Mercurial > repos > marie-tremblay-metatoul > nmr_bucketing

annotate NmrBucketing_xml.xml @ 10:06b7a5815a1c draft

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planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit e936eab761415f9337f8b4ab0ff0337e27a5b090
author lecorguille
date Fri, 21 Apr 2017 09:08:00 -0400
parents 62c62e31fc80
children
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06b7a5815a1c planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit e936eab761415f9337f8b4ab0ff0337e27a5b090
lecorguille
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1 <tool id="NmrBucketing" name="NMR_Bucketing" version="2.0.2">
9
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3 <description> Bucketing and integration of NMR Bruker raw data</description>
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4
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5 <requirements>
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6 <requirement type="package" version="1.1_4">r-batch</requirement>
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7 <requirement type="package" version="1.8.8">r-pracma</requirement>
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8 </requirements>
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10 <stdio>
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11 <exit_code range="1:" level="fatal" />
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12 </stdio>
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62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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14 <command>
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15 Rscript '$__tool_directory__/NmrBucketing_wrapper.R'
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17 #if $inputs.input == "tsv_file":
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18 tsvfile '$inputs.tsv_file'
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19 #elif $inputs.input == "zip_file":
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20 zipfile '$inputs.zip_file'
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21 #end if
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24 ## Bucket width
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25 bucket_width $bucket_width
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27 ## Spectra borders
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28 left_border $left_border
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29 right_border $right_border
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32 ## Spectra representation
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33 graphType $graphType
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35 ## Exclusion zone
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36 zone_exclusion_choices.choice ${zone_exclusion_choices.choice}
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37 #if str($zone_exclusion_choices.choice) == 'yes':
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38 #for $i in $zone_exclusion_choices.conditions:
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39 zone_exclusion_left ${i.zone_exclusion_left}
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40 zone_exclusion_right ${i.zone_exclusion_right}
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41 #end for
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42 #end if
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44 ## Outputs
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45 logOut log.log
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46 dataMatrixOut '$dataMatrixOut'
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47 sampleOut '$sampleOut'
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48 variableOut '$variableOut'
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49 graphOut '$graphOut'; cat log.log
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50 </command>
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51
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52 <inputs>
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53 <conditional name="inputs">
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54 <param name="input" type="select" label="Choose your inputs method" >
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55 <option value="zip_file" selected="true">Zip file from your history containing your Bruker directories</option>
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56 <option value="tsv_file">Tsv file containing preprocessed spectra (from your history)</option>
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57 </param>
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58 <when value="zip_file">
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59 <param name="zip_file" type="data" format="no_unzip.zip" label="Zip file" />
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60 </when>
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61 <when value="tsv_file">
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62 <param name="tsv_file" type="data" format="tabular" label="Tsv file" />
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63 </when>
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64 </conditional>
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65
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66 <param name="bucket_width" label="Bucket width" type="float" value="0.04" help="Default value is 0.04 ppm"/>
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67
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68 <param name="left_border" label="Left Border" type="float" value="10.0" size="10" help="Default value is 10 ppm"/>
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69 <param name="right_border" label="Right Border" type="float" value="0.5" size="10" help="Default value is 0.5 ppm"/>
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70
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71 <conditional name="zone_exclusion_choices">
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72 <param name="choice" type="select" label="Exclusion zone(s)" help="Choose if you want to exclude particular zone(s)" >
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73 <option value="yes" > yes </option>
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74 <option value="no" selected="true"> no </option>
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75 </param>
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76 <when value="yes">
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77 <repeat name="conditions" title="exclusion zones">
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78 <param name="zone_exclusion_left" label="Left exclusion zone border" type="float" value="10.0" />
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79 <param name="zone_exclusion_right" label="Right exclusion zone border" type="float" value="10.0" />
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80 </repeat>
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81 </when>
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82 <when value="no">
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83 </when>
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84 </conditional>
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85
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86 <param name="graphType" label="Spectra representation" type="select" help="Select 'None' for no representation,'Overlay' to overlay all spectra on a unique chart and 'One per individual' to generate an individual chart for each observation">
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87 <option value="None"> none </option>
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88 <option value="Overlay"> Overlay </option>
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89 <option value="One_per_individual"> One_per_individual </option>
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90 </param>
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91
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92 </inputs>
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93
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94 <outputs>
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95 <data format="tabular" name="sampleOut" label="${tool.name}_sampleMetadata" />
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96 <data format="tabular" name="variableOut" label="${tool.name}_variableMetadata" />
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97 <data format="tabular" name="dataMatrixOut" label="${tool.name}_bucketedData" />
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98 <data format="pdf" name="graphOut" label="${tool.name}_spectra" >
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99 <filter> graphType != "None" </filter>
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100 </data>
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101 </outputs>
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102
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103 <tests>
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104 <test>
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105 <param name="inputs|input" value="zip_file" />
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106 <param name="inputs|zip_file" value="MTBLS1.zip" ftype="zip" />
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107 <param name="bucket_width" value="0.01" ftype="zip" />
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108 <param name="left_border" value="9.3" />
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109 <param name="right_border" value="0.8" />
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110 <param name="zone_exclusion_choices|choice" value="yes" />
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111 <param name="zone_exclusion_choices|conditions_0|zone_exclusion_left" value="6.0" />
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112 <param name="zone_exclusion_choices|conditions_0|zone_exclusion_right" value="4.24" />
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113 <param name="zone_exclusion_choices|conditions_1|zone_exclusion_left" value="3.99" />
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114 <param name="zone_exclusion_choices|conditions_1|zone_exclusion_right" value="3.19" />
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115 <param name="graphType" value="Overlay" />
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116 <output name="dataMatrixOut" file="MTBLS1_bucketedData.tabular" />
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117 <output name="sampleOut" file="MTBLS1_sampleMetadata.tabular" />
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118 <output name="variableOut" file="MTBLS1_variableMetadata.tabular" />
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119 </test>
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120 </tests>
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121
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122 <help>
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123
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124 .. class:: infomark
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125
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126 **Authors** Marie Tremblay-Franco (marie.tremblay-franco@toulouse.inra.fr), Marion Landi (marion.landi@clermont.inra.fr) and Franck Giacomoni (fgiacomoni@clermont.inra.fr)
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127
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128
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129 =============
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130 NMR Bucketing
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131 =============
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132
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133 -----------
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134 Description
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135 -----------
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136
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137 Bucketing / Binning (spectra segmentation in fixed-size windows) and integration (sum of absolute intensities inside each bucket) to preprocess NMR data
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138
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139 -----------------
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140 Workflow position
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141 -----------------
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142
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143 **Upstream tools**
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144
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145 ========================= ============================ =======
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146 Name output file format
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147 ========================= ============================ =======
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148 NMRAlignment NMR_Alignment_alignedSpectra tsv
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149 ========================= ============================ =======
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150
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151 **Downstream tools**
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152
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153 +---------------------------+----------------------+--------+
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154 | Name | Output file | Format |
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155 +===========================+======================+========+
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156 |NmrNormalization | dataMatrix.tsv | Tabular|
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157 +---------------------------+----------------------+--------+
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158 |Univariate | variableMetadata.tsv | Tabular|
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159 +---------------------------+----------------------+--------+
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160 |Multivariate | sampleMetadata.tsv | Tabular|
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161 +---------------------------+----------------------+--------+
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162 | | variableMetadata.tsv | Tabular|
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163 +---------------------------+----------------------+--------+
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164
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165
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166 -----------
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167 Input files
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168 -----------
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169
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170 +---------------------------+------------+
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171 | Parameter : num + label | Format |
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172 +===========================+============+
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173 | 1 : Choose your inputs | zip |
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174 +---------------------------+------------+
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175 | 1 : Choose your inputs | tsv |
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176 +---------------------------+------------+
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177
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178 **Choose your inputs**
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179
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180 You have three methods for your inputs:
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181
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182 | Zip file (recommended): You can put a zip file containing your inputs as raw Bruker files: myinputs.zip (containing all your conditions as sub-directories).
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183 | Tsv file: You can put a tsv file containing your inputs as preprocessed spectra: myinputs.tsv (containing all your conditions in columns and chemical shifts in rows).
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184
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185 .. image:: ./static/images/Mth_Architecture_Repertoire_Bruker.png
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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186 :width: 800
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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187
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188 ----------
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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189 Parameters
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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190 ----------
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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191
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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192 Bucket width
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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193 | size of windows
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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194 |
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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195
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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196 Left limit
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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197 | Upper boundary: values greater than this value are not used in the bucketing. Default value is 10.0 ppm
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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198 |
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199
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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200 Right limit
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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201 | Lower boundary: values lower than this value are not used in the bucketing. Default value is 0.5 ppm
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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202 |
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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203
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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204 Exclusion zone(s)
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205 | Spectral regions to exclude, water, solvents, ... resonance
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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206 | If YES: parameters **Lower exclusion zone** and **Upper exclusion zone** are visible,
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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207 | If NO: no zone to exclude
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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208 | Default value is NO
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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209 |
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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210
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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211 Left exclusion zone
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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212 | Upper boundary of exclusion zone
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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213 |
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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214
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215 Right exclusion zone
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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216 | Lower boundary of exclusion zone
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217
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218 | *Notes:*
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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219 | - these parameters can be used several times using the "Add new exclusion zones" button
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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220 |
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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221
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222 Spectra representation:
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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223 | Graphical chart of bucketed and integrated raw files
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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224 | If "Overlay": the n (sample number) spectra are overlaid on the same figure
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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225 | If "One_per_individual": pdf file includes n pages (1 per sample)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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226 |
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227
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228
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229 ------------
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230 Output files
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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231 ------------
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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232
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233
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234 bucketedData.tsv
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235 | tabular output
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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236 | Data matrix with p rows (buckets) and n columns (samples) containing the intensities
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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237 |
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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238
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239 sampleMetadata.tsv
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240 | tabular output
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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241 | file with n rows (samples) and 2 columns containing sample identifier (rownames) and sample order: the rownames of sampleMetadata must be identical to the colnames of the bucketedData. Can add columns with numeric and/or character sample metadata. This file is optional in the normalization step and mandatory in the statistical analysis step of the workflow.
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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242 |
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243
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244 variableMetadata.tsv
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245 | tabular output
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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246 | file with p rows (buckets) and 2 columns containing variable identifier (rownames) and bucket order: the rownames of variableMetadata must be identical to the rownames of the bucketedData. Can add columns with numeric and/or character variable metadata. This file is mandatory in the statistical analysis step of the workflow.
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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247 |
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248
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249 spectra.pdf
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250 | pdf output
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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251 | Graphical chart of bucketed and integrated data
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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252 |
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253
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254
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255 ---------------------------------------------------
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256
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257 ---------------
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258 Working example
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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259 ---------------
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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260
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261
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262 .. class:: warningmark
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263
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264 Under construction
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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265
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266 .. image:: ./static/images/Mth_Travaux.png
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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267 :width: 100
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268
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269 ---------------------------------------------------
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270
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271 Changelog/News
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272 --------------
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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273
10
06b7a5815a1c planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit e936eab761415f9337f8b4ab0ff0337e27a5b090
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274 **Version 2.0.2 - 21/04/2017**
9
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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275
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276 - IMPROVEMENT: Add “zoomed” representations of bucketed spectra, depending on exclusion zone borders
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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277
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278 **Version 1.0.3 - 24/10/2016**
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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279
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280 - ENHANCEMENT: add possibility of bucketing processed files (upstream tools)
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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281
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282 **Version 1.0.2 - 12/08/2016**
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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283
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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284 - ENHANCEMENT: x-axis customization: add chemical shift labels
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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285
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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286 **Version 1.0.1 - 04/04/2016**
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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287
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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288 - TEST: refactoring to pass planemo test using conda dependencies
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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289
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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290
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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291 **Version 2015-01-08 - 08/01/2015**
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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292
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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293 </help>
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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294 <citations>
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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295 <citation type="doi">10.1093/bioinformatics/btu813</citation>
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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296 </citations>
62c62e31fc80 planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit fc2be0f9fa66f830d592d74d14b47a63e761647b
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297 </tool>