Mercurial > repos > marie-tremblay-metatoul > normalization

annotate NmrNormalization_xml.xml @ 5:3d00a98974b7 draft

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planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
author lecorguille
date Tue, 02 Oct 2018 12:14:47 -0400
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children 221cbd549c40
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3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
lecorguille
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1 <tool id="normalization" name="Normalization" version="1.0.6">
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
lecorguille
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3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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3 <description> Normalization of (preprocessed) spectra </description>
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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5 <requirements>
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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6 <requirement type="package" version="1.1_4">r-batch</requirement>
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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7 </requirements>
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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9 <stdio>
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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10 <exit_code range="1:" level="fatal" />
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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11 </stdio>
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3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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13 <command><![CDATA[
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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14 Rscript $__tool_directory__/NmrNormalization_wrapper.R
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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16 ## Data matrix of bucketed and integrated spectra
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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17 dataMatrix $dataMatrix
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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19 ## Normalization method
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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20 scalingMethod $scalingMethod.method
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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21 #if $scalingMethod.method == "PQN":
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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22 ## Sample metadata matrix
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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23 sampleMetadata $scalingMethod.sampleMetadata
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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25 ## Biological factor of interest (column number in samplemetadata)
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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26 factor $scalingMethod.factor
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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28 ## Reference class
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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29 controlGroup $scalingMethod.controlGroup
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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30 #end if
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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31 #if $scalingMethod.method == "QuantitativeVariable":
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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32 ## Sample metadata matrix
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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33 sampleMetadata $scalingMethod.sampleMetadata
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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34
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35 ## Biological factor of interest (column number in samplemetadata)
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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36 factor $scalingMethod.factor
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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37 #end if
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38
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39 ## Spectra representation
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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40 graphType $graphType
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41
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42 ## Outputs
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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43 logOut $logOut
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44 dataMatrixOut $dataMatrixOut
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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45 graphOut $graphOut
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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46 ]]></command>
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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47
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48 <inputs>
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49 <param name="dataMatrix" type="data" label="Data matrix of preprocessed data" help="" format="tabular" />
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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50
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51 <conditional name="scalingMethod" >
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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52 <param name="method" label="Normalization method" type="select" help="Default method is total intensity" >
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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53 <option value="None">None normalization</option>
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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54 <option value="Total">Total intensity</option>
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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55 <option value="PQN">Probabilistic Quotient Normalization</option>
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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56 <option value="QuantitativeVariable">Quantitative variable</option>
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57 </param>
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58 <when value="None" />
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59 <when value="Total" />
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60 <when value="PQN">
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61 <param name="sampleMetadata" type="data" label="Sample metadata matrix" help="" format="tabular" />
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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62 <param name="factor" label="Name of the column of the biological factor of interest (for PQN method)" type="text" />
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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63 <param name="controlGroup" label="Name of reference level for PQN normalization" type="text" help=""/>
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64 </when>
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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65 <when value="QuantitativeVariable">
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66 <param name="sampleMetadata" type="data" label="Sample metadata matrix" help="" format="tabular" />
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67 <param name="factor" label="Name of the column of the numerical variable for normalization (weight, osmolality, ...)" type="text" />
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68 </when>
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69 </conditional>
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70
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71 <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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72 <option value="None"> none </option>
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73 <option value="Overlay"> Overlay </option>
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74 <option value="One_per_individual"> One_per_individual </option>
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75 </param>
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76 </inputs>
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77
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78
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79 <outputs>
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80 <data format="txt" name="logOut" label="${tool.name}_log" />
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81 <data format="tabular" name="dataMatrixOut" label="${tool.name}_dataMatrix" />
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82 <data format="pdf" name="graphOut" label="${tool.name}_spectra" >
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83 <filter> graphType != "None" </filter>
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84 </data>
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85 </outputs>
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86
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87 <tests>
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88 <test>
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89 <param name="dataMatrix" value="MTBLS1_bucketedData.tabular" ftype="tabular" />
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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90 <conditional name="scalingMethod" >
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91 <param name="method" value="Total" />
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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92 </conditional>
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93 <param name="graphType" value="Overlay" />
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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94 <output name="dataMatrixOut" file="MTBLS1_bucketedData_normalized.tabular" />
3d00a98974b7 planemo upload for repository https://github.com/workflow4metabolomics/normalization commit 1aedb0fe77d56139bc8f5ded1fee1e455e8e9495
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95 </test>
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96 </tests>
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97
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98 <help>
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99
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100 .. class:: infomark
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101
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102 **Authors** Marie Tremblay-Franco (marie.tremblay-franco@toulouse.inra.fr) and Marion Landi (marion.landi@clermont.inra.fr)
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103 MetaboHUB: The French National Infrastructure for Metabolomics and Fluxomics (http://www.metabohub.fr/en)
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104
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105 ---------------------------------------------------
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106
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107 .. class:: infomark
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108
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109 **Please cite**
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110
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111 F. Dieterle, A. Ross, G. Schlotterbeck, and H. Senn (2006). Probabilistic Quotient Normalization as Robust Method to Account for Dilution of Complex Biological Mixtures. Application in 1H NMR Metabonomics.
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112 Analytical Chemistry 78(13): 4281-4290.
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113
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114 ---------------------------------------------------
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115
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116 ===============
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117 Normalization
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118 ===============
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119
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120 -----------
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121 Description
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122 -----------
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123
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124 Normalization (operation applied on each (preprocessed) individual spectrum) of preprocessed data
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125
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126 -----------------
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127 Workflow position
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128 -----------------
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129
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130 **Upstream tools**
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131
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132 +----------------------+------------------------------------+---------+-------------+
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133 | Name | output file | format | parameter |
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134 +======================+====================================+=========+=============+
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135 | NMR_Bucketing | Normalization_bucketedData.tsv | tabular | Ions Matrix |
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136 +----------------------+------------------------------------+---------+-------------+
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137
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138
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139
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140
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141 **Downstream tools**
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142
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143 +---------------------------+----------------------+--------+
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144 | Name | Output file | Format |
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145 +===========================+======================+========+
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146 |Univariate | variableMetadata.tsv | Tabular|
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147 +---------------------------+----------------------+--------+
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148 |Multivariate | sampleMetadata.tsv | Tabular|
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149 +---------------------------+----------------------+--------+
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150 | | variableMetadata.tsv | Tabular|
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151 +---------------------------+----------------------+--------+
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152
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153
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154 -----------
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155 Input files
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156 -----------
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157
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158 +---------------------------+------------+
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159 | Parameter : num + label | Format |
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160 +===========================+============+
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161 | DataMatrix | Tabular |
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162 +---------------------------+------------+
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163
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164 **DataMAtrix**
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165
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166 | variable x sample dataMatrix tabular separated file containing (preprocessed) spectra, with . as decimal, and NA for missing values
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167
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168
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169 ----------
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170 Parameters
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171 ----------
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172
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173 DataMatrix
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174 | see "Input files" section above
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175 |
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176
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177 Normalization method
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178 | normalization to apply on each spectrum:
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179
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180 +---------------------------+--------------------------------------+
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181 | Name | Normalization |
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182 +===========================+======================================+
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183 |None | No |
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184 +---------------------------+--------------------------------------+
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185 |Total | Total intensity |
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186 +---------------------------+--------------------------------------+
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187 |PQN | Probabilistic Quotient Normalization |
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188 +---------------------------+--------------------------------------+
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189 |QuantitativeVariable | Weight, osmolality, ... |
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190 +---------------------------+--------------------------------------+
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191
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192
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193 sampleMetadata
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194 | sample x metadata **sample** tabular separated file of the numeric and/or character sample metadata, with . as decimal and NA for missing values
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195 | Mandatory for "PQN" or "Quantitative" normalization method
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196 | The row names must be identical to the column names of the dataMatrix file
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197 |
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198
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199
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200 Spectra representation:
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201 | Graphical chart of bucketed and integrated raw files
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202 | If "Overlay": the n (sample number) spectra are overlaid on the same figure
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203 | If "One_per_individual": pdf file includes n pages (1 per sample)
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204 |
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205
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206
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207 ------------
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208 Output files
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209 ------------
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210
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211
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212 dataMatrix.tsv
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213 | tabular output
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214 | Data matrix with p rows (variable) and n columns (samples) containing the intensities
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215 |
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216
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217 spectra.pdf
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218 | pdf output
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219 | Graphical chart of bucketed and integrated data
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220 |
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221
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222
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223 ---------------------------------------------------
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224
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225 ---------------
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226 Working example
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227 ---------------
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228
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229
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230 .. class:: warningmark
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231
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232 Under construction
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233
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234 .. image:: ./static/images/Mth_Travaux.png
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235 :width: 100
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236
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237
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238 ---------------------------------------------------
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239
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240 --------------
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241 Changelog/News
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242 --------------
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243
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244 **Version 1.0.3 - 30/01/2017**
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245
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246 - BUGFIX: Fix a bug: stack overflow for integers
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247
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248 **Version 1.0.2 - 22/10/2016**
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249
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250 - NEW: this tool was previously named NMR Normalization. It had been generalize to deal with all kind of preprocessed data
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251
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252 **Version 1.0.1 - 14/04/2016**
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253
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254 - TEST: refactoring to pass planemo test using conda dependencies
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255
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256 **Version 2015-01-28 - 28/01/2015**
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257
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258 </help>
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259 <citations>
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260 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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261 </citations>
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262 </tool>