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annotate bbmerge.xml @ 0:fc029a9b4d07 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 18:06:47 +0000
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children 82ced0e47b9d
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fc029a9b4d07 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_bbmerge" name="BBTools: BBMerge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
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2 <description>Merge overlapping mates of a read pair</description>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
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3 <macros>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
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4 <import>macros.xml</import>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
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5 </macros>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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6 <expand macro="edam_ontology"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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7 <expand macro="requirements"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
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8 <command detect_errors="exit_code"><![CDATA[
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
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9 #import os
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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10 #import re
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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11
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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12 #if str($input_type_cond.input_type) in ['single', 'pair']:
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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13 #set read1 = $input_type_cond.read1
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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14 ## bbmerge uses the file extension to determine the input format.
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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15 #set ext = '.fastq'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
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16 #if $read1.ext.endswith('.gz'):
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
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17 #set ext = $ext + '.gz'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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18 #end if
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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19 #set read1_file = 'forward' + $ext
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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20 ln -s '${read1}' '${read1_file}' &&
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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21 #if str($input_type_cond.input_type) == 'pair':
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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22 #set read2 = $input_type_cond.read2
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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23 #set read2_file = 'reverse' + $ext
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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24 ln -s '${read2}' '${read2_file}' &&
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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25 #end if
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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26 #else:
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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27 #set read1 = $input_type_cond.reads_collection['forward']
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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28 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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29 ## bbmap uses the file extension to determine the input format.
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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30 #set ext = $read1_identifier + '.fastq'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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31 #if $read1.ext.endswith('.gz'):
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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32 #set ext = $ext + '.gz'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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33 #end if
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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34 #set read1_file = $read1_identifier + $ext
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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35 ln -s '${read1}' '${read1_file}' &&
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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36 #set read2 = $input_type_cond.reads_collection['reverse']
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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37 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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38 #set read2_file = $read2_identifier + $ext
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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39 ln -s '${read2}' '${read2_file}' &&
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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40 #end if
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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41
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42 bbmerge.sh
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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43 #### Input parameters
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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44 #if str($input_type_cond.input_type) == 'single':
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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45 in='${read1_file}'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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46 interleaved=t
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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47 #else:
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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48 in1='${read1_file}' in2='${read2_file}'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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49 interleaved=f
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50 #end if
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51
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52 #### Output options
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53 out=merged.fastq
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54 outu=unmerged.fastq
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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55 ihist=ihist.tabular
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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56 touppercase=t
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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57
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58 #### Quality and trimming parameters
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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59 qtrim='$qt_options.qtrim'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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60 trimq='$qt_options.trimq'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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61 minlength='$qt_options.minlength_after_trim'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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62 usequality='$qt_options.usequality'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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63
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64 #### Merging parameters
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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65 usejni=f ## Do overlapping in C code, which is faster.
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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66 ecco='$merge_options.ecco'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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67 trimnonoverlapping='$merge_options.trimnonoverlapping'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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68 mininsert='$merge_options.mininsert'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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69 minoverlap='$merge_options.minoverlap'
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70 minq='$merge_options.minq'
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71 maxq='$merge_options.maxq'
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72 entropy='$merge_options.entropy'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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73 efilter='$merge_options.efilter'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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74 pfilter='$merge_options.pfilter'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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75 kfilter='$merge_options.kfilter'
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76 usequality='$merge_options.usequality'
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77
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78 #if $merge_options.adapters.selector == "with_adaptors":
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79 adapter1='$merge_options.adapter1'
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80 adapter2='$merge_options.adapter2'
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81 #end if
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82
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83 #if $merge_options.merge_mode.selector == 'Ratio mode':
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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84 maxratio='$merge_options.merge_mode.maxratio'
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85 ratiomargin='$merge_options.merge_mode.ratiomargin'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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86 ratiooffset='$merge_options.merge_mode.ratiooffset'
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87 maxmismatches='$merge_options.merge_mode.maxmismatches'
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88 ratiominoverlapreduction=0
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89 minsecondratio='$merge_options.merge_mode.minsecondratio'
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90 #else:
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91 margin='$merge_options.merge_mode.margin'
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92 mismatches='$merge_options.merge_mode.mismatches'
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93 requireratiomatch='$merge_options.merge_mode.requireratiomatch'
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94 #end if
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95
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96 $merge_options.strictness=t
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97 ]]></command>
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98 <inputs>
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99 <expand macro="input_type_cond"/>
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100
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101 <section name="qt_options" title="Quality and trimming options">
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102 <param name="qtrim" type="select" label="Select option for quality trimming ends before mapping">
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103 <option value="f" selected="true">No trimming</option>
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104 <option value="l">Trim left</option>
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105 <option value="r">Trim right</option>
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106 <option value="lr">Trim both</option>
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107 </param>
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108 <param argument="trimq" type="integer" value="6" label="Trim regions with average quality below this value"/>
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109 <param argument="minlength_after_trim" type="integer" value="60" label="Don't trim reads to be shorter than this value"/>
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110 <param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Use quality scores when determining which read kmers to use as seeds?"/>
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111 </section>
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112
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113 <section name="merge_options" title="Merging parameters">
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114 <param name="strictness" type="select" label="Select option for quality trimming ends before mapping">
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115 <option value="xstrict">max strict</option>
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116 <option value="ustrict">ultra strict</option>
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117 <option value="vstrict">very strict</option>
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118 <option value="strict">strict</option>
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119 <option value="default" selected="true">default</option>
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120 <option value="loose">loose</option>
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121 <option value="vloose">very loose</option>
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122 <option value="uloose">ultra loose</option>
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123 <option value="xloose">max loose</option>
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124 <option value="fast">fastest possible, less accurate</option>
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125 </param>
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126 <param argument="ecco" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Error-correct the overlapping part, but don't merge." help="If selected, the tool with find the overlaps as if merging reads, use this overlap information to correct sequencing errors on both strands. However, the strands from the mates will not be merged but provided as two separate reads after error correction."/>
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127 <param argument="trimnonoverlapping" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Trim all non-overlapping portions, leaving only consensus sequence. By default, only sequence to the right of the overlap (adapter sequence) is trimmed."/>
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128 <param argument="mininsert" type="integer" value="35" label="Minimum insert size to merge reads"/>
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129 <param argument="minoverlap" type="integer" value="12" label="Minimum number of overlapping bases to allow merging"/>
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130
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131 <param argument="minq" type="integer" value="9" label="Ignore bases with quality below this"/>
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132 <param argument="maxq" type="integer" value="41" label="Cap output quality scores at this"/>
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133
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134 <param argument="entropy" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Increase the minimum overlap requirement for low-complexity reads"/>
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135 <param argument="efilter" type="integer" value="6" label="Ban overlaps with over this many times the expected number of errors." help="Lower is more strict, -1 disables."/>
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136 <param argument="pfilter" type="float" value="0.00004" label="Probability filter to disallow improbable overlaps." help="Higher is stricter. 0 will disable the filter; 1 will allow only perfect overlaps."/>
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137 <param argument="kfilter" type="integer" value="41" label="Ban overlaps that create kmers with count below this value" help="Requires good coverage, 0 disables."/>
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138 <param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Take quality factors into account" help="If disabled, quality values are completely ignored, both for overlap detection and filtering. May be useful for data with inaccurate quality values."/>
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139
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140 <conditional name="adapters">
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141 <param name="selector" type="select" label="Provide adapter sequences to improve accuracy?">
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142 <option value="wout_adapters" selected="true">No</option>
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143 <option value="with_adapters">Yes, use these adapter sequences</option>
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144 </param>
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145 <when value="wout_adapters"/>
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146 <when value="with_adapters">
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147 <param argument="adapter1" type="text" value="" label="Left adapter sequence"/>
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148 <param argument="adapter2" type="text" value="" label="Right adapter sequence"/>
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149 </when>
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150 </conditional>
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151
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152 <conditional name="merge_mode">
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153 <param name="selector" type="select" label="Evaluate overlaps via..." help="In the ratio mode, overlaps are decided based on the ratio of matching to mismatching bases. Flat mode scores overlaps based on the total number of mismatching bases only.">
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154 <option value="Ratio mode" selected="true">Ratio mode</option>
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155 <option value="Flat mode">Flat mode</option>
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156 </param>
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157 <when value="Ratio mode">
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158 <param argument="maxratio" type="float" value="0.09" label="Max error rate; higher increases merge rate."/>
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159 <param argument="ratiomargin" type="float" value="5.5" label="Lower increases merge rate; min is 1."/>
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160 <param argument="ratiooffset" type="float" value="0.55" label="Lower increases merge rate; min is 0."/>
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161 <param argument="maxmismatches" type="integer" value="20" label="Maximum mismatches allowed in overlapping region."/>
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162 <param argument="minsecondratio" type="float" value="0.1" label="Cutoff for second-best overlap ratio."/>
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163 </when>
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164 <when value="Flat mode">
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165 <param argument="margin" type="integer" value="2" label="The best overlap must have at least 'margin' fewer mismatches than the second best."/>
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166 <param argument="mismatches" type="integer" value="3" label="Do not allow more than this many mismatches."/>
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167 <param argument="requireratiomatch" type="boolean" value="false" label="Require the answer from flat mode and ratio mode to agree, reducing false positives if both are enabled."/>
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168 </when>
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169 </conditional>
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170 </section>
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171 </inputs>
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172 <outputs>
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173 <data format="fastq" name="output_merged_reads" from_work_dir="merged.fastq" label="${tool.name} on ${on_string} (merged reads)"/>
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174 <data format="fastq" name="output_unmerged_reads" from_work_dir="unmerged.fastq" label="${tool.name} on ${on_string} (unmerged reads)"/>
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175 <data format="tabular" name="output_insertlen_hist" from_work_dir="ihist.tabular" label="${tool.name} on ${on_string} (insert size histogram)"/>
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176 </outputs>
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177 <tests>
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178 <!-- Single interleaved file -->
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179 <test expect_num_outputs="3">
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180 <param name="input_type" value="single"/>
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181 <param name="read1" value="bbmerge/input_interleaved.fastq"/>
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182 <output name="output_unmerged_reads" ftype="fastq" value="bbmerge/unmerged.fastq"/>
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183 <output name="output_merged_reads" ftype="fastq" value="bbmerge/merged.fastq"/>
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184 <output name="output_insertlen_hist" ftype="tabular" value="bbmerge/insert_length_hist.tabular"/>
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185 </test>
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186 <!-- Paired mates in 2 separate files -->
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187 <test expect_num_outputs="3">
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188 <param name="input_type" value="pair"/>
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189 <param name="read1" value="bbmerge/input_R1.fastq"/>
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190 <param name="read2" value="bbmerge/input_R2.fastq"/>
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191 <output name="output_unmerged_reads" ftype="fastq" value="bbmerge/unmerged.fastq"/>
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192 <output name="output_merged_reads" ftype="fastq" value="bbmerge/merged.fastq"/>
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193 <output name="output_insertlen_hist" ftype="tabular" value="bbmerge/insert_length_hist.tabular"/>
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194 </test>
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195 <!-- Paired mates provided via a paired collection -->
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196 <test expect_num_outputs="3">
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197 <param name="input_type" value="paired"/>
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198 <param name="reads_collection">
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199 <collection type="paired">
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200 <element name="forward" value="bbmerge/input_R1.fastq"/>
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201 <element name="reverse" value="bbmerge/input_R2.fastq"/>
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202 </collection>
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203 </param>
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204 <output name="output_unmerged_reads" ftype="fastq" value="bbmerge/unmerged.fastq"/>
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205 <output name="output_merged_reads" ftype="fastq" value="bbmerge/merged.fastq"/>
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206 <output name="output_insertlen_hist" ftype="tabular" value="bbmerge/insert_length_hist.tabular"/>
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207 </test>
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208 </tests>
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209 <help>
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210 **What it does**
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211
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212 BBMerge merges two overlapping paired reads into a single read. A 2x100nt read pair, for instance can be merged into a single read of length 150nt if the last 50nt of the first read mate and the last 50nt of the second read map overlap. The accuracy of the base calling can also improve as a result of such a reconciliation between the read pairs. BBMerge is also capable of error-correcting the overlapping portion of reads without merging them, as well as merging nonoverlapping reads, if enough coverage is available.
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213
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214 -----
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215
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216 **A Martian PE sequencing result is expected to be processed as follows:**
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217
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218 input_R1.fastq::
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219
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220 @read_header_1/1
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221 AAAAATTTTTAAAAACCCCCGGGGG
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222 +
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223 FFFFFFFFFFFFFFFEFFFFFF,FF
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224 @read_header_2/1
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225 AAAATTTTAAAACCCCCGGGGG
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226 +
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227 FFFFFFFFFFFFFFFEFFFFFF
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228
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229
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230 input_R2.fastq::
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231
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232 @read_header_1/2
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233 TTAATTAATTCCCCCGGGGG
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234 +
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235 FFFFFFFFFFFFFFFFFFFF
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236 @read_header_2/2
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237 TTTAAATTTAAACCCCCGGGGG
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238 +
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239 FFFFFFFFFFFFFFFFFFFFEF
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240
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241
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242 output.fastq::
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243
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244 @read_header_1
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245 AAAAATTTTTAAAAACCCCCGGGGGAATTAATTAA
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246 +
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247 FFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFF
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248 @read_header_2
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249 AAAATTTTAAAACCCCCGGGGGTTTAAATTTAAA
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250 +
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251 FFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFF
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252 </help>
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253 <expand macro="citations"/>
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254 </tool>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
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