Mercurial > repos > iuc > bbtools_bbduk

annotate bbduk.xml @ 3:008b8c6f6b26 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
author iuc
date Mon, 06 Feb 2023 18:04:39 +0000
parents ff3b87a0d205
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
008b8c6f6b26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents: 1
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1 <tool id="bbtools_bbduk" name="BBTools: BBduk" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
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2 <description>decontamination using kmers</description>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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3 <macros>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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4 <import>macros.xml</import>
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5 </macros>
3
008b8c6f6b26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
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6 <expand macro="edam_ontology"/>
0
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 #import os
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10 #import re
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11
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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12 #if str($input_type_cond.input_type) in ['single', 'pair']:
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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13 #set read1 = $input_type_cond.read1
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14 ## bbduk uses the file extension to determine the input format.
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ff3b87a0d205 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
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15 #set ext = '.fastq'
0
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16 #if $read1.ext.endswith('.gz'):
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17 #set ext = $ext + '.gz'
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18 #end if
1
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19 #set read1_file = 'forward' + $ext
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20 ln -s '${read1}' '${read1_file}' &&
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21 #if str($input_type_cond.input_type) == 'pair':
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22 #set read2 = $input_type_cond.read2
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23 #set read2_file = 'reverse' + $ext
0
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24 ln -s '${read2}' '${read2_file}' &&
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25 #end if
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26 #else:
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27 #set read1 = $input_type_cond.reads_collection['forward']
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28 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.name))
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29 ## bbduk uses the file extension to determine the input format.
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30 #set ext = $read1_identifier + '.fastq'
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31 #if $read1.ext.endswith('.gz'):
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32 #set ext = $ext + '.gz'
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33 #end if
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34 #set read1_file = $read1_identifier + $ext
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35 ln -s '${read1}' '${read1_file}' &&
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36 #set read2 = $input_type_cond.reads_collection['reverse']
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37 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.name))
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38 #set read2_file = $read2_identifier + $ext
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39 ln -s '${read2}' '${read2_file}' &&
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40 #end if
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41
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42 #if str($reference_type_cond.reference_type) == 'files':
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43 #set refs = list()
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44 #for ref in $reference_type_cond.reference:
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45 ## bbduk looks at the file extension.
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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46 #set ref_name = str($os.path.basename($ref.file_name)) + '.fa'
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47 #if $ref.ext.endswith('.gz'):
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48 gunzip -c '$ref' > '$ref_name' &&
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49 #else:
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50 ln -s '$ref' '$ref_name' &&
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51 #end if
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52 $refs.append(str($ref_name))
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53 #end for
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54 #set refs = ','.join($refs)
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55 #else if str($reference_type_cond.reference_type) == 'keywords':
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56 #set refs = str($reference_type_cond.reference)
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57 #end if
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58
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59 bbduk.sh
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60 in='${read1_file}'
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61
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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62 #if str($input_type_cond.input_type) in ['pair', 'paired']:
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63 in2='${read2_file}'
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64 #end if
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65 #if str($outputs_select).find('outu') >= 0:
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66 out='${outputu}'
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67 #if str($input_type_cond.input_type) in ['pair', 'paired']:
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68 out2='${outputu2}'
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69 #end if
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70 #end if
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71 #if str($outputs_select).find('outm') >= 0:
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72 outm='${outputm}'
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73 #if str($input_type_cond.input_type) in ['pair', 'paired']:
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74 outm2='${outputm2}'
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75 #end if
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76 #end if
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77 #if str($outputs_select).find('outs') >= 0:
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78 outs='${outputs}'
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79 #end if
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80
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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81 #if str($reference_type_cond.reference_type) != 'no_reference':
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82 ref='$refs'
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83 #if str($reference_type_cond.ktrim_cond.ktrim_select) == 'yes':
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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84 ktrim='${reference_type_cond.ktrim_cond.ktrim}'
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85 minlength=$reference_type_cond.ktrim_cond.minlength
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86 #end if
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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87 #end if
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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88
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89 k=$advanced_options.k
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90 rcomp='${advanced_options.rcomp}'
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91 maskmiddle='${advanced_options.maskmiddle}'
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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92 minkmerhits='${advanced_options.minkmerhits}'
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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93 minkmerfraction=$advanced_options.minkmerfraction
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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94 mincovfraction=$advanced_options.mincovfraction
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95 hammingdistance=$advanced_options.hammingdistance
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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96 qhdist=$advanced_options.qhdist
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97 editdistance=$advanced_options.editdistance
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98 forbidn='${advanced_options.forbidn}'
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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99 trimfailures='${advanced_options.trimfailures}'
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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100 findbestmatch='${advanced_options.findbestmatch}'
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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101 skipr1='${advanced_options.skipr1}'
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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102 skipr2='${advanced_options.skipr2}'
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103
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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104 #if str($output_stats_cond.output_stats) == 'yes':
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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105 #if str($output_stats_cond.output_stats_select).find('stats') >= 0:
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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106 stats='${output_stats}'
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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107 #end if
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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108 #if str($output_stats_cond.output_stats_select).find('ref') >= 0:
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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109 refstats='${output_ref}'
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110 #end if
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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111 #if str($output_stats_cond.output_stats_select).find('rpkm') >= 0:
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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112 rpkm='${output_rpkm}'
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113 #end if
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114 #if str($output_stats_cond.output_stats_select).find('dump') >= 0:
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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115 dump='${output_dump}'
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116 #end if
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117 #end if
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118 #if str($output_hists_cond.output_hists) == 'yes':
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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119 #if str($output_hists_cond.output_hists_select).find('bhist') >= 0:
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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120 bhist='${output_bhist}'
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121 #end if
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122 #if str($output_hists_cond.output_hists_select).find('quhist') >= 0:
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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123 qhist='${output_quhist}'
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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124 #end if
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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125 #if str($output_hists_cond.output_hists_select).find('quchist') >= 0:
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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126 qchist='${output_quchist}'
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127 #end if
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128 #if str($output_hists_cond.output_hists_select).find('aqhist') >= 0:
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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129 aqhist='${output_aqhist}'
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130 #end if
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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131 #if str($output_hists_cond.output_hists_select).find('bqhist') >= 0:
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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132 bqhist='${output_bqhist}'
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133 #end if
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134 #if str($output_hists_cond.output_hists_select).find('lhist') >= 0:
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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135 lhist='${output_lhist}'
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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diff changeset
136 #end if
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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137 #if str($output_hists_cond.output_hists_select).find('phist') >= 0:
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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138 phist='${output_phist}'
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139 #end if
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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140 #if str($output_hists_cond.output_hists_select).find('gchist') >= 0:
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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141 gchist='${output_gchist}'
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142 #end if
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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diff changeset
143 #if str($output_hists_cond.output_hists_select).find('enthist') >= 0:
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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diff changeset
144 enthist='${output_enthist}'
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diff changeset
145 #end if
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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diff changeset
146 #end if
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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147 t=\${GALAXY_SLOTS:-4}
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parents:
diff changeset
148 ]]></command>
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diff changeset
149 <inputs>
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parents:
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150 <expand macro="input_type_cond"/>
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iuc
parents:
diff changeset
151 <conditional name="reference_type_cond">
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152 <param name="reference_type" type="select" label="Choose the reference type" help="Optional, no reference is the default">
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iuc
parents:
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153 <option value="no_reference" selected="true">No reference</option>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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154 <option value="files">files</option>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
155 <option value="keywords">keywords</option>
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iuc
parents:
diff changeset
156 </param>
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iuc
parents:
diff changeset
157 <when value="no_reference"/>
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parents:
diff changeset
158 <when value="files">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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diff changeset
159 <param name="reference" type="data" format="fasta,fasta.gz" multiple="true" optional="false" label="Select one or more fasta file"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
160 <expand macro="ktrim_cond"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
161 </when>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
162 <when value="keywords">
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parents:
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163 <param name="reference" type="select" multiple="true" optional="false" label="Select one or more keywords">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
164 <option value="adapters">adapters</option>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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165 <option value="artifacts">artifacts</option>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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diff changeset
166 <option value="phix">phix</option>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
167 <option value="lambda">lambda</option>
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168 <option value="pjet">pjet</option>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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169 <option value="mtst">mtst</option>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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170 <option value="kapa">kapa</option>
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diff changeset
171 </param>
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parents:
diff changeset
172 <expand macro="ktrim_cond"/>
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iuc
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diff changeset
173 </when>
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174 </conditional>
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175 <section name="advanced_options" title="Advanced options" expanded="false">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
176 <param argument="k" type="integer" value="27" min="1" label="Kmer length used for finding contaminants"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
177 <param argument="rcomp" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Look for reverse-complements of kmers in addition to forward kmers?"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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178 <param argument="maskmiddle" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Treat the middle base of a kmer as a wildcard to increase sensitivity in the presence of errors?"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
179 <param argument="minkmerhits" type="integer" value="1" min="1" label="Reads need at least this many matching kmers to be considered as matching the reference"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
diff changeset
180 <param argument="minkmerfraction" type="float" value="0" min="0" label="A read needs at least this fraction of its total kmers to hit a ref in order to be considered a match"/>
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181 <param argument="mincovfraction" type="float" value="0" min="0" label="A read needs at least this fraction of its total bases to be covered by ref kmers to be considered a match"/>
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182 <param argument="hammingdistance" type="integer" value="0" min="0" label="Maximum Hamming distance for ref kmers (subs only)"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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183 <param argument="qhdist" type="integer" value="0" min="0" label="Hamming distance for query kmers"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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184 <param argument="editdistance" type="integer" value="0" min="0" label="Maximum edit distance from ref kmers (subs and indels)"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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185 <param argument="forbidn" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Do not match kmers comntaining N?"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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186 <param argument="trimfailures" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Trim failed reads to 1bp instead of discarding them?"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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187 <param argument="findbestmatch" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Associate read with sequence sharing most kmers if multiple matches?"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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188 <param argument="skipr1" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Don't do kmer-based operations on read 1?"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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189 <param argument="skipr2" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Don't do kmer-based operations on read 2?"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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190 </section>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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191 <param name="outputs_select" type="select" multiple="true" optional="false" label="Specify outputs">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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192 <option value="outu">Unmatched</option>
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193 <option value="outm">Matched</option>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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194 <option value="outs">Single</option>
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195 </param>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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196 <conditional name="output_stats_cond">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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197 <param name="output_stats" type="select" label="Output statistics?">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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198 <option value="no" selected="true">No</option>
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199 <option value="yes">Yes</option>
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200 </param>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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201 <when value="no"/>
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parents:
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202 <when value="yes">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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203 <param name="output_stats_select" type="select" multiple="true" optional="false" label="Specify statistics outputs">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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204 <option value="stats">Statistics about which contamininants were detected</option>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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205 <option value="ref">Statistics on a per-reference-file basis</option>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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206 <option value="rpkm">RPKM for each reference sequence (for RNA-seq)</option>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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207 <option value="dump">kmer tables in fasta format</option>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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208 </param>
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209 </when>
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210 </conditional>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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211 <conditional name="output_hists_cond">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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212 <param name="output_hists" type="select" label="Output histograms?">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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213 <option value="no" selected="true">No</option>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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214 <option value="yes">Yes</option>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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215 </param>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
216 <when value="no"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
217 <when value="yes">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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218 <param name="output_hists_select" type="select" multiple="true" optional="false" label="Specify statistics outputs">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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219 <option value="bhist">Base composition histogram by position</option>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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220 <option value="quhist">Quality histogram by position</option>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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221 <option value="quchist">Count of bases with each quality value</option>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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222 <option value="aqhist">Histogram of average read quality</option>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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223 <option value="bqhist">Quality histogram designed for box plots</option>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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224 <option value="lhist">Read length histogram</option>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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225 <option value="phist">Polymer length histogram</option>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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226 <option value="gchist">Read GC content histogram</option>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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227 <option value="enthist">Read entropy histogram</option>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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228 </param>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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229 </when>
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230 </conditional>
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231 </inputs>
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232 <outputs>
1
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parents: 0
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233 <data name="outputu" format="fastqsanger" label="${tool.name} on ${on_string} (Forward Unmatched)">
0
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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234 <filter>str(outputs_select).find('outu') >= 0</filter>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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235 <filter>'outu' in outputs_select</filter>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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236 </data>
1
ff3b87a0d205 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
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parents: 0
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237 <data name="outputu2" format="fastqsanger" label="${tool.name} on ${on_string} (Reverse Unmatched)">
0
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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238 <filter>'outu' in outputs_select and input_type_cond['input_type'] != 'single'</filter>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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239 </data>
1
ff3b87a0d205 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
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parents: 0
diff changeset
240 <data name="outputm" format="fastqsanger" label="${tool.name} on ${on_string} (Forward Matched)">
0
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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241 <filter>'outm' in outputs_select</filter>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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242 </data>
1
ff3b87a0d205 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
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parents: 0
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243 <data name="outputm2" format="fastqsanger" label="${tool.name} on ${on_string} (Reverse Matched)">
0
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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244 <filter>'outm' in outputs_select and input_type_cond['input_type'] != 'single'</filter>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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245 </data>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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246 <data name="outputs" format="fastqsanger" label="${tool.name} on ${on_string} (Single)">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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247 <filter>'outs' in outputs_select</filter>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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248 </data>
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249 <data name="output_stats" format="tabular" label="${tool.name} on ${on_string} (Detected contaminates stats)">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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250 <filter>output_stats_cond['output_stats'] == 'yes' and 'stats' in output_stats_cond['output_stats_select']</filter>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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251 </data>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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252 <data name="output_ref" format="tabular" label="${tool.name} on ${on_string} (Per reference file stats)">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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253 <filter>output_stats_cond['output_stats'] == 'yes' and 'ref' in output_stats_cond['output_stats_select']</filter>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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254 </data>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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255 <data name="output_rpkm" format="tabular" label="${tool.name} on ${on_string} (RPKM for each ref seq)">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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256 <filter>output_stats_cond['output_stats'] == 'yes' and 'rpkm' in output_stats_cond['output_stats_select']</filter>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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257 </data>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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258 <data name="output_dump" format="fasta" label="${tool.name} on ${on_string} (kmer tables)">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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259 <filter>output_stats_cond['output_stats'] == 'yes' and 'dump' in output_stats_cond['output_stats_select']</filter>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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260 </data>
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parents:
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261 <data name="output_bhist" format="tabular" label="${tool.name} on ${on_string} (Base composition py poition)">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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262 <filter>output_hists_cond['output_hists'] == 'yes' and 'bhist' in output_hists_cond['output_hists_select']</filter>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
parents:
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263 </data>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
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264 <data name="output_quhist" format="tabular" label="${tool.name} on ${on_string} (Quality by position)">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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265 <filter>output_hists_cond['output_hists'] == 'yes' and 'quhist' in output_hists_cond['output_hists_select']</filter>
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266 </data>
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267 <data name="output_quchist" format="tabular" label="${tool.name} on ${on_string} (Bases w/ each quality value)">
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268 <filter>output_hists_cond['output_hists'] == 'yes' and 'quchist' in output_hists_cond['output_hists_select']</filter>
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269 </data>
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270 <data name="output_aqhist" format="tabular" label="${tool.name} on ${on_string} (average read quality)">
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271 <filter>output_hists_cond['output_hists'] == 'yes' and 'aqhist' in output_hists_cond['output_hists_select']</filter>
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272 </data>
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273 <data name="output_bqhist" format="tabular" label="${tool.name} on ${on_string} (Quality for box plots)">
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274 <filter>output_hists_cond['output_hists'] == 'yes' and 'bqhist' in output_hists_cond['output_hists_select']</filter>
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275 </data>
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276 <data name="output_lhist" format="tabular" label="${tool.name} on ${on_string} (Read length)">
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277 <filter>output_hists_cond['output_hists'] == 'yes' and 'lhist' in output_hists_cond['output_hists_select']</filter>
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278 </data>
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279 <data name="output_phist" format="tabular" label="${tool.name} on ${on_string} (Polymer length)">
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280 <filter>output_hists_cond['output_hists'] == 'yes' and 'phist' in output_hists_cond['output_hists_select']</filter>
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281 </data>
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282 <data name="output_gchist" format="tabular" label="${tool.name} on ${on_string} (Read GC content)">
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283 <filter>output_hists_cond['output_hists'] == 'yes' and 'gchist' in output_hists_cond['output_hists_select']</filter>
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284 </data>
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285 <data name="output_enthist" format="tabular" label="${tool.name} on ${on_string} (Read entropy)">
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286 <filter>output_hists_cond['output_hists'] == 'yes' and 'enthist' in output_hists_cond['output_hists_select']</filter>
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287 </data>
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288 </outputs>
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289 <tests>
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290 <!-- Single read -->
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291 <test expect_num_outputs="1">
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292 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
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293 <param name="reference" value="adapters.fa.gz" ftype="fasta.gz"/>
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294 <param name="reference_type" value="files"/>
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295 <param name="outputs_select" value="outu"/>
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296 <output name="outputu" file="bduk_outputu1.fastqsanger" ftype="fastqsanger" compare="contains"/>
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297 </test>
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298 <!-- Paired reads in separate datasets -->
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299 <test expect_num_outputs="4">
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300 <param name="input_type" value="pair"/>
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301 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
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302 <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz"/>
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303 <param name="reference_type" value="files"/>
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304 <param name="reference" value="adapters.fa.gz" ftype="fasta.gz"/>
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305 <param name="outputs_select" value="outu"/>
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306 <param name="output_stats" value="yes"/>
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307 <param name="output_stats_select" value="dump"/>
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308 <param name="output_hists" value="yes"/>
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309 <param name="output_hists_select" value="quhist"/>
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310 <output name="outputu" file="bduk_outputu1.fastqsanger" ftype="fastqsanger" compare="contains"/>
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311 <output name="outputu2" file="bduk_outputu2.fastqsanger" ftype="fastqsanger" compare="contains"/>
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312 <output name="output_dump" file="bduk_output_dump1.fasta" ftype="fasta" compare="contains"/>
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313 <output name="output_quhist" file="bduk_output_quhist1.tabular" ftype="tabular"/>
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314 </test>
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315 <!-- Collection of Paired reads -->
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316 <test expect_num_outputs="2">
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317 <param name="input_type" value="paired"/>
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318 <param name="reads_collection">
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319 <collection type="paired">
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320 <element name="forward" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/>
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321 <element name="reverse" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/>
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322 </collection>
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323 </param>
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324 <param name="reference_type" value="keywords"/>
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325 <param name="reference" value="adapters,artifacts,phix,lambda,pjet,mtst,kapa"/>
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326 <param name="outputs_select" value="outu"/>
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327 <output name="outputu" file="bduk_outputu1.fastqsanger" ftype="fastqsanger" compare="contains"/>
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328 <output name="outputu2" file="bduk_outputu2.fastqsanger" ftype="fastqsanger" compare="contains"/>
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329 </test>
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330 </tests>
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331 <help>
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332 **What it does**
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333
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334 BBDuk was developed to combine most common data-quality-related trimming, filtering, and masking operations into a single
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335 high-performance tool. It is capable of quality-trimming and filtering, adapter-trimming, contaminant-filtering via kmer
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336 matching, sequence masking, GC-filtering, length filtering, entropy-filtering, format conversion, histogram generation,
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337 subsampling, quality-score recalibration, kmer cardinality estimation, and various other operations in a single pass.
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338 Specifically, any combination of operations is possible in a single pass with the exception of kmer-based operations (kmer
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339 trimming, kmer masking, or kmer filtering). At most 1 kmer-based operation can be done in a single pass.
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340
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341 **Options**
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342
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343 * **Reference** - if a reference is specified, BBDuk will operate on kmers in one of 4 modes: right-trimming, left-trimming, masking, or filtering. The default is filtering - any read matching a reference kmer will be discarded.
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344
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345 * **Trim reads to remove bases matching reference kmers** - When trimming to the right, once a reference kmer is matched in a read, that kmer and all the bases to the right will be trimmed, leaving only the bases to the left. When trimming to the left, trimming will be done to the left instead.
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346
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347 **Outputs**
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348
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349 * **Unmatched** - All the reads that pass all filtering criteria. Reads will be at least as long as **Minimum read length** after any trimming operations and reads will not match any reference kmer if kmer-filtering is being performed. A read’s average quality will be at least as high as the specified **Minimum average quality**.
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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350 * **Matched** - Reads failing any filter criteria (such as matching a reference kmer). By default, if either read in a pair fails, both will be included in *Matched*.
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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351 * **Single** - Singleton reads whose mate was trimmed shorter than the value of **Minimum read length**.
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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352 </help>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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353 <expand macro="citations"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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354 </tool>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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355