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1 <tool id="NMR_Read" name="NMR_Read" version="1.2.0">
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2 <description> Read Bruker NMR raw files</description>
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3
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4 <stdio>
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5 <exit_code range="1:" level="fatal" />
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6 </stdio>
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7
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8 <command>
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9 ## Wrapper
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10 Rscript $__tool_directory__/ReadFids_wrapper.R
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11
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12 ## File input
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13 fidzipfile $fidzipfile
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14
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15 ## Title line
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16 title_line $title_line
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17
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18 ## Subdirectories
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19 subdirectories $subdirectories
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20
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21 ## Use subdirectories names as FID names?
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22 dirs_names $dirs_names
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23
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24 ## Outputs
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25 dataMatrix $dataMatrix
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26 sampleMetadata $sampleMetadata
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27 logOut $logOut
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28 graphOut $graphOut
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29
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30 </command>
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31
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32 <inputs>
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33 <param name="fidzipfile" type="data" format="no_unzip.zip" label="Bruker FID file" />
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34
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35 <param name="title_line" label="Specify the line in the title file to recover the FID names (usually in pdata/1/title)" type="integer" value="1" size="100" help="Default value is line 1"/>
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36
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37 <param name="subdirectories" label="Presence of subdirectories?" type="select" help="Select 'FALSE' when there is no subdirectories, 'TRUE' if there are subdirectories">
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38 <option value="FALSE"> FALSE </option>
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39 <option value="TRUE"> TRUE </option>
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40 </param>
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41
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42 <param name="dirs_names" label="Use (sub)directories names as FID names?" type="select" help="Select 'TRUE' to use the subdirectories names as the FID names (instead of looking in the title file)">
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43 <option value="FALSE"> FALSE </option>
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44 <option value="TRUE"> TRUE </option>
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45 </param>
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46 </inputs>
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47
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48
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49
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50 <outputs>
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51 <data format="tabular" name="dataMatrix" label="${tool.name}_dataMatrix" />
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52 <data format="tabular" name="sampleMetadata" label="${tool.name}_sampleMetadata" />
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53 <data format="txt" name="logOut" label="${tool.name}_log" />
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54 <data format="pdf" name="graphOut" label="${tool.name}_graph" />
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55 </outputs>
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56
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57
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58 <tests>
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59 <test>
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60 <param name="fidzipfile" value="MTBLS1.zip" ftype="zip" />
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61 <param name="title_line" value="1" />
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62 <param name="subdirectories" value="TRUE" />
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63 <param name="dirs_names" value="TRUE" />
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64
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65 <output name="dataMatrix" value="NMR_ReadFids_dataMatrix.tabular" />
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66
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67 </test>
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68 </tests>
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69
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70
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71
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72 <help>
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73
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74 .. class:: infomark
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75
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76 **Authors** Manon Martin (manon.martin@uclouvain.be) and Marie Tremblay-Franco (marie.tremblay-franco@inra.fr; Galaxy integration)
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77
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78 .. class:: infomark
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79
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80
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81 =============
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82 NMR Read
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83 =============
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84
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85 -----------
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86 Description
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87 -----------
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88
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89 Nuclear Magnetic Resonance Bruker files reading (from the PEPS-NMR R package (https://github.com/ManonMartin/PEPSNMR))
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90
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91 -----------------
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92 Workflow position
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93 -----------------
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94
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95 **Upstream tools**
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96
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97 ========================= ================= =======
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98 Name output file format
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99 ========================= ================= =======
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100 NA NA NA
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101 ========================= ================= =======
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102
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103
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104 **Downstream tools**
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105
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106 +-----------------------+--------------------------+--------+
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107 | Name | Output file | Format |
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108 +=======================+==========================+========+
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109 |NMR_Preprocessing | dataMatrix | Tabular|
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110 +-----------------------+--------------------------+--------+
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111 |NMR_Preprocessing | sampleMetadata | Tabular|
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112 +-----------------------+--------------------------+--------+
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113 |NMR_Preprocessing | NMR_Read_log | TXT |
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114 +-----------------------+--------------------------+--------+
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115 |NMR_Preprocessing | NMR_Read_graph | PDF |
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116 +-----------------------+--------------------------+--------+
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117 |NMR_Alignement | dataMatrix | Tabular|
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118 +-----------------------+--------------------------+--------+
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119 |NMR_Bucketing | dataMatrix | Tabular|
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120 +-----------------------+--------------------------+--------+
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121 |Normalization | dataMatrix | Tabular|
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122 +-----------------------+--------------------------+--------+
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123 |Univariate | variableMetadata | Tabular|
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124 +-----------------------+--------------------------+--------+
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125 |Multivariate | sampleMetadata | Tabular|
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126 +-----------------------+--------------------------+--------+
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127 | | variableMetadata | Tabular|
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128 +-----------------------+--------------------------+--------+
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129
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130
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131 -----------
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132 Input files
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133 -----------
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134
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135 +---------------------------+-----------------+
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136 | Parameter : num + label | Format |
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137 +===========================+=================+
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138 | 1 : Choose your inputs | zip |
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139 +---------------------------+-----------------+
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140
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141
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142 **Choose your inputs**
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143
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144 | Zip file (recommended) of FID Bruker files: you can put a zip file containing your FID Bruker files: myinputs.zip.
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145
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146
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147 ----------
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148 Parameters
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149 ----------
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150
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151 FID Title line
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152 | Line in the acqus file to find the FID title (name)
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153 |
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154
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155 subdirectories
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156 | Organization of individual's files
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157 | TRUE: will search inside subdirectories for FIDs and will merge them to have unique FID and info matrices.
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158 |
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159
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160 dirs_names
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161 | Use the (sub)directories names as FID names?
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162 |
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163
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164
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165 ------------
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166 Output files
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167 ------------
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168
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169 NMR_Read_dataMatrix
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170 | tabular output
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171 | Data matrix with n rows (samples) and p columns (time) containing the raw FIDs.
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172 |
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173
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174 NMR_Read_sampleMetadata
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175 | tabular output
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176 | Data matrix with n rows (samples) containing the acquisition parameters for each sample.
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177 |
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178
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179 NMR_Read_log
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180 | Text output
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181 | Contains warnings
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182 |
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183
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184
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185 NMR_Read_graph
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186 | pdf output
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187 | line plots of FID
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188 |
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189
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190
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191 Creating the zip file
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192 -----------------------
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193
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194 .. class:: warningmark you must use the 7Zip software (http://www.7-zip.org/) to zip under Windows.
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195
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196 Must contain at least the following files for every sample: fid, acqu and acqus
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197
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198 .. image:: ./static/images/ReadFids.png
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199 :height: 400
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200
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201
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202
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203 **Possible structure and parameters values:**
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204
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205
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206 (1) use title file and presence of sub-directories: set the FID Title line, subdirectories = TRUE, dirs_names = FALSE
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207 (2) use title file and no sub-directories: set the FID Title line, subdirectories = FALSE, dirs_names = FALSE
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208 (3) don't use title file and presence of sub-directories: subdirectories = TRUE, dirs_names = TRUE
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209 (4) don't use title file and no sub-directories: subdirectories = FALSE, dirs_names = TRUE
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210
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211
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212
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213 </help>
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214
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215
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216 <citations>
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217
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218 <citation type="bibtex">@PhDThesis{Rousseau2011,
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219 title = {Statistical contribution to the analysis of metabonomics data in $^1$H NMR spectroscopy},
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220 author = {Rousseau, R.},
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221 school = {Institut de Statistique, Biostatistique et Sciences Actuarielles, Universit{\'e} catholique de Louvain},
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222 year = {2011}}
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223 </citation>
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224
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225 </citations>
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226
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227
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228 </tool>
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