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1 <tool id="motiffinding_weeder2" name="Weeder2" version="2.0.0">
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2 <description>Motif discovery in sequences from coregulated genes of a single species</description>
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3 <command interpreter="bash">weeder2_wrapper.sh
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4 $sequence_file $species_code
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5 $output_motifs_file $output_matrix_file
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6 $strands
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7 #if $chipseq.use_chipseq
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8 -chipseq -top $chipseq.top
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9 #end if
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10 #if str( $advanced_options.advanced_options_selector ) == "on"
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11 -maxm $advanced_options.n_motifs_report
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12 -b $advanced_options.n_motifs_build
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13 -sim $advanced_options.sim_threshold
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14 -em $advanced_options.em_cycles
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15 #end if
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16 </command>
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17 <requirements>
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18 <requirement type="package" version="2.0">weeder</requirement>
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19 </requirements>
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20 <inputs>
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21 <param name="sequence_file" type="data" format="fasta" label="Input sequence" />
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22 <param name="species_code" type="select" label="Species to use for background comparison">
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23 <!-- Hard code options for now
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24 See weeder's "organisms.txt" for full list
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25 -->
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26 <option value="HS">Homo sapiens (HS)</option>
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27 <option value="MM">Mus musculus (MM)</option>
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28 <option value="DM">Drosophila melanogaster (DM)</option>
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29 <option value="SC">Saccharomyces cerevisiae (SC)</option>
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30 <option value="AT">Arabidopsis thaliana (AT)</option>
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31 </param>
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32 <param name="strands" label="Use both strands of sequence" type="boolean"
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33 truevalue="" falsevalue="-ss" checked="True"
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34 help="If not checked then use -ss option" />
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35 <conditional name="chipseq">
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36 <param name="use_chipseq" type="boolean"
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37 label="Use the ChIP-seq heuristic"
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38 help="Speeds up the computation (-chipseq)"
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39 truevalue="yes" falsevalue="no" checked="on" />
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40 <when value="yes">
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41 <param name="top" type="integer" value="100"
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42 label="Number of top input sequences with oligos to scan for"
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43 help="Increase this value to improve the chance of finding motifs enriched only in a subset of your input sequences (-top)" />
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44 </when>
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45 <when value="no"></when>
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46 </conditional>
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47 <conditional name="advanced_options">
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48 <param name="advanced_options_selector" type="select"
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49 label="Display advanced options">
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50 <option value="off">Hide</option>
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51 <option value="on">Display</option>
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52 </param>
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53 <when value="on">
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54 <param name="n_motifs_report" type="integer" value="25"
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55 label="Number of discovered motifs to report" help="(-maxm)" />
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56 <param name="n_motifs_build" type="integer" value="50"
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57 label="Number of top scoring motifs to build occurrences matrix profiles and outputs for"
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58 help="(-b)" />
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59 <param name="sim_threshold" type="float" min="0.0" max="1.0" value="0.95"
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60 label="Similarity threshold for the redundancy filter"
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61 help="Remove motifs that are too similar, with lower values imposing a stricter filter. Must be between 0.0 and 1.0 (-sim)" />
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62 <param name="em_cycles" type="integer" min="0" max="100" value="1"
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63 label="Number of expectation maximization (EM) cycles to perform"
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64 help="Number of cycles must be between 0 and 100 (-em)" />
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65 </when>
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66 <when value="off">
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67 </when>
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68 </conditional>
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69 </inputs>
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70 <outputs>
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71 <data name="output_motifs_file" format="txt" label="Weeder2 on ${on_string} (motifs)" />
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72 <data name="output_matrix_file" format="txt" label="Weeder2 on ${on_string} (matrix)" />
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73 </outputs>
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74 <tests>
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75 <test>
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76 <param name="sequence_file" value="weeder_in.fa" ftype="fasta" />
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77 <param name="species_code" value="MM" />
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78 <output name="output_motifs_file" file="weeder2_motifs.out" lines_diff="2" />
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79 <output name="output_matrix_file" file="weeder2_matrix.out" />
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80 </test>
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81 </tests>
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82 <help>
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83
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84 .. class:: infomark
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85
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86 **What it does**
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87
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88 Weeder2 is a program for finding novel motifs (transcription factor binding sites)
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89 conserved in a set of regulatory regions of related genes.
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90
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91 -------------
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92
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93 .. class:: infomark
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94
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95 **Usage advice**
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96
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97 Guidelines on how to use this tool can be seen in Zambelli et al. 2014 (see link
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98 below), but the following is a brief guide. Please note that **motifs** are a model
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99 or matrix that describes a set of sequences that may differ in the base composition.
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100 **Oligos** are specific sequences found within the input sequences or genomic
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101 background.
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102
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103 **Input sequence** (in FASTA format) should be short (100-200bp) and be reasonably
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104 expected to contain an enriched motif(s). This is not generally an issue with
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105 transcription factor ChIP-seq derived sequences centred on the summit of binding
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106 regions that are expected to contain a dominant motif and possibly secondary motifs.
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107
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108 There is **no need to mask sequence for repetitive sequence** as factors may
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109 legitimately bind repetitive sequence.
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110
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111 **Use both strands of sequence** by default, unless there is a specific reason not
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112 to do so.
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113
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114 **Species to use for background comparison** should match the genome used to
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115 generate the **input sequence**. The background genome motif frequencies are
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116 generated from within the promoter regions of annotated genes and are shown to be a
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117 good background for both promoter and other regulatory regions.
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118
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119 **Use the ChIP-seq heuristic** (-chipseq) when there are a large number of
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120 input sequences (hundreds or thousands). When -chipseq is used Weeder will use
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121 only oligos from the first 100 sequences to build motifs with which it scans
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122 all of the input sequences. This speeds up the computational time without too much
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123 risk of losing important motifs. Even if not strictly necessary it's advisable to
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124 order input sequences by their significance, e.g. fold enrichment or Pvalue. For
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125 large data sets (-top) should be set to a number equating at least 10 to 20% of
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126 input sequences (as recommended by the authors).
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127
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128 **Number of discovered motifs to report** (-maxm) limits the number of reported
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129 motifs even if there are more than -maxm. **Number of top scoring motifs to build
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130 occurrences matrix profiles and outputs for** (-b) changes the number of top
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131 scoring motifs of length 6, 8 and 10 for which the occurrence matrix is built.
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132 Increasing -b may result in a larger number of reported motifs, but with potentially
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133 more of low significance and increases the computational time. If increasing -b does
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134 not result in more motifs in your results it means that the additional motifs are
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135 filtered out by the redundancy filter or that the maximum number of reported motifs
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136 set by -maxm has been reached.
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137
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138 **Similarity threshold for the redundancy filter** (-sim) default setting is
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139 recommended.
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140
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141 **Number of expectation maximization (EM) cycles to perform** (-em) default is
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142 recommended. The option is included to help "clean up" the resulting motif matrices.
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143 In this version the number of EM steps can be increased, which can be useful for
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144 motifs with highly redundant stretches of sequence.
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145
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146 -------------
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147
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148 .. class:: infomark
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149
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150 **A note on the results**
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151
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152 The resulting matrices are the result of scanning (by default both strands) for
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153 oligos of length 6, 8 and 8, allowing 1, 2 and 3 substitutions respectively. The
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154 matrices within the matrix.w2 file can be input into other tools. The recommended
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155 next step is to use **STAMP** (http://www.benoslab.pitt.edu/stamp/), which displays
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156 the motifs as logos and identifies matches with libraries of known DNA binding
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157 motifs, such as TRANSFAC or JASPAR.
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158
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159 -------------
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160
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161 .. class:: infomark
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162
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163 **Credits**
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164
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165 This Galaxy tool has been developed by Peter Briggs and Ian Donaldson within the
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166 Bioinformatics Core Facility at the University of Manchester, and runs the Weeder2
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167 motif discovery package:
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168
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169 * Zambelli, F., Pesole, G. and Pavesi, G. 2014. Using Weeder, Pscan, and PscanChIP
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170 for the Discovery of Enriched Transcription Factor Binding Site Motifs in
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171 Nucleotide Sequences. Current Protocols in Bioinformatics. 47:2.11:2.11.1–2.11.31.
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172 * http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi0211s47/full
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173
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174 This tool is compatible with Weeder 2.0:
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175
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176 * http://159.149.160.51/modtools/downloads/weeder2.html
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177
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178 Please kindly acknowledge both this Galaxy tool, the Weeder package and the utility
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179 scripts if you use it in your work.
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180 </help>
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181 <citations>
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182 <!--
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183 See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
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184 Can be either DOI or Bibtex
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185 Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex
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186 -->
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187 <citation type="doi">10.1002/0471250953.bi0211s47</citation>
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188 </citations>
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189 </tool>
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