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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="EICExtractor" name="EICExtractor" version="2.0.0">
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3 <description>Extracts intensities from dedicates positions in a LC/MS map</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">EICExtractor</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>EICExtractor
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11
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12 -in
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13 #for token in $param_in:
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14 $token
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15 #end for
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16 -in_header
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17 #for token in $param_in_header:
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18 $token
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19 #end for
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20 #if $param_pos:
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21 -pos $param_pos
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22 #end if
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23 #if $param_rt_tol:
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24 -rt_tol $param_rt_tol
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25 #end if
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26 #if $param_mz_tol:
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27 -mz_tol $param_mz_tol
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28 #end if
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29 #if $param_rt_collect:
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30 -rt_collect $param_rt_collect
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31 #end if
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32 #if $param_out:
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33 -out $param_out
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34 #end if
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35 -threads \${GALAXY_SLOTS:-24}
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36 #if $param_auto_rt_enabled:
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37 -auto_rt:enabled
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38 #end if
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39 #if $param_auto_rt_out_debug_TIC:
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40 -auto_rt:out_debug_TIC $param_auto_rt_out_debug_TIC
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41 #end if
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42 #if $adv_opts.adv_opts_selector=='advanced':
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43 #if $adv_opts.param_out_separator:
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44 -out_separator "$adv_opts.param_out_separator"
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45 #end if
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46 #if $adv_opts.param_force:
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47 -force
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48 #end if
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49 #if $adv_opts.param_auto_rt_FHWM:
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50 -auto_rt:FHWM $adv_opts.param_auto_rt_FHWM
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51 #end if
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52 #if $adv_opts.param_auto_rt_SNThreshold:
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53 -auto_rt:SNThreshold $adv_opts.param_auto_rt_SNThreshold
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54 #end if
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55 #end if
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56 </command>
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57 <inputs>
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58 <param name="param_in" type="data" format="mzml" multiple="true" optional="False" size="30" label="Input raw data file" help="(-in) ">
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59 <sanitizer>
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60 <valid initial="string.printable">
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61 <remove value="'"/>
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62 <remove value="""/>
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63 </valid>
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64 </sanitizer>
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65 </param>
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66 <param name="param_in_header" type="data" format="txt" multiple="true" optional="True" size="30" label="[for Waters data only] Read additional information from _HEADER.TXT" help="(-in_header) Provide one for each raw input file">
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67 <sanitizer>
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68 <valid initial="string.printable">
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69 <remove value="'"/>
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70 <remove value="""/>
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71 </valid>
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72 </sanitizer>
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73 </param>
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74 <param name="param_pos" type="data" format="tabular" optional="False" label="Input config file stating where to find signal" help="(-pos) "/>
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75 <param name="param_rt_tol" type="float" value="3.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help="(-rt_tol) "/>
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76 <param name="param_mz_tol" type="float" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help="(-mz_tol) "/>
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77 <param name="param_rt_collect" type="integer" value="1" label="# of scans up & down in RT from highest point for ppm estimation in result" help="(-rt_collect) "/>
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78 <param name="param_auto_rt_enabled" type="boolean" truevalue="-auto_rt:enabled" falsevalue="" checked="false" optional="True" label="Automatically detect injection peaks from TIC and quantify all m/z x RT combinations" help="(-enabled) "/>
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79 <expand macro="advanced_options">
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80 <param name="param_out_separator" type="text" size="30" value="," label="Separator character for output CSV file" help="(-out_separator) ">
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81 <sanitizer>
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82 <valid initial="string.printable">
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83 <remove value="'"/>
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84 <remove value="""/>
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85 </valid>
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86 </sanitizer>
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87 </param>
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88 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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89 <param name="param_auto_rt_FHWM" type="float" value="5.0" label="Expected full width at half-maximum of each raw RT peak in [s]" help="(-FHWM) Gaussian smoothing filter with this width is applied to TIC"/>
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90 <param name="param_auto_rt_SNThreshold" type="float" value="5.0" label="S/N threshold for a smoothed raw peak to pass peak picking" help="(-SNThreshold) Higher thesholds will result in less peaks"/>
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91 </expand>
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92 </inputs>
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93 <outputs>
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94 <data name="param_out" format="tabular"/>
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95 <data name="param_auto_rt_out_debug_TIC" format="mzml"/>
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96 </outputs>
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97 <help>**What it does**
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98
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99 Extracts intensities from dedicates positions in a LC/MS map
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100
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101
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102 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_EICExtractor.html</help>
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103 <expand macro="references"/>
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104 </tool>
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