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1 <tool id="2021_05_hdf5_to_dat" name="MS .h5 -> MS .dat " version="0.0.1">
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2
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3 <description> from an Orbitrap MS </description>
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4
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5
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6 <requirements>
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7 <requirement type="package" >scilab</requirement>
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8 </requirements>
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9
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10
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11 <stdio>
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12 <exit_code range="1:" level="fatal" />
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13 </stdio>
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14
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15
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16 <command> <![CDATA[
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17 if [ -d $__root_dir__/packages/scilab-6.1.0 ]; then $__root_dir__/packages/scilab-6.1.0/bin/scilab-cli -nb -quit -f $* < ${script_file}; else scilab-cli -nb -quit -f $* < ${script_file}; fi
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18 ]]>
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19 </command>
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20
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21
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22 <configfiles>
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23 <configfile name="script_file">
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24 <![CDATA[ exec("$__tool_directory__/src/mz_hdf5tosci.sci",-1); ...
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25 if ~isdef('pls') then ...
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26 atomsSystemUpdate(); ...
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27 atomsInstall('FACT'); ...
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28 atomsLoad('FACT'); ...
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29 end; ...
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30 lasterror(); ...
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31 res=mz_hdf5tosci("${filein}"); ...
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32 save("${res}",'res'); ...
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33 if ~isempty(lasterror(%f)) then ...
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34 write(0,lasterror()); ...
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35 end ]]>
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36 </configfile>
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37 </configfiles>
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38
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39
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40 <inputs>
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41 <param name="filein" format="h5" type="data" label="Mass spectrum, .h5 format" />
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42 </inputs>
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43
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44
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45 <outputs>
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46
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47 <data name="res" format="mat" label="${filein.name}.dat" />
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48
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49 </outputs>
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50
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51
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52 <tests>
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53 <test>
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54 <param name="filein" value="VI2016_AC_4Areduit_1.h5"/>
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55 <output name="res" file="VI2016_AC_4Areduit_1.dat" compare="sim_size" delta="500" />
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56 </test>
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57 </tests>
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58
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59 <help>
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60
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61
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62 **Author** Jean-Claude Boulet (INRAE).
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63
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64
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65 ---------------------------------------------------
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66
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67 =================
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68 MS .h5 -> MS .dat
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69 =================
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70
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71 -----------
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72 Description
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73 -----------
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74
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75 This function converts an Orbitrap HDF5 mass spectrum into a Scilab mass spectrum
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76
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77 -----
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78 Input
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79 -----
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80
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81 **an .h5 hrms**
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82
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83 Previously, Orbitrap devices yielded .raw files.
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84
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85 MSconvert selected MS1 and performed the conversion .raw -> .md5
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86
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87 Then HDF5View performed the conversion .md5 -> .h5
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88 which is the format of the input file.
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89
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90
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91 -------
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92 Outputs
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93 -------
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94
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95 **a .dat mass spectrum**
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96
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97 This is an HDF5 file whose structure is specific to Scilab.
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98
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99 It contains two fields:
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100
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101 - time: the retention times, a vector;
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102
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103 - mzdata: a list containing a MS1 spectrum (m/z + signals) for each retention time.
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104
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105
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106 </help>
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107
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108 <citations>
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109
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110 </citations>
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111
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112
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113
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114 </tool>
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