0%)
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1199 Pairs written (passing filters): 96 (97.0%)
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1200
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1201 Total basepairs processed: 48,291 bp
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1202 Read 1: 24,147 bp
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1203 Read 2: 24,144 bp
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1204 Total written (filtered): 48,171 bp (99.8%)
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1205 Read 1: 24,090 bp
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1206 Read 2: 24,081 bp
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1207
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1208
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1209 **Info file**
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1210
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1211 The info file contains information about the found adapters. The output is a tab-separated text file. Each line corresponds to one read of the input file.
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1212
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1213 Columns contain the following data:
9
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
1214
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1215 * **1st**: Read name
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1216 * **2nd**: Number of errors
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1217 * **3rd**: 0-based start coordinate of the adapter match
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1218 * **4th**: 0-based end coordinate of the adapter match
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1219 * **5th**: Sequence of the read to the left of the adapter match (can be empty)
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1220 * **6th**: Sequence of the read that was matched to the adapter
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1221 * **7th**: Sequence of the read to the right of the adapter match (can be empty)
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1222 * **8th**: Name of the found adapter
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1223 * **9th**: Quality values corresponding to sequence left of the adapter match (can be empty)
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1224 * **10th**: Quality values corresponding to sequence matched to the adapter (can be empty)
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1225 * **11th**: Quality values corresponding to sequence to the right of the adapter (can be empty)
9
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
1226
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1227 The concatenation of columns 5-7 yields the full read sequence. Column 8 identifies the found adapter. Adapters without a name are numbered starting from 1. Fields 9-11 are empty if quality values are not available. Concatenating them yields the full sequence of quality values.
9
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
1228
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
1229 If no adapter was found, the format is as follows:
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
1230
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1231 #. Read name
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1232 #. The value -1
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1233 #. The read sequence
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1234 #. Quality values
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1235
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1236 When parsing the file, be aware that additional columns may be added in the future. Note also that some fields can be empty, resulting in consecutive tabs within a line.
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1237
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1238 If the --times option is used and greater than 1, each read can appear more than once in the info file. There will be one line for each found adapter, all with identical read names. Only for the first of those lines will the concatenation of columns 5-7 be identical to the original read sequence (and accordingly for columns 9-11). For subsequent lines, the shown sequence are the ones that were used in subsequent rounds of adapter trimming, that is, they get successively shorter.
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1239
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1240
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1241 --------------------
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1242
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1243 **Rename Reads**
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1244
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1245 --------------------
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1246
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1247
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1248 The --rename option expects a template string such as {id} extra_info {adapter_name} as a parameter. It can contain regular text and placeholders that consist of a name enclosed in curly braces ({placeholdername}).
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1249
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1250 The read name will be set to the template string in which the placeholders are replaced with the actual values relevant for the current read.
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1251
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1252 The following placeholders are currently available for single-end reads:
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1253
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1254 * {header} – the full, unchanged header
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1255 * {id} – the read ID, that is, the part of the header before the first whitespace
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1256 * {comment} – the part of the header after the whitespace following the ID
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1257 * {adapter_name} – the name of adapter that was found in this read or no_adapter if there was none adapter match. If you use --times to do multiple rounds of adapter matching, this is the name of the last found adapter.
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1258 * {cut_prefix} – the prefix removed by the --cut (or -u) option (that is, when used with a positive length argument)
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1259 * {cut_suffix} – the suffix removed by the --cut (or -u) option (that is, when used with a negative length argument)
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1260
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1261 If the --rename option is used with paired-end data, the template is applied separately to both R1 and R2. That is, for R1, the placeholders are replaced with values from R1, and for R2, the placeholders are replaced with values from R2. For example, {comment} becomes R1’s comment in R1 and it becomes R2’s comment in R2.
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1262
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1263
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1264 --------------------
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1265
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1266 **More Information**
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1267
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1268 --------------------
9
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
1269
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1270 See the excellent `Cutadapt documentation`_
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1271
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1272 .. _Cutadapt: https://cutadapt.readthedocs.io/en/stable/
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1273 .. _`Cutadapt documentation`: https://cutadapt.readthedocs.io/en/latest/index.html
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1274 .. _`Illumina TruSeq Adapters De-Mystified`: http://tucf-genomics.tufts.edu/documents/protocols/TUCF_Understanding_Illumina_TruSeq_Adapters.pdf
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1275
9
93d58ffe39f1 Updated to version 1.6
lparsons
parents: 8
diff changeset
1276
11
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1277 --------------------
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1278
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1279 **Galaxy Wrapper Development**
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1280
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1281 --------------------
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1282
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1283 Author: Lance Parsons <lparsons@princeton.edu>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1284
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
diff changeset
1285 ]]></help>
24
288f97432497 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
iuc
parents: 23
diff changeset
1286 <expand macro="citations" />
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
diff changeset
1287 </tool>