Mercurial > repos > marie-tremblay-metatoul > nmr_preprocessing

annotate ReadFids.xml @ 7:122df1bf0a8c draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
author workflow4metabolomics
date Fri, 11 Jul 2025 08:33:38 +0000
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122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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1 <tool id="NMR_Read" name="NMR_Read" version="@WRAPPER_VERSION@+galaxy1">
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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>
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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6 </macros>
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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8 <expand macro="requirements"/>
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122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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10 <required_files>
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11 <include path="DrawFunctions.R" />
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12 <include path="ReadFids_wrapper.R" />
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13 <include path="ReadFids_script.R" />
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14 </required_files>
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122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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16 <command detect_errors="aggressive"><![CDATA[
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17 Rscript
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18 -e "source('${__tool_directory__}/DrawFunctions.R')"
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19 -e "source('${__tool_directory__}/ReadFids_script.R')"
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20 -e "source('${__tool_directory__}/ReadFids_wrapper.R')"
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21 --fidzipfile "$fidzipfile"
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22 --title_line $title_line
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23 $subdirectories
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24 $dirs_names
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25 ]]></command>
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27 <inputs>
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28 <param name="fidzipfile" type="data" format="zip" label="Bruker FID file" />
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29 <param name="title_line" label="Specify the line in the title file to recover the FID names (usually in pdata/1/title)" type="integer" value="1" help="Default value is line 1"/>
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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30 <param name="subdirectories" label="Presence of subdirectories?" type="boolean" truevalue="--subdirectories" falsevalue="" checked="false" help="Select 'FALSE' when there is no subdirectories, 'TRUE' if there are subdirectories"/>
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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31 <param name="dirs_names" label="Use (sub)directories names as FID names?" type="boolean" truevalue="--dirs_names" falsevalue="" checked="false" help="Select 'TRUE' to use the subdirectories names as the FID names (instead of looking in the title file)"/>
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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32 </inputs>
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34 <outputs>
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35 <data format="tabular" name="dataMatrix" from_work_dir="dataMatrix.tsv" label="${tool.name}_dataMatrix" />
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36 <data format="tabular" name="sampleMetadata" from_work_dir="sampleMetadata.tsv" label="${tool.name}_sampleMetadata" />
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37 <data format="txt" name="logOut" from_work_dir="logOut.txt" label="${tool.name}_log" />
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38 <data format="pdf" name="graphOut" from_work_dir="graphOut.pdf" label="${tool.name}_graph" />
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39 </outputs>
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42 <tests>
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43 <test>
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44 <param name="fidzipfile" location="https://nextcloud.inrae.fr/s/ksGZq9GZfL9R6PD/download/MTBLS1.zip" ftype="zip" />
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45 <param name="title_line" value="1" />
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46 <param name="subdirectories" value="TRUE" />
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47 <param name="dirs_names" value="TRUE" />
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49 <output name="dataMatrix" location="https://nextcloud.inrae.fr/s/aMs9eM4RwRjeign/download/NMR_ReadFids_dataMatrix.tabular" />
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50 <output name="sampleMetadata" value="NMR_ReadFids_sampleMetadata.tabular" />
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51 <output name="logOut" value="NMR_ReadFids_log.txt" compare="diff" lines_diff="100" />
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52 <output name="graphOut" value="NMR_ReadFids_graph.pdf" compare="diff" lines_diff="100" />
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53 </test>
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54 </tests>
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56 <help>
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58 @HELP_AUTHORS@
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61 =============
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62 NMR Read
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63 =============
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65 -----------
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66 Description
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67 -----------
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69 Nuclear Magnetic Resonance Bruker files reading (from the PEPS-NMR R package (https://github.com/ManonMartin/PEPSNMR))
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71 -----------------
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72 Workflow position
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73 -----------------
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75 **Upstream tools**
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77 ========================= ================= =======
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78 Name output file format
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79 ========================= ================= =======
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80 NA NA NA
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81 ========================= ================= =======
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84 **Downstream tools**
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86 +-----------------------+--------------------------+--------+
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87 | Name | Output file | Format |
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88 +=======================+==========================+========+
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89 |NMR_Preprocessing | dataMatrix | Tabular|
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90 +-----------------------+--------------------------+--------+
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91 |NMR_Preprocessing | sampleMetadata | Tabular|
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92 +-----------------------+--------------------------+--------+
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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93 |NMR_Preprocessing | NMR_Read_log | TXT |
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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94 +-----------------------+--------------------------+--------+
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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95 |NMR_Preprocessing | NMR_Read_graph | PDF |
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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96 +-----------------------+--------------------------+--------+
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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97 |NMR_Alignement | dataMatrix | Tabular|
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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98 +-----------------------+--------------------------+--------+
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99 |NMR_Bucketing | dataMatrix | Tabular|
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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100 +-----------------------+--------------------------+--------+
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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101 |Normalization | dataMatrix | Tabular|
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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102 +-----------------------+--------------------------+--------+
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103 |Univariate | variableMetadata | Tabular|
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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104 +-----------------------+--------------------------+--------+
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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105 |Multivariate | sampleMetadata | Tabular|
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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106 +-----------------------+--------------------------+--------+
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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107 | | variableMetadata | Tabular|
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108 +-----------------------+--------------------------+--------+
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109
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110
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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111 -----------
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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112 Input files
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113 -----------
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114
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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115 +---------------------------+-----------------+
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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116 | Parameter : num + label | Format |
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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117 +===========================+=================+
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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118 | 1 : Choose your inputs | zip |
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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119 +---------------------------+-----------------+
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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120
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121
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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122 **Choose your inputs**
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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123
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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124 | Zip file (recommended) of FID Bruker files: you can put a zip file containing your FID Bruker files: myinputs.zip.
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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125
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126
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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127 ----------
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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128 Parameters
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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129 ----------
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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130
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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131 FID Title line
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132 | Line in the acqus file to find the FID title (name)
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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133 |
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134
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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135 subdirectories
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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136 | Organization of individual's files
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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137 | TRUE: will search inside subdirectories for FIDs and will merge them to have unique FID and info matrices.
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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138 |
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139
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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140 dirs_names
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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141 | Use the (sub)directories names as FID names?
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142 |
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143
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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144
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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145 ------------
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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146 Output files
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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147 ------------
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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148
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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149 NMR_Read_dataMatrix
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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150 | tabular output
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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151 | Data matrix with n rows (samples) and p columns (time) containing the raw FIDs.
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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152 |
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153
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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154 NMR_Read_sampleMetadata
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155 | tabular output
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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156 | Data matrix with n rows (samples) containing the acquisition parameters for each sample.
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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157 |
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158
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159 NMR_Read_log
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160 | Text output
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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161 | Contains warnings
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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162 |
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163
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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164
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165 NMR_Read_graph
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166 | pdf output
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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167 | line plots of FID
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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168 |
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169
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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170
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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171 Creating the zip file
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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172 -----------------------
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173
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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174 .. class:: warningmark you must use the 7Zip software (http://www.7-zip.org/) to zip under Windows.
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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175
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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176 Must contain at least the following files for every sample: fid, acqu and acqus
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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177
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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178 .. image:: ./static/images/ReadFids.png
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179
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180
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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181
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182 **Possible structure and parameters values:**
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183
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184
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185 (1) use title file and presence of sub-directories: set the FID Title line, subdirectories = TRUE, dirs_names = FALSE
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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186 (2) use title file and no sub-directories: set the FID Title line, subdirectories = FALSE, dirs_names = FALSE
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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187 (3) don't use title file and presence of sub-directories: subdirectories = TRUE, dirs_names = TRUE
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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188 (4) don't use title file and no sub-directories: subdirectories = FALSE, dirs_names = TRUE
122df1bf0a8c planemo upload for repository https://github.com/workflow4metabolomics/nmr_preprocessing commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
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189
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191 @HELP_CHANGELOG@
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193 </help>
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195 <expand macro="citation" />
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197 </tool>