Mercurial > repos > iuc > bbtools_bbduk

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 4aa44523d9df9bf1773ed724735120476d773a19
author iuc
date Thu, 06 Mar 2025 11:49:54 +0000
parents 4f4e34a75de9
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
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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>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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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"/>
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ed2c532794c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
iuc
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7 <expand macro="bio.tools"/>
0
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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8 <expand macro="requirements"/>
6
c456a40153af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 46992fbb9d79da3d3c45b0c10f2936cf2af2dbcd
iuc
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9 <command detect_errors="aggressive"><![CDATA[
0
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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10 #import os
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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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
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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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'):
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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17 #set ext = $ext + '.gz'
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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18 #end if
1
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19 #set read1_file = 'forward' + $ext
0
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20 ln -s '${read1}' '${read1_file}' &&
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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21 #if str($input_type_cond.input_type) == 'pair':
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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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
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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26 #else:
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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27 #set read1 = $input_type_cond.reads_collection['forward']
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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28 ## bbduk uses the file extension to determine the input format.
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ed2c532794c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
iuc
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29 #set ext = '.fastq'
0
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30 #if $read1.ext.endswith('.gz'):
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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31 #set ext = $ext + '.gz'
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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32 #end if
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ed2c532794c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
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33 #set read1_file = 'forward' + $ext
0
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34 ln -s '${read1}' '${read1_file}' &&
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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35 #set read2 = $input_type_cond.reads_collection['reverse']
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ed2c532794c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
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36 #set read2_file = 'reverse' + $ext
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37 ln -s '${read2}' '${read2_file}' &&
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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38 #end if
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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39
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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40 #if str($reference_type_cond.reference_type) == 'files':
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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41 #set refs = list()
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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42 #for ref in $reference_type_cond.reference:
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43 ## bbduk looks at the file extension.
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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44 #set ref_name = str($os.path.basename($ref.file_name)) + '.fa'
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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45 #if $ref.ext.endswith('.gz'):
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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46 gunzip -c '$ref' > '$ref_name' &&
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47 #else:
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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48 ln -s '$ref' '$ref_name' &&
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49 #end if
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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50 $refs.append(str($ref_name))
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51 #end for
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52 #set refs = ','.join($refs)
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53 #else if str($reference_type_cond.reference_type) == 'keywords':
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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54 #set refs = str($reference_type_cond.reference)
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55 #end if
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56
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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57 bbduk.sh
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58 in='${read1_file}'
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59
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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60 #if str($input_type_cond.input_type) in ['pair', 'paired']:
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61 in2='${read2_file}'
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62 #end if
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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63 #if str($outputs_select).find('outu') >= 0:
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64 out='${outputu}'
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65 #if str($input_type_cond.input_type) in ['pair', 'paired']:
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66 out2='${outputu2}'
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67 #end if
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68 #end if
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69 #if str($outputs_select).find('outm') >= 0:
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70 outm='${outputm}'
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71 #if str($input_type_cond.input_type) in ['pair', 'paired']:
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72 outm2='${outputm2}'
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73 #end if
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74 #end if
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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75 #if str($outputs_select).find('outs') >= 0:
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76 outs='${outputs}'
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77 #end if
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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78
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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79 #if str($reference_type_cond.reference_type) != 'no_reference':
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80 ref='$refs'
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81 #if str($reference_type_cond.ktrim_cond.ktrim_select) == 'yes':
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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82 ktrim='${reference_type_cond.ktrim_cond.ktrim}'
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83 minlength=$reference_type_cond.ktrim_cond.minlength
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84 #end if
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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85 #end if
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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86
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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87 k=$advanced_options.k
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88 rcomp='${advanced_options.rcomp}'
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89 maskmiddle='${advanced_options.maskmiddle}'
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90 minkmerhits='${advanced_options.minkmerhits}'
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91 minkmerfraction=$advanced_options.minkmerfraction
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92 mincovfraction=$advanced_options.mincovfraction
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93 hammingdistance=$advanced_options.hammingdistance
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94 qhdist=$advanced_options.qhdist
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95 editdistance=$advanced_options.editdistance
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96 forbidn='${advanced_options.forbidn}'
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97 trimfailures='${advanced_options.trimfailures}'
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98 findbestmatch='${advanced_options.findbestmatch}'
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99 skipr1='${advanced_options.skipr1}'
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100 skipr2='${advanced_options.skipr2}'
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101
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102 #if str($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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103 #if str($output_stats_cond.output_stats_select).find('stats') >= 0:
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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104 stats='${output_stats}'
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105 #end if
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106 #if str($output_stats_cond.output_stats_select).find('ref') >= 0:
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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107 refstats='${output_ref}'
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108 #end if
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109 #if str($output_stats_cond.output_stats_select).find('rpkm') >= 0:
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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110 rpkm='${output_rpkm}'
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111 #end if
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112 #if str($output_stats_cond.output_stats_select).find('dump') >= 0:
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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113 dump='${output_dump}'
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114 #end if
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115 #end if
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116 #if str($output_hists_cond.output_hists) == 'yes':
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117 #if str($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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118 bhist='${output_bhist}'
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119 #end if
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120 #if str($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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121 qhist='${output_quhist}'
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122 #end if
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123 #if str($output_hists_cond.output_hists_select).find('quchist') >= 0:
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124 qchist='${output_quchist}'
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125 #end if
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126 #if str($output_hists_cond.output_hists_select).find('aqhist') >= 0:
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127 aqhist='${output_aqhist}'
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128 #end if
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129 #if str($output_hists_cond.output_hists_select).find('bqhist') >= 0:
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130 bqhist='${output_bqhist}'
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131 #end if
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132 #if str($output_hists_cond.output_hists_select).find('lhist') >= 0:
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133 lhist='${output_lhist}'
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134 #end if
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135 #if str($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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136 phist='${output_phist}'
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137 #end if
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138 #if str($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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139 gchist='${output_gchist}'
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140 #end if
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141 #if str($output_hists_cond.output_hists_select).find('enthist') >= 0:
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142 enthist='${output_enthist}'
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143 #end if
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144 #end if
7
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145 #if $log_file
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146 2> >(tee '$log_output' >&2)
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147 #end if
0
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148 t=\${GALAXY_SLOTS:-4}
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149 ]]></command>
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150 <inputs>
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151 <expand macro="input_type_cond"/>
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152 <conditional name="reference_type_cond">
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153 <param name="reference_type" type="select" label="Choose the reference type" help="Optional, no reference is the default">
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154 <option value="no_reference" selected="true">No reference</option>
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155 <option value="files">files</option>
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156 <option value="keywords">keywords</option>
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diff changeset
157 </param>
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158 <when value="no_reference"/>
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159 <when value="files">
5
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parents: 3
diff changeset
160 <param name="reference" type="data" format="fasta,fasta.gz" optional="false" label="Select one or more fasta file" multiple="true"/>
0
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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161 <expand macro="ktrim_cond"/>
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diff changeset
162 </when>
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163 <when value="keywords">
5
ed2c532794c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
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parents: 3
diff changeset
164 <param name="reference" type="select" optional="false" label="Select one or more keywords" multiple="true">
0
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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165 <option value="adapters">adapters</option>
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166 <option value="artifacts">artifacts</option>
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167 <option value="phix">phix</option>
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168 <option value="lambda">lambda</option>
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169 <option value="pjet">pjet</option>
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170 <option value="mtst">mtst</option>
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171 <option value="kapa">kapa</option>
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172 </param>
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173 <expand macro="ktrim_cond"/>
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174 </when>
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175 </conditional>
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176 <section name="advanced_options" title="Advanced options" expanded="false">
5
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diff changeset
177 <param argument="k" type="integer" min="1" value="27" label="Kmer length used for finding contaminants"/>
0
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178 <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"
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179 <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?"/>
5
ed2c532794c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb
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parents: 3
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180 <param argument="minkmerhits" type="integer" min="1" value="1" label="Reads need at least this many matching kmers to be considered as matching the reference"/>
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181 <param argument="minkmerfraction" type="float" min="0" value="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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182 <param argument="mincovfraction" type="float" min="0" value="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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183 <param argument="hammingdistance" type="integer" min="0" value="0" label="Maximum Hamming distance for ref kmers (subs only)"/>
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184 <param argument="qhdist" type="integer" min="0" value="0" label="Hamming distance for query kmers"/>
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185 <param argument="editdistance" type="integer" min="0" value="0" label="Maximum edit distance from ref kmers (subs and indels)"/>
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186 <param argument="forbidn" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Do not match kmers comntaining N?"/>
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187 <param argument="trimfailures" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Trim failed reads to 1bp instead of discarding them?"/>
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188 <param argument="findbestmatch" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Associate read with sequence sharing most kmers if multiple matches?"/>
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189 <param argument="skipr1" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Don't do kmer-based operations on read 1?"/>
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190 <param argument="skipr2" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Don't do kmer-based operations on read 2?"/>
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191 </section>
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192 <param name="outputs_select" type="select" optional="false" label="Specify outputs" multiple="true">
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193 <option value="outu">Unmatched</option>
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194 <option value="outm">Matched</option>
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195 <option value="outs">Single</option>
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196 </param>
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197 <conditional name="output_stats_cond">
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198 <param name="output_stats" type="select" label="Output statistics?">
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199 <option value="no" selected="true">No</option>
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200 <option value="yes">Yes</option>
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201 </param>
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202 <when value="no"/>
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203 <when value="yes">
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204 <param name="output_stats_select" type="select" optional="false" label="Specify statistics outputs" multiple="true">
0
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205 <option value="stats">Statistics about which contamininants were detected</option>
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206 <option value="ref">Statistics on a per-reference-file basis</option>
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207 <option value="rpkm">RPKM for each reference sequence (for RNA-seq)</option>
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208 <option value="dump">kmer tables in fasta format</option>
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209 </param>
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210 </when>
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211 </conditional>
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212 <conditional name="output_hists_cond">
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213 <param name="output_hists" type="select" label="Output histograms?">
0
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214 <option value="no" selected="true">No</option>
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215 <option value="yes">Yes</option>
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216 </param>
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217 <when value="no"/>
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218 <when value="yes">
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219 <param name="output_hists_select" type="select" optional="false" label="Specify statistics outputs" multiple="true">
0
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220 <option value="bhist">Base composition histogram by position</option>
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221 <option value="quhist">Quality histogram by position</option>
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222 <option value="quchist">Count of bases with each quality value</option>
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223 <option value="aqhist">Histogram of average read quality</option>
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224 <option value="bqhist">Quality histogram designed for box plots</option>
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225 <option value="lhist">Read length histogram</option>
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226 <option value="phist">Polymer length histogram</option>
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227 <option value="gchist">Read GC content histogram</option>
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228 <option value="enthist">Read entropy histogram</option>
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229 </param>
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230 </when>
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231 </conditional>
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232 <param name="log_file" type="boolean" label="Generate a log file" help="Generates a log file, which can be used as MultiQC input"/>
0
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233 </inputs>
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234 <outputs>
1
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235 <data name="outputu" format="fastqsanger" label="${tool.name} on ${on_string} (Forward Unmatched)">
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236 <filter>str(outputs_select).find('outu') &gt;= 0</filter>
0
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237 <filter>'outu' in outputs_select</filter>
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238 </data>
1
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239 <data name="outputu2" format="fastqsanger" label="${tool.name} on ${on_string} (Reverse Unmatched)">
0
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240 <filter>'outu' in outputs_select and input_type_cond['input_type'] != 'single'</filter>
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241 </data>
1
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242 <data name="outputm" format="fastqsanger" label="${tool.name} on ${on_string} (Forward Matched)">
0
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243 <filter>'outm' in outputs_select</filter>
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244 </data>
1
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245 <data name="outputm2" format="fastqsanger" label="${tool.name} on ${on_string} (Reverse Matched)">
0
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246 <filter>'outm' in outputs_select and input_type_cond['input_type'] != 'single'</filter>
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247 </data>
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248 <data name="outputs" format="fastqsanger" label="${tool.name} on ${on_string} (Single)">
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249 <filter>'outs' in outputs_select</filter>
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250 </data>
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251 <data name="output_stats" format="tabular" label="${tool.name} on ${on_string} (Detected contaminates stats)">
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252 <filter>output_stats_cond['output_stats'] == 'yes' and 'stats' in output_stats_cond['output_stats_select']</filter>
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253 </data>
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254 <data name="output_ref" format="tabular" label="${tool.name} on ${on_string} (Per reference file stats)">
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255 <filter>output_stats_cond['output_stats'] == 'yes' and 'ref' in output_stats_cond['output_stats_select']</filter>
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256 </data>
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257 <data name="output_rpkm" format="tabular" label="${tool.name} on ${on_string} (RPKM for each ref seq)">
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258 <filter>output_stats_cond['output_stats'] == 'yes' and 'rpkm' in output_stats_cond['output_stats_select']</filter>
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259 </data>
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260 <data name="output_dump" format="fasta" label="${tool.name} on ${on_string} (kmer tables)">
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261 <filter>output_stats_cond['output_stats'] == 'yes' and 'dump' in output_stats_cond['output_stats_select']</filter>
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262 </data>
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263 <data name="output_bhist" format="tabular" label="${tool.name} on ${on_string} (Base composition py poition)">
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264 <filter>output_hists_cond['output_hists'] == 'yes' and 'bhist' in output_hists_cond['output_hists_select']</filter>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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265 </data>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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266 <data name="output_quhist" format="tabular" label="${tool.name} on ${on_string} (Quality by position)">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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267 <filter>output_hists_cond['output_hists'] == 'yes' and 'quhist' in output_hists_cond['output_hists_select']</filter>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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268 </data>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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269 <data name="output_quchist" format="tabular" label="${tool.name} on ${on_string} (Bases w/ each quality value)">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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270 <filter>output_hists_cond['output_hists'] == 'yes' and 'quchist' in output_hists_cond['output_hists_select']</filter>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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271 </data>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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272 <data name="output_aqhist" format="tabular" label="${tool.name} on ${on_string} (average read quality)">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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273 <filter>output_hists_cond['output_hists'] == 'yes' and 'aqhist' in output_hists_cond['output_hists_select']</filter>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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274 </data>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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275 <data name="output_bqhist" format="tabular" label="${tool.name} on ${on_string} (Quality for box plots)">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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276 <filter>output_hists_cond['output_hists'] == 'yes' and 'bqhist' in output_hists_cond['output_hists_select']</filter>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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277 </data>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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278 <data name="output_lhist" format="tabular" label="${tool.name} on ${on_string} (Read length)">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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279 <filter>output_hists_cond['output_hists'] == 'yes' and 'lhist' in output_hists_cond['output_hists_select']</filter>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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280 </data>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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281 <data name="output_phist" format="tabular" label="${tool.name} on ${on_string} (Polymer length)">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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282 <filter>output_hists_cond['output_hists'] == 'yes' and 'phist' in output_hists_cond['output_hists_select']</filter>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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283 </data>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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284 <data name="output_gchist" format="tabular" label="${tool.name} on ${on_string} (Read GC content)">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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285 <filter>output_hists_cond['output_hists'] == 'yes' and 'gchist' in output_hists_cond['output_hists_select']</filter>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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286 </data>
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287 <data name="output_enthist" format="tabular" label="${tool.name} on ${on_string} (Read entropy)">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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288 <filter>output_hists_cond['output_hists'] == 'yes' and 'enthist' in output_hists_cond['output_hists_select']</filter>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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289 </data>
7
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290 <data name="log_output" format="txt" label="${tool.name} on ${on_string} (Log file)">
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291 <filter>log_file</filter>
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292 </data>
0
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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293 </outputs>
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294 <tests>
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295 <!-- Single read -->
7
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296 <test expect_num_outputs="2">
0
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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297 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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298 <param name="reference" value="adapters.fa.gz" ftype="fasta.gz"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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299 <param name="reference_type" value="files"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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300 <param name="outputs_select" value="outu"/>
7
4f4e34a75de9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit b3c4dcad33ad59a50c953f409896dc2279e776ab
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301 <param name="log_file" value="true"/>
0
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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302 <output name="outputu" file="bduk_outputu1.fastqsanger" ftype="fastqsanger" compare="contains"/>
7
4f4e34a75de9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit b3c4dcad33ad59a50c953f409896dc2279e776ab
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303 <output name="log_output" ftype="txt">
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304 <assert_contents>
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305 <has_text text="Executing jgi.BBDuk"/>
4f4e34a75de9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit b3c4dcad33ad59a50c953f409896dc2279e776ab
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306 <has_text text="Input"/>
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307 <has_text text="Contaminants"/>
4f4e34a75de9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit b3c4dcad33ad59a50c953f409896dc2279e776ab
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308 <has_text text="Total Removed"/>
4f4e34a75de9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit b3c4dcad33ad59a50c953f409896dc2279e776ab
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309 <has_text text="Result"/>
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310 <has_text text="10000 bases"/>
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311 <has_text text="100 reads"/>
4f4e34a75de9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit b3c4dcad33ad59a50c953f409896dc2279e776ab
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312 <has_text text="0 reads"/>
4f4e34a75de9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit b3c4dcad33ad59a50c953f409896dc2279e776ab
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313 <has_text text="0 bases"/>
4f4e34a75de9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit b3c4dcad33ad59a50c953f409896dc2279e776ab
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314 </assert_contents>
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315 </output>
0
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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316 </test>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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317 <!-- Paired reads in separate datasets -->
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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318 <test expect_num_outputs="4">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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319 <param name="input_type" value="pair"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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320 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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321 <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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322 <param name="reference_type" value="files"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
iuc
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323 <param name="reference" value="adapters.fa.gz" ftype="fasta.gz"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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324 <param name="outputs_select" value="outu"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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325 <param name="output_stats" value="yes"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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326 <param name="output_stats_select" value="dump"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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327 <param name="output_hists" value="yes"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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328 <param name="output_hists_select" value="quhist"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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329 <output name="outputu" file="bduk_outputu1.fastqsanger" ftype="fastqsanger" compare="contains"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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330 <output name="outputu2" file="bduk_outputu2.fastqsanger" ftype="fastqsanger" compare="contains"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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331 <output name="output_dump" file="bduk_output_dump1.fasta" ftype="fasta" compare="contains"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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332 <output name="output_quhist" file="bduk_output_quhist1.tabular" ftype="tabular"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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333 </test>
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334 <!-- Collection of Paired reads -->
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335 <test expect_num_outputs="2">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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336 <param name="input_type" value="paired"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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337 <param name="reads_collection">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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338 <collection type="paired">
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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339 <element name="forward" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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340 <element name="reverse" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/>
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diff changeset
341 </collection>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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diff changeset
342 </param>
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343 <param name="reference_type" value="keywords"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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344 <param name="reference" value="adapters,artifacts,phix,lambda,pjet,mtst,kapa"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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345 <param name="outputs_select" value="outu"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
346 <output name="outputu" file="bduk_outputu1.fastqsanger" ftype="fastqsanger" compare="contains"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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parents:
diff changeset
347 <output name="outputu2" file="bduk_outputu2.fastqsanger" ftype="fastqsanger" compare="contains"/>
132af91f11b9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit ae31a678eb5c04fb74b94161db95705d597990ad"
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348 </test>
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349 </tests>
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350 <help>
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351 **What it does**
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352
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353 BBDuk was developed to combine most common data-quality-related trimming, filtering, and masking operations into a single
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354 high-performance tool. It is capable of quality-trimming and filtering, adapter-trimming, contaminant-filtering via kmer
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355 matching, sequence masking, GC-filtering, length filtering, entropy-filtering, format conversion, histogram generation,
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356 subsampling, quality-score recalibration, kmer cardinality estimation, and various other operations in a single pass.
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357 Specifically, any combination of operations is possible in a single pass with the exception of kmer-based operations (kmer
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358 trimming, kmer masking, or kmer filtering). At most 1 kmer-based operation can be done in a single pass.
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359
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360 **Options**
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361
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362 * **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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363
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364 * **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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365
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366 **Outputs**
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367
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368 * **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**.
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369 * **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*.
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370 * **Single** - Singleton reads whose mate was trimmed shorter than the value of **Minimum read length**.
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371 </help>
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372 <expand macro="citations"/>
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373 </tool>