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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="OpenSwathChromatogramExtractor" name="OpenSwathChromatogramExtractor" version="2.0.0">
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3 <description>Extract chromatograms (XIC) from a MS2 map file.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">OpenSwathChromatogramExtractor</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>OpenSwathChromatogramExtractor
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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 #if $param_tr:
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17 -tr $param_tr
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18 #end if
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19 #if $param_rt_norm:
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20 -rt_norm $param_rt_norm
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21 #end if
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22 #if $param_out:
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23 -out $param_out
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24 #end if
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25 #if $param_min_upper_edge_dist:
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26 -min_upper_edge_dist $param_min_upper_edge_dist
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27 #end if
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28 #if $param_mz_window:
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29 -mz_window $param_mz_window
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30 #end if
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31 #if $param_rt_window:
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32 -rt_window $param_rt_window
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33 #end if
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34 #if $param_is_swath:
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35 -is_swath
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36 #end if
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37 #if $param_ppm:
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38 -ppm
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39 #end if
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40 #if $param_extract_MS1:
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41 -extract_MS1
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42 #end if
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43 #if $param_extraction_function:
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44 -extraction_function
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45 #if " " in str($param_extraction_function):
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46 "$param_extraction_function"
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47 #else
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48 $param_extraction_function
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49 #end if
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50 #end if
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51 -threads \${GALAXY_SLOTS:-24}
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52 #if $param_model_type:
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53 -model:type
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54 #if " " in str($param_model_type):
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55 "$param_model_type"
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56 #else
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57 $param_model_type
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58 #end if
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59 #end if
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60 #if $param_model_symmetric_regression:
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61 -model:symmetric_regression
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62 #end if
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63 #if $adv_opts.adv_opts_selector=='advanced':
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64 #if $adv_opts.param_force:
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65 -force
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66 #end if
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67 #end if
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68 </command>
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69 <inputs>
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70 <param name="param_in" type="data" format="mzml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
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71 <sanitizer>
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72 <valid initial="string.printable">
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73 <remove value="'"/>
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74 <remove value="""/>
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75 </valid>
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76 </sanitizer>
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77 </param>
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78 <param name="param_tr" type="data" format="tabular,traml" optional="False" label="transition file ('TraML' or 'csv')" help="(-tr) "/>
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79 <param name="param_rt_norm" type="data" format="trafoxml" optional="True" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help="(-rt_norm) "/>
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80 <param name="param_min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson" help="(-min_upper_edge_dist) "/>
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81 <param name="param_mz_window" type="float" min="0.0" optional="True" value="0.05" label="Extraction window in m/z dimension (in Thomson, to use ppm see -ppm flag). This is the full window size," help="(-mz_window) e.g. 100 ppm would extract 50 ppm on either side"/>
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82 <param name="param_rt_window" type="float" value="-1.0" label="Extraction window in RT dimension (-1 means extract over the whole range). This is the full window size," help="(-rt_window) e.g. a value of 1000 seconds would extract 500 seconds on either side"/>
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83 <param name="param_is_swath" type="boolean" truevalue="-is_swath" falsevalue="" checked="false" optional="True" label="Set this flag if the data is SWATH data" help="(-is_swath) "/>
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84 <param name="param_ppm" type="boolean" truevalue="-ppm" falsevalue="" checked="false" optional="True" label="m/z extraction_window is in ppm" help="(-ppm) "/>
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85 <param name="param_extract_MS1" type="boolean" truevalue="-extract_MS1" falsevalue="" checked="false" optional="True" label="Extract the MS1 transitions based on the precursor values in the TraML file" help="(-extract_MS1) "/>
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86 <param name="param_extraction_function" type="select" optional="True" value="tophat" label="Function used to extract the signal" help="(-extraction_function) ">
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87 <option value="tophat">tophat</option>
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88 <option value="bartlett">bartlett</option>
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89 </param>
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90 <param name="param_model_type" type="select" optional="True" value="linear" label="Type of model" help="(-type) ">
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91 <option value="linear">linear</option>
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92 <option value="b_spline">b_spline</option>
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93 <option value="interpolated">interpolated</option>
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94 </param>
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95 <param name="param_model_symmetric_regression" type="boolean" truevalue="-model:symmetric_regression" falsevalue="" checked="false" optional="True" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" help="(-symmetric_regression) 'y + x', instead of on 'y' vs. 'x'"/>
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96 <expand macro="advanced_options">
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97 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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98 </expand>
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99 </inputs>
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100 <outputs>
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101 <data name="param_out" format="mzml"/>
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102 </outputs>
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103 <help>**What it does**
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104
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105 Extract chromatograms (XIC) from a MS2 map file.
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106
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107
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108 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathChromatogramExtractor.html</help>
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109 <expand macro="references"/>
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110 </tool>
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