Mercurial > repos > artbio > sr_bowtie_dataset_annotation

annotate sr_bowtie_dataset_annotation.xml @ 8:3519c2de7fac draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit e62066428e669516e024d081933ee8c7f953ba1b"
author artbio
date Sat, 09 Apr 2022 22:45:21 +0000
parents 3bddd7ab96e3
children 6bf9de09aa74
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3519c2de7fac "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit e62066428e669516e024d081933ee8c7f953ba1b"
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1 <tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.6">
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2 <description>by iterative alignments with sRbowtie</description>
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3 <requirements>
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4 <requirement type="package" version="1.3.1">bowtie</requirement>
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5 <requirement type="package" version="1.7.1">r-optparse</requirement>
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6 <requirement type="package" version="3.3.5">r-ggplot2</requirement>
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7 <requirement type="package" version="0.9.1">r-ggrepel</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 #if $refGenomeSource1.genomeSource == "history":
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11 bowtie-build -f $refGenomeSource1.ownFile genome 1>/dev/null &&
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12 #set index_path = 'genome'
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13 #else:
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14 #set index_path = $refGenomeSource1.index.fields.path
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15 #end if
5
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16
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17 #for $i in $AdditionalQueries:
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18 bowtie-build -f $i.ownFile $i.ownFile.name 1>/dev/null &&
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19 #end for
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20
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21 #set method_prefix = "-v %s -k 1 --best" % str($mismatches)
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22 #if $input[0].is_of_type('fasta'):
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23 #set format = "-f"
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24 #elif $input[0].is_of_type('fastq'):
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25 #set format = "-q"
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26 #end if
4
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27
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28 #for $file in $input:
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29 #set sample=$file.element_identifier
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30 bowtie -p \${GALAXY_SLOTS:-4}
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31 $method_prefix
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32 --al matched.fa
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33 --un unmatched.fa
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34 --suppress 6,7,8
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35 $index_path $format $file > tabular_bowtie_output.tab &&
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36 genome_aligned=\$(wc -l < matched.fa) &&
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37 genome_aligned=\$(( \$genome_aligned/2)) &&
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38 #set counter = 0
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39 #for $i in $AdditionalQueries:
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40 #set $counter += 1
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41 #if $counter != 1:
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42 #set to_align = "class_unmatched.fa"
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43 #else:
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44 #set to_align = "matched.fa"
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45 #end if
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46 touch tmp_class_matched.fa tmp_class_unmatched.fa &&
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47 bowtie -p \${GALAXY_SLOTS:-4}
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48 $method_prefix
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49 --al tmp_class_matched.fa
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50 --un tmp_class_unmatched.fa
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51 --suppress 6,7,8
5
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52 $i.ownFile.name $format '$to_align' > tabular_bowtie_output.tab &&
4
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53 class_aligned=\$(( \$(wc -l < tmp_class_matched.fa)/2)) &&
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54 class_unaligned=\$(( \$(wc -l < tmp_class_unmatched.fa)/2)) &&
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55 echo -e "$sample\t$i.ownFile.name\t\$class_aligned\t\${genome_aligned}" >> $output &&
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56 mv tmp_class_unmatched.fa class_unmatched.fa &&
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57 rm tmp_class_matched.fa &&
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58 #end for
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59 remaining=\$(( \$(wc -l < class_unmatched.fa)/2)) &&
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60 echo -e "$sample\tNot classified\t\${remaining}\t\${genome_aligned}" >> $output &&
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61 #end for
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62 Rscript $__tool_directory__/barplot.r --input $output --barplot $barplot
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63 #if $format == '-q':
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64 && mv class_unmatched.fa class_unmatched.fastq
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65 && sed -n '1~4s/^@/>/p;2~4p' class_unmatched.fastq > class_unmatched.fa
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66 #end if
0
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67 ]]></command>
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68 <inputs>
4
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69 <param name="input" type="data" multiple="True" format="fasta,fastq" label="Input file: reads clipped from their adapter" help="Only with clipped, raw fasta or fastq files"/>
0
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70 <param name="mismatches" type="select" label="Number of mismatches allowed" help="specify the number of mismatches allowed during alignments">
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71 <option value="0">0</option>
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72 <option value="1" selected="true">1</option>
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73 <option value="2">2</option>
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74 <option value="3">3</option>
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75 </param>
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76 <!-- First bowtie index selection -->
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77 <conditional name="refGenomeSource1">
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78 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Bowtie Built-ins were indexed using default options">
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79 <option value="indexed">Use a built-in index</option>
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80 <option value="history">Use one from the history</option>
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81 </param>
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82 <when value="indexed">
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83 <param name="index" type="select" label="Select a DNA reference index" help="if your genome of interest is not listed - contact instance administrator">
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84 <options from_data_table="bowtie_indexes"/>
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85 </param>
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86 </when>
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87 <when value="history">
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88 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
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89 </when>
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90 </conditional>
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91 <!-- End of first bowtie index selection -->
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92 <!-- other bowtie index selections from fasta in history (mandatory) -->
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93 <repeat name="AdditionalQueries" title="Additional Alignment Step">
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94 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
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95 </repeat>
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96 <!-- End of other bowtie index selections -->
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97 </inputs>
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98 <outputs>
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99 <data format="fasta" name="unmatched" label="Annotate smRNAs: Unmatched reads" from_work_dir="class_unmatched.fa" />
3
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100 <data format="tabular" name="output" label="Cascade Annotation Analysis">
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101 <actions>
4
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102 <action name="column_names" type="metadata" default="Sample,Reference Index,Number of reads, Total reads" />
3
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103 </actions>
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104 </data>
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105 <data name="barplot" format="pdf" label="barplot from ${on_string}" />
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106 </outputs>
0
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107 <tests>
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108 <test>
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109 <param name="input" value ="sample1.fa" ftype="fasta" />
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110 <param name="genomeSource" value="history" />
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111 <param name="ownFile" value ="2L-tail.fa" ftype="fasta" />
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112 <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
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113 <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
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114 <output name="output" ftype="tabular" file="sample1_output.tab" />
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115 <output name="barplot" ftype="pdf" file="sample1_output.pdf" compare="sim_size" delta="500"/>
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116 <output name="unmatched" ftype="fasta" file="unmatched_1.fa" />
0
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117 </test>
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118 <test>
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119 <param name="input" value ="sample.fastq" ftype="fastq" />
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120 <param name="genomeSource" value="history" />
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121 <param name="ownFile" value ="2L-tail.fa" ftype="fasta" />
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122 <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
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123 <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
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124 <output name="output" ftype="tabular" file="sample_output.tab" />
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125 <output name="barplot" ftype="pdf" file="sample_output.pdf" compare="sim_size" delta="500"/>
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126 <output name="unmatched" ftype="fasta" file="unmatched_2.fa" />
4
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127 </test>
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128 <test>
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129 <param name="input" value ="sample5.fa,sample4.fa,sample3.fa,sample2.fa,sample1.fa" ftype="fasta" />
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130 <param name="genomeSource" value="history" />
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131 <param name="ownFile" value ="2L-tail.fa" ftype="fasta" />
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132 <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
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133 <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
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134 <output name="output" ftype="tabular" file="multisample5_output.tab" />
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135 <output name="barplot" ftype="pdf" file="multisample5_output.pdf" compare="sim_size" delta="500" />
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136 <output name="unmatched" ftype="fasta" file="unmatched_3.fa" />
0
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137 </test>
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138 </tests>
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139 <help>
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140
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141 **Introduction**
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142
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143 Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient.
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144 A generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution.
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145
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146 Here The sRbowtie wrapper specifically works with short reads FASTA or FASTQ inputs
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147 (-v bowtie mode, with -k 1) which has to be clipped from adapter before alignment.
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148
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149 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
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150
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151
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152 ------
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153
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154 **What it does**
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155
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156 .. class:: infomark
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157
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158 This script uses the sRbowtie wrapper to iteratively match reads on a reference indexes.
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159 Read that aligned to the first reference are realigned to the second reference.
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160 From this point, unaligned reads are taken as input for alignment to the third reference, etc.
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161
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163 Reads are Matched on DNA references (both strands) as fast as possible, without taking care of mapping issues
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165 *-v [0,1,2,3] -k 1 --best -p 12 --suppress 6,7,8*
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167 unaligned reads at step N are used as input for sRbowtie at step N+1
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169 -----
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171 **Input formats**
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173 .. class:: warningmark
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175 *Reads must be clipped from their adapter and provided in a FASTA or FASTQ format*
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177 -----
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179 **OUTPUTS**
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180
8
3519c2de7fac "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit e62066428e669516e024d081933ee8c7f953ba1b"
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181 **- Annotation table in a tabular format**
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182
3519c2de7fac "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit e62066428e669516e024d081933ee8c7f953ba1b"
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183 **- Pie Charts of class abundances**
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184
3519c2de7fac "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit e62066428e669516e024d081933ee8c7f953ba1b"
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185 **- Unmatched reads in fasta format**
0
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186
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187 </help>
8
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188
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189 <citations>
3519c2de7fac "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit e62066428e669516e024d081933ee8c7f953ba1b"
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190 <citation type="doi">10.1038/nature11416</citation>
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191 </citations>
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192
0
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193 </tool>