annotate ReadFids_xml.xml @ 6:6e837e9352a2 draft default tip

"planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 62fed9acaee7410de763b756cfa7de48ee258929"
author workflow4metabolomics
date Wed, 13 May 2020 03:52:09 -0400
parents 5e64657b4fe5
children
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1 <tool id="NMR_Read" name="NMR_Read" version="@WRAPPER_VERSION@">
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2 <description> Read Bruker NMR raw files</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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8 <expand macro="requirements" />
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10 <expand macro="stdio"/>
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12 <command>
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13 ## Wrapper
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14 Rscript $__tool_directory__/ReadFids_wrapper.R
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16 ## File input
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17 fidzipfile $fidzipfile
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19 ## Title line
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20 title_line $title_line
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22 ## Subdirectories
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23 subdirectories $subdirectories
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25 ## Use subdirectories names as FID names?
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26 dirs_names $dirs_names
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28 ## Outputs
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29 dataMatrix $dataMatrix
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30 sampleMetadata $sampleMetadata
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31 logOut $logOut
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32 graphOut $graphOut
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34 </command>
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36 <inputs>
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37 <param name="fidzipfile" type="data" format="no_unzip.zip,zip" label="Bruker FID file" />
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38 <param name="title_line" label="Specify the line in the title file to recover the FID names (usually in pdata/1/title)" type="integer" value="1" size="100" help="Default value is line 1"/>
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40 <param name="subdirectories" label="Presence of subdirectories?" type="select" help="Select 'FALSE' when there is no subdirectories, 'TRUE' if there are subdirectories">
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41 <option value="FALSE"> FALSE </option>
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42 <option value="TRUE"> TRUE </option>
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43 </param>
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45 <param name="dirs_names" label="Use (sub)directories names as FID names?" type="select" help="Select 'TRUE' to use the subdirectories names as the FID names (instead of looking in the title file)">
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46 <option value="FALSE"> FALSE </option>
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47 <option value="TRUE"> TRUE </option>
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48 </param>
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49 </inputs>
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51 <outputs>
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52 <data format="tabular" name="dataMatrix" label="${tool.name}_dataMatrix" />
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53 <data format="tabular" name="sampleMetadata" label="${tool.name}_sampleMetadata" />
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54 <data format="txt" name="logOut" label="${tool.name}_log" />
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55 <data format="pdf" name="graphOut" label="${tool.name}_graph" />
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56 </outputs>
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59 <tests>
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60 <test>
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61 <param name="fidzipfile" value="MTBLS1.zip" ftype="zip" />
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62 <param name="title_line" value="1" />
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63 <param name="subdirectories" value="TRUE" />
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64 <param name="dirs_names" value="TRUE" />
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66 <output name="dataMatrix" value="NMR_ReadFids_dataMatrix.tabular" />
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67 </test>
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68 </tests>
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70 <help>
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72 @HELP_AUTHORS@
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75 =============
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76 NMR Read
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77 =============
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79 -----------
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80 Description
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81 -----------
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83 Nuclear Magnetic Resonance Bruker files reading (from the PEPS-NMR R package (https://github.com/ManonMartin/PEPSNMR))
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85 -----------------
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86 Workflow position
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87 -----------------
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89 **Upstream tools**
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91 ========================= ================= =======
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92 Name output file format
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93 ========================= ================= =======
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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94 NA NA NA
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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95 ========================= ================= =======
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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96
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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97
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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98 **Downstream tools**
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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99
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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100 +-----------------------+--------------------------+--------+
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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101 | Name | Output file | Format |
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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102 +=======================+==========================+========+
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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103 |NMR_Preprocessing | dataMatrix | Tabular|
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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104 +-----------------------+--------------------------+--------+
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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105 |NMR_Preprocessing | sampleMetadata | Tabular|
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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106 +-----------------------+--------------------------+--------+
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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107 |NMR_Preprocessing | NMR_Read_log | TXT |
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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108 +-----------------------+--------------------------+--------+
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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109 |NMR_Preprocessing | NMR_Read_graph | PDF |
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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110 +-----------------------+--------------------------+--------+
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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111 |NMR_Alignement | dataMatrix | Tabular|
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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112 +-----------------------+--------------------------+--------+
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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113 |NMR_Bucketing | dataMatrix | Tabular|
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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114 +-----------------------+--------------------------+--------+
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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115 |Normalization | dataMatrix | Tabular|
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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116 +-----------------------+--------------------------+--------+
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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117 |Univariate | variableMetadata | Tabular|
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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118 +-----------------------+--------------------------+--------+
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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119 |Multivariate | sampleMetadata | Tabular|
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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120 +-----------------------+--------------------------+--------+
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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121 | | variableMetadata | Tabular|
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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122 +-----------------------+--------------------------+--------+
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123
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124
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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125 -----------
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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126 Input files
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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127 -----------
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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128
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129 +---------------------------+-----------------+
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130 | Parameter : num + label | Format |
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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131 +===========================+=================+
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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132 | 1 : Choose your inputs | zip |
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133 +---------------------------+-----------------+
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134
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135
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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136 **Choose your inputs**
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137
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138 | Zip file (recommended) of FID Bruker files: you can put a zip file containing your FID Bruker files: myinputs.zip.
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139
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140
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141 ----------
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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142 Parameters
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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143 ----------
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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144
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145 FID Title line
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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146 | Line in the acqus file to find the FID title (name)
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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147 |
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148
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149 subdirectories
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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150 | Organization of individual's files
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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151 | TRUE: will search inside subdirectories for FIDs and will merge them to have unique FID and info matrices.
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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152 |
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153
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154 dirs_names
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155 | Use the (sub)directories names as FID names?
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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156 |
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157
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158
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159 ------------
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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160 Output files
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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161 ------------
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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162
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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163 NMR_Read_dataMatrix
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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164 | tabular output
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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165 | Data matrix with n rows (samples) and p columns (time) containing the raw FIDs.
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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166 |
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167
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168 NMR_Read_sampleMetadata
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169 | tabular output
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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170 | Data matrix with n rows (samples) containing the acquisition parameters for each sample.
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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171 |
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173 NMR_Read_log
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174 | Text output
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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175 | Contains warnings
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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176 |
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177
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179 NMR_Read_graph
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180 | pdf output
5e64657b4fe5 planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 22ca8782d7c4c0211e13c95b425d4f29f53f995e
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181 | line plots of FID
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182 |
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183
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185 Creating the zip file
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186 -----------------------
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188 .. class:: warningmark you must use the 7Zip software (http://www.7-zip.org/) to zip under Windows.
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190 Must contain at least the following files for every sample: fid, acqu and acqus
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191
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192 .. image:: ./static/images/ReadFids.png
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193
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194
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195
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196 **Possible structure and parameters values:**
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197
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198
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199 (1) use title file and presence of sub-directories: set the FID Title line, subdirectories = TRUE, dirs_names = FALSE
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200 (2) use title file and no sub-directories: set the FID Title line, subdirectories = FALSE, dirs_names = FALSE
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201 (3) don't use title file and presence of sub-directories: subdirectories = TRUE, dirs_names = TRUE
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202 (4) don't use title file and no sub-directories: subdirectories = FALSE, dirs_names = TRUE
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203
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204
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205 @HELP_CHANGELOG@
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206
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207 </help>
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208
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209 <expand macro="citation" />
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210
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211 </tool>