Mercurial > repos > lecorguille > mnsbase_readmsdata

annotate msnbase_readmsdata.xml @ 0:3f0a218e2ebc draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
author lecorguille
date Tue, 03 Apr 2018 11:45:58 -0400
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3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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1 <tool id="mnsbase_readmsdata" name="MSnbase readMSData" version="@WRAPPER_VERSION@.0">
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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2 <description>Imports mass-spectrometry raw data files</description>
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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3
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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4 <macros>
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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5 <import>macros.xml</import>
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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6 <import>macros_msnbase.xml</import>
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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7 </macros>
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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9 <expand macro="requirements"/>
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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10 <expand macro="stdio"/>
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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12 <command><![CDATA[
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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13 @COMMAND_RSCRIPT@/msnbase_readmsdata.r
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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15 #if $input.is_of_type("mzxml") or $input.is_of_type("mzml") or $input.is_of_type("mzdata") or $input.is_of_type("netcdf"):
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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16 singlefile_galaxyPath '$input' singlefile_sampleName '$input.name'
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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17 #else
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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18 zipfile '$input'
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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19 #end if
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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21 @COMMAND_LOG_EXIT@
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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22 ]]></command>
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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24 <inputs>
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26 <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" 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." />
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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28 </inputs>
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30 <outputs>
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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31 <data name="xsetRData" format="rdata.msnbase.raw" label="${input.name.rsplit('.',1)[0]}.raw.RData" from_work_dir="readmsdata.RData" />
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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32 <data name="sampleMetadata" format="tabular" label="${input.name.rsplit('.',1)[0]}.sampleMetadata.tsv" from_work_dir="sampleMetadata.tsv" >
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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33 <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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34 </data>
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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35 </outputs>
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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37 <tests>
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39 <test>
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40 <param name="input" value="faahKO_reduce.zip" ftype="zip" />
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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41 <assert_stdout>
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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42 <has_text text="rowNames: faahKO_reduce/KO/ko15.CDF faahKO_reduce/KO/ko16.CDF" />
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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43 <has_text text="faahKO_reduce/WT/wt15.CDF faahKO_reduce/WT/wt16.CDF" />
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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44 <has_text text="featureNames: F1.S0001 F1.S0002 ... F4.S1278 (5112 total)" />
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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45 <has_text text="fvarLabels: fileIdx spIdx ... spectrum (27 total)" />
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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46 <has_text text="faahKO_reduce/KO/ko15.CDF ko15 KO" />
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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47 <has_text text="faahKO_reduce/KO/ko16.CDF ko16 KO" />
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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48 <has_text text="faahKO_reduce/WT/wt15.CDF wt15 WT" />
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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49 <has_text text="faahKO_reduce/WT/wt16.CDF wt16 WT" />
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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50 </assert_stdout>
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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51 <output name="sampleMetadata" value="sampleMetadata.tsv" />
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52 </test>
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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53 <test>
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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54 <param name="input" value="ko15.CDF" ftype="netcdf" />
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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55 <assert_stdout>
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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56 <has_text text="rowNames: ./ko15.CDF" />
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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57 <has_text text="ko15.CDF" />
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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58 <has_text text="featureNames: F1.S0001 F1.S0002 ... F1.S1278 (1278 total)" />
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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59 <has_text text="fvarLabels: fileIdx spIdx ... spectrum (27 total)" />
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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60 <has_text text="./ko15.CDF ko15 ." />
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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61 </assert_stdout>
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62 </test>
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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63 <!-- DISABLE FOR TRAVIS
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64 Useful to generate test-data for the further steps
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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65 <test>
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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66 <param name="input" value="ko16.CDF" ftype="netcdf" />
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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67 <assert_stdout>
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68 <has_text text="rowNames: ./ko16.CDF" />
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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69 <has_text text="ko16.CDF" />
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70 <has_text text="./ko16.CDF ko16 ." />
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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71 </assert_stdout>
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72 </test>
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73 <test>
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74 <param name="input" value="wt15.CDF" ftype="netcdf" />
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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75 <assert_stdout>
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76 <has_text text="rowNames: ./wt15.CDF" />
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77 <has_text text="wt15.CDF" />
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78 <has_text text="./wt15.CDF wt15 ." />
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79 </assert_stdout>
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80 </test>
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81 <test>
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82 <param name="input" value="wt16.CDF" ftype="netcdf" />
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83 <assert_stdout>
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84 <has_text text="rowNames: ./wt16.CDF" />
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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85 <has_text text="wt16.CDF" />
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86 <has_text text="./wt16.CDF wt16 ." />
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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87 </assert_stdout>
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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88 </test>
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89 -->
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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90 </tests>
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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91
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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92 <help><![CDATA[
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93
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94 @HELP_AUTHORS@
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95
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96 ==================
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97 MSnbase readMSData
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98 ==================
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99
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100 -----------
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101 Description
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102 -----------
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103
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104 Reads as set of XML-based mass-spectrometry data files and
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105 generates an MSnExp object. This function uses the functionality
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106 provided by the ‘mzR’ package to access data and meta data in
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107 ‘mzData’, ‘mzXML’ and ‘mzML’.
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108
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109 .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html
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110 .. _here: http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformXcmsPreprocessing_v02.pdf
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111
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112
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113 -----------------
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114 Workflow position
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115 -----------------
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116
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117 **Upstream tools**
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118
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119 ========================= ================= ======= =========
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120 Name output file format parameter
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121 ========================= ================= ======= =========
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122 NA NA zip NA
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123 ========================= ================= ======= =========
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124
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125
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126 **Downstream tools**
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127
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128 =========================== ==================== ====================
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129 Name Output file Format
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130 =========================== ==================== ====================
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131 xcms.findChromPeaks xset.RData rdata.msnbase.raw
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132 --------------------------- -------------------- --------------------
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133 PCA ellipsoid by factors sampleMetadata.tsv Tabular
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134 --------------------------- -------------------- --------------------
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135 Anova sampleMetadata.tsv Tabular
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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 **Example of a metabolomic workflow**
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141
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142 .. image:: mnsbase_readmsdata_workflow.png
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143
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144 ---------------------------------------------------
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145
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146
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147
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148 -----------
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149 Input files
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150 -----------
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151
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152 =========================== ==================================
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153 Parameter : num + label Format
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154 =========================== ==================================
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155 OR : Zip file zip
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156 --------------------------- ----------------------------------
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157 OR : Single file mzXML, mzML, mzData, netCDF
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158 =========================== ==================================
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159
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160 **Choose your inputs**
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161
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162 You have two methods for your inputs:
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163
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164 | Single file (recommended): You can put a single file as input. That way, you will be able to launch several xcmsSet in parallel and use "xcms.xcmsSet Merger" before "xcms.group"
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165 | Zip file: You can put a zip file containing your inputs: myinputs.zip (containing all your conditions as sub-directories).
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166
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167 Zip file: Steps for creating the zip file
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168 -----------------------------------------
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169
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170 **Step1: Creating your directory and hierarchize the subdirectories**
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171
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172
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173 VERY IMPORTANT: If you zip your files under Windows, you must use the 7Zip_ software, otherwise your zip will not be well unzipped on the platform W4M (zip corrupted bug).
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174
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175 .. _7Zip: http://www.7-zip.org/
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176
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177 Your zip should contain all your conditions as sub-directories. For example, two conditions (mutant and wild):
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178 arabidopsis/wild/01.raw
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179 arabidopsis/mutant/01.raw
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180
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181 **Step2: Creating a zip file**
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182
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183 Create your zip file (e.g.: arabidopsis.zip).
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184
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185 **Step 3 : Uploading it to our Galaxy server**
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186
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187 If your zip file is less than 2Gb, you get use the Get Data tool to upload it.
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188
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189 Otherwise if your zip file is larger than 2Gb, please refer to the HOWTO_ on workflow4metabolomics.org.
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190
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191 .. _HOWTO: http://application.sb-roscoff.fr/download/w4m/howto/galaxy_upload_up_2Go.pdf
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192
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193 For more informations, don't hesitate to send us an email at supportATworkflow4metabolomics.org).
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194
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195 Advices for converting your files for the XCMS input
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196 ----------------------------------------------------
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197
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198 We recommend you to convert your raw files to **mzXML** in centroid mode (smaller files) and the files will be compatible with the xmcs centWave method.
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199
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200 **We recommend you the following parameters:**
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201
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202 Use Filtering: **True**
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203
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204 Use Peak Picking: **True**
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205
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206 Peak Peaking -Apply to MS Levels: **All Levels (1-)** : Centroid Mode
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207
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208 Use zlib: **64**
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209
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210 Binary Encoding: **64**
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211
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212 m/z Encoding: **64**
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213
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214 Intensity Encoding: **64**
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215
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216
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217 ------------
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218 Output files
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219 ------------
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220
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221 sampleMetadata.tsv
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222
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223 | Tabular file that contains for each sample, it's associated class and polarity (positive,negative and mixed).
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224 | This file is necessary in the Anova and PCA step of the workflow.
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225
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226 xset.RData: rdata.msnbase.raw format
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227
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228 | Rdata file that is necessary in the second step of the workflow "xcms.findChromPeaks".
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229
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230 ---------------------------------------------------
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231
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232 Changelog/News
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233 --------------
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234
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235
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236 **Version 2.4.0.0 - 29/03/2018**
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237
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238 - NEW: a new dedicated tool to read the raw data. This function was previously included in xcms.findChromPeaks. This way, you will now be able to display TICs and BPCs before xcms.findChromPeaks.
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239
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240 ]]></help>
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241
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242 <expand macro="citation" />
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243 </tool>