Mercurial > repos > workflow4metabolomics > xcms_refine

annotate macros_xcms.xml @ 0:eb115eb8f25c draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
author workflow4metabolomics
date Thu, 17 Jun 2021 07:42:55 +0000
parents
children 20f8ebc3a391
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eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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1 <?xml version="1.0"?>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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2 <macros>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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3
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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4 <token name="@TOOL_VERSION@">3.12.0</token>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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5 <xml name="requirements">
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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6 <requirements>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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7 <requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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8 <requirement type="package" version="1.1_5">r-batch</requirement>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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9 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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10 <requirement type="package" version="6.0">unzip</requirement>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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11 <yield />
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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12 </requirements>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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13 </xml>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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15 <!-- FILE_LOAD for planemo test -->
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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16 <token name="@COMMAND_FILE_LOAD@">
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17 #if $file_load_section.file_load_conditional.file_load_select == "yes":
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18 #if $file_load_section.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section.file_load_conditional.input[0].is_of_type("netcdf"):
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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19 #set singlefile_galaxyPath = '|'.join( [ str( $single_file ) for $single_file in $file_load_section.file_load_conditional.input ] )
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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20 #set singlefile_sampleName = '|'.join( [ str( $single_file.name ) for $single_file in $file_load_section.file_load_conditional.input ] )
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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21
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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22 singlefile_galaxyPath '$singlefile_galaxyPath' singlefile_sampleName '$singlefile_sampleName'
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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23 #else
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24 zipfile '$file_load_section.file_load_conditional.input'
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25 #end if
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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26 #end if
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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27 </token>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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28
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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29 <xml name="input_file_load">
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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30 <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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31 <conditional name="file_load_conditional">
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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32 <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message saying that your original dataset or zip file have been deleted on the server." >
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33 <option value="no" >no need</option>
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34 <option value="yes" >yes</option>
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35 </param>
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36 <when value="no">
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37 </when>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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38 <when value="yes">
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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39 <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." />
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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40 </when>
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41 </conditional>
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42 </section>
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43 </xml>
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44
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45 <xml name="test_file_load_zip">
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46 <section name="file_load_section">
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47 <conditional name="file_load_conditional">
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48 <param name="file_load_select" value="yes" />
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49 <param name="input" value="faahKO_reduce.zip" ftype="zip" />
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50 </conditional>
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51 </section>
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52 </xml>
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53
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54 <xml name="test_file_load_zip_sacuri">
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55 <section name="file_load_section">
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56 <conditional name="file_load_conditional">
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57 <param name="file_load_select" value="yes" />
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58 <param name="input" value="sacuri_dir_root.zip" ftype="zip" />
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59 </conditional>
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60 </section>
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61 </xml>
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62
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63 <xml name="test_file_load_single">
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64 <section name="file_load_section">
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65 <conditional name="file_load_conditional">
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66 <param name="file_load_select" value="yes" />
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67 <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" />
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68 </conditional>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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69 </section>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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70 </xml>
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eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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72 <xml name="test_file_load_single_file" token_filename="">
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73 <section name="file_load_section">
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74 <conditional name="file_load_conditional">
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75 <param name="file_load_select" value="yes" />
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76 <param name="input" value="@FILENAME@.CDF" ftype="netcdf" />
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77 </conditional>
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78 </section>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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79 </xml>
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80
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81 <!-- PEAKLIST -->
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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82 <token name="@COMMAND_PEAKLIST@">
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83 #if $peaklist.peaklistBool
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84 convertRTMinute $peaklist.convertRTMinute
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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85 numDigitsMZ $peaklist.numDigitsMZ
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86 numDigitsRT $peaklist.numDigitsRT
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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87 intval $peaklist.intval
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88 naTOzero $peaklist.naTOzero
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89 #end if
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90 </token>
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91
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92 <xml name="input_peaklist">
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93 <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
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94 <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
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95 <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
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96 <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below">
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97 <option value="into" selected="true">into</option>
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98 <option value="maxo">maxo</option>
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99 <option value="intb">intb</option>
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100 </param>
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101 <param name="naTOzero" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="If NA values remain, replace them by 0 in the dataMatrix" help="Mandatory for some of the downstream tools (data processing, statistics) that do not accept NA values"/>
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102 </xml>
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103
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104 <xml name="input_peaklist_section">
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105 <section name="peaklist" title="Peak List" expanded="True">
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106 <param name="peaklistBool" type="hidden" label="Get the Peak List" value="True" />
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107 <expand macro="input_peaklist"/>
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108 </section>
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109 </xml>
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110
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111 <xml name="input_peaklist_conditional">
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112 <conditional name="peaklist">
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113 <param name="peaklistBool" type="boolean" label="Get the Peak List" />
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114 <when value="true">
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115 <expand macro="input_peaklist"/>
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116 </when>
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117 <when value="false" />
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118 </conditional>
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119 </xml>
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120
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121 <xml name="output_peaklist" token_function="">
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122 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.@FUNCTION@.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" >
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123 <filter>(peaklist['peaklistBool'])</filter>
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124 </data>
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125 <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.@FUNCTION@.dataMatrix.tsv" from_work_dir="dataMatrix.tsv" >
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126 <filter>(peaklist['peaklistBool'])</filter>
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127 </data>
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128 </xml>
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129
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130 <token name="@HELP_PEAKLIST@">
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131
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132 Get a Peak List
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133 ---------------
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134
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135 If 'true', the module generates two additional files corresponding to the peak list:
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136 - the variable metadata file (corresponding to information about extracted ions such as mass or retention time)
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137 - the data matrix (corresponding to related intensities)
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138
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139 **decimal places for [mass or retention time] values in identifiers**
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140
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141 | Ions' identifiers are constructed as MxxxTyyy where 'xxx' is the ion median mass and 'yyy' the ion median retention time.
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142 | Two parameters are used to adjust the number of decimal places wanted in identifiers for mass and retention time respectively.
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143 | Theses parameters do not affect decimal places in columns other than the identifier one.
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144
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145 **Reported intensity values**
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146
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147 | This parameter determines which values should be reported as intensities in the dataMatrix table; it correspond to xcms 'intval' parameter:
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148 | - into: integrated area of original (raw) peak
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149 | - maxo: maximum intensity of original (raw) peak
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150 | - intb: baseline corrected integrated peak area (only available if peak detection was done by ‘findPeaks.centWave’)
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151
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152 </token>
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153
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154 <token name="@HELP_PEAKLIST_OUTPUT@">
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155 xset.variableMetadata.tsv : tabular format
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156
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157 | Table containing information about ions; can be used as one input of **Quality_Metrics** or **Generic_filter** modules.
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158
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159 xset.dataMatrix.tsv : tabular format
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160
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161 | Table containing ions' intensities; can be used as one input of **Quality_Metrics** or **Generic_filter** modules.
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162 </token>
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163
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164 <!-- CENTWAVE -->
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165 <token name="@COMMAND_CENTWAVE@">
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166 ppm $methods.ppm
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167 peakwidth "c($methods.peakwidth)"
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168
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169 ## Advanced
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170 snthresh $methods.CentWaveAdv.snthresh
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171 prefilter "c($methods.CentWaveAdv.prefilter)"
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172 mzCenterFun $methods.CentWaveAdv.mzCenterFun
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173 integrate $methods.CentWaveAdv.integrate
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174 mzdiff $methods.CentWaveAdv.mzdiff
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175 fitgauss $methods.CentWaveAdv.fitgauss
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176 noise $methods.CentWaveAdv.noise
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177 verboseColumns $methods.CentWaveAdv.verboseColumns
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178 </token>
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179
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180 <xml name="input_centwave">
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181 <param argument="ppm" type="float" value="25" label="Max tolerated ppm m/z deviation in consecutive scans in ppm" help="for the initial ROI definition." />
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182 <param argument="peakwidth" type="text" value="20,50" label="Min,Max peak width in seconds" help="with the expected approximate peak width in chromatographic space.">
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183 <expand macro="input_validator_range_float"/>
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184 </param>
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185 </xml>
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186
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187 <xml name="input_centwaveAdv">
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188 <param argument="snthresh" type="integer" value="10" label="Signal to Noise ratio cutoff" />
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189 <param argument="prefilter" type="text" value="3,100" label="Prefilter step for for the first analysis step (ROI detection)" help="Separate by coma k, I. Mass traces are only retained if they contain at least ‘k‘ peaks with intensity ‘>= I‘.">
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190 <expand macro="input_validator_range_integer"/>
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191 </param>
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192 <param argument="mzCenterFun" type="select" label="Name of the function to calculate the m/z center of the chromatographic peak" >
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193 <option value="wMean">intensity weighted mean of the peak's m/z values</option>
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194 <option value="mean">mean of the peak's m/z values</option>
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195 <option value="apex">use the m/z value at the peak apex</option>
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196 <option value="wMeanApex3">intensity weighted mean of the m/z value at the peak apex and the m/z values left and right of it</option>
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197 <option value="meanApex3">mean of the m/z value of the peak apex and the m/z values left and right of it</option>
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198 </param>
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199 <param argument="integrate" type="select" label="Integration method" >
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200 <option value="1">peak limits are found through descent on the mexican hat filtered data (more robust, but less exact)</option>
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201 <option value="2">peak limits based on real data (more accurate but prone to noise)</option>
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202 </param>
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203 <param argument="mzdiff" type="float" value="-0.001" label="Minimum difference in m/z for peaks with overlapping retention times" help="can be negative to allow overlap" />
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204 <param argument="fitgauss" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="fitgauss" help="whether or not a Gaussian should be fitted to each peak" />
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205 <param argument="noise" type="integer" value="0" label="Noise filter" help="allowing to set a minimum intensity required for centroids to be considered in the first analysis step (centroids with intensity lower than ‘noise’ are omitted from ROI detection)." />
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206 <param argument="verboseColumns" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="verbose Columns" help="whether additional peak meta data columns should be returned" />
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207 </xml>
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208
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209 <token name="@COMMAND_CENTWAVEADVROI@">
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210 #if $sectionROI.roiList:
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211 roiList '$sectionROI.roiList'
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212 firstBaselineCheck $sectionROI.firstBaselineCheck
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213 #if $sectionROI.roiScales != "":
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214 roiScales "c($sectionROI.roiScales)"
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215 #end if
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216 #end if
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217 </token>
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218
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219 <xml name="input_centwaveAdvROI" token_optional="true">
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220 <param argument="roiList" type="data" format="tabular" optional="@OPTIONAL@" label="List of regions-of-interest (ROI) representing detected mass traces" help="If ROIs are submitted the first analysis step is omitted and chromatographic peak detection is performed on the submitted ROIs. Each ROI is expected to have the following elements specified: ‘scmin’ (start scan index), ‘scmax’ (end scan index), ‘mzmin’ (minimum m/z), ‘mzmax’ (maximum m/z), ‘length’ (number of scans), ‘intensity’ (summed intensity)." />
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221 <param argument="firstBaselineCheck" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Is continuous data within regions of interest is checked to be above the first baseline." />
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222 <param argument="roiScales" type="text" value="" optional="true" label="Numeric vector defining the scale for each region of interest in ‘roiList’" help="Length equal to ‘roiList’ - Should be used for the centWave-wavelets (format 0.9,1,0.2)">
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223 <expand macro="input_validator_range_float"/>
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224 </param>
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225 </xml>
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226
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227 <!-- MISC -->
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228 <token name="@HELP_AUTHORS@">
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229 .. class:: infomark
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230
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231 **Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu
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232
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233 @HELP_AUTHORS_WRAPPERS@
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234
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235 ---------------------------------------------------
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236
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237 </token>
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238
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239 <token name="@HELP_XCMS_MANUAL@">
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240
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241 For details and explanations concerning all the parameters and workflow of xcms_ package, see its manual_ and this example_
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242
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243 .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html
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244 .. _manual: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf
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245 .. _example: https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html
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246 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
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247
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248 </token>
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249
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250 <token name="@HELP_XCMS_NEWVERSION_3440@">
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251 **Version 3.4.4.0 - 08/02/2019**
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252
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253 - UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_)
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254 </token>
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255 <token name="@HELP_XCMS_NEWVERSION_3610@">
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256 **Version 3.6.1+galaxy* - 03/09/2019**
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257
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258 - UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS News_)
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259 </token>
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260 <token name="@HELP_XCMS_NEWVERSION_31200@">
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261 **Version 3.12.0+galaxy* - 03/03/2020**
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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262
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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263 - UPGRADE: upgrade the xcms version from 3.6.1 to 3.12.0 (see XCMS News_)
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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264 </token>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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265
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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266 <xml name="citation">
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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267 <citations>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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268 <citation type="doi">10.1021/ac051437y</citation>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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269 <expand macro="citation_w4m"/>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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270 </citations>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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271 </xml>
eb115eb8f25c "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit d4bb3c31e2beca6b4059758c9e76d42c26f8aa55"
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272 </macros>