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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="SpectraMerger" name="SpectraMerger" version="2.0.0">
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3 <description>Merges spectra (each MS level separately), increasing S/N ratios.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">SpectraMerger</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>SpectraMerger
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11
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12 #if $param_in:
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13 -in $param_in
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14 #end if
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15 #if $param_out:
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16 -out $param_out
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17 #end if
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18 #if $param_merging_method:
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19 -merging_method
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20 #if " " in str($param_merging_method):
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21 "$param_merging_method"
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22 #else
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23 $param_merging_method
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24 #end if
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25 #end if
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26 -threads \${GALAXY_SLOTS:-24}
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27
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28 #if $rep_param_algorithm_block_method_ms_levels:
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29 -algorithm:block_method:ms_levels
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30 #for token in $rep_param_algorithm_block_method_ms_levels:
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31 #if " " in str(token):
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32 "$token.param_algorithm_block_method_ms_levels"
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33 #else
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34 $token.param_algorithm_block_method_ms_levels
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35 #end if
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36 #end for
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37 #end if
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38 #if $param_algorithm_block_method_rt_block_size:
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39 -algorithm:block_method:rt_block_size $param_algorithm_block_method_rt_block_size
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40 #end if
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41 #if $param_algorithm_block_method_rt_max_length:
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42 -algorithm:block_method:rt_max_length $param_algorithm_block_method_rt_max_length
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43 #end if
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44 #if $param_algorithm_precursor_method_mz_tolerance:
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45 -algorithm:precursor_method:mz_tolerance $param_algorithm_precursor_method_mz_tolerance
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46 #end if
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47 #if $param_algorithm_precursor_method_rt_tolerance:
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48 -algorithm:precursor_method:rt_tolerance $param_algorithm_precursor_method_rt_tolerance
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49 #end if
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50 #if $adv_opts.adv_opts_selector=='advanced':
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51 #if $adv_opts.param_force:
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52 -force
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53 #end if
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54 #if $adv_opts.param_algorithm_mz_binning_width:
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55 -algorithm:mz_binning_width $adv_opts.param_algorithm_mz_binning_width
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56 #end if
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57 #if $adv_opts.param_algorithm_mz_binning_width_unit:
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58 -algorithm:mz_binning_width_unit
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59 #if " " in str($adv_opts.param_algorithm_mz_binning_width_unit):
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60 "$adv_opts.param_algorithm_mz_binning_width_unit"
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61 #else
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62 $adv_opts.param_algorithm_mz_binning_width_unit
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63 #end if
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64 #end if
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65 #if $adv_opts.param_algorithm_sort_blocks:
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66 -algorithm:sort_blocks
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67 #if " " in str($adv_opts.param_algorithm_sort_blocks):
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68 "$adv_opts.param_algorithm_sort_blocks"
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69 #else
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70 $adv_opts.param_algorithm_sort_blocks
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71 #end if
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72 #end if
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73 #end if
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74 </command>
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75 <inputs>
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76 <param name="param_in" type="data" format="mzml" optional="False" label="Input mzML file" help="(-in) "/>
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77 <param name="param_merging_method" type="select" optional="True" value="block_method" label="Method of merging which should be used" help="(-merging_method) ">
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78 <option value="precursor_method">precursor_method</option>
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79 <option value="block_method">block_method</option>
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80 </param>
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81 <repeat name="rep_param_algorithm_block_method_ms_levels" min="0" max="1" title="param_algorithm_block_method_ms_levels">
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82 <param name="param_algorithm_block_method_ms_levels" type="text" min="1" optional="True" size="30" value="1" label="Merge spectra of this level" help="(-ms_levels) All spectra with other MS levels remain untouched">
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83 <sanitizer>
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84 <valid initial="string.printable">
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85 <remove value="'"/>
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86 <remove value="""/>
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87 </valid>
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88 </sanitizer>
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89 </param>
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90 </repeat>
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91 <param name="param_algorithm_block_method_rt_block_size" type="integer" min="1" optional="True" value="5" label="Maximum number of scans to be summed up" help="(-rt_block_size) "/>
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92 <param name="param_algorithm_block_method_rt_max_length" type="float" min="0.0" max="1e+11" optional="True" value="0.0" label="Maximum RT size of the block in seconds (0.0 = no size restriction)" help="(-rt_max_length) "/>
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93 <param name="param_algorithm_precursor_method_mz_tolerance" type="float" min="0.0" optional="True" value="0.0001" label="Max m/z distance of the precursor entries of two spectra to be merged in [Da]" help="(-mz_tolerance) "/>
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94 <param name="param_algorithm_precursor_method_rt_tolerance" type="float" min="0.0" optional="True" value="5.0" label="Max RT distance of the precursor entries of two spectra to be merged in [s]" help="(-rt_tolerance) "/>
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95 <expand macro="advanced_options">
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96 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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97 <param name="param_algorithm_mz_binning_width" type="float" min="0.0" optional="True" value="0.0001" label="Max m/z distance of two peaks to be merged" help="(-mz_binning_width) "/>
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98 <param name="param_algorithm_mz_binning_width_unit" type="select" optional="True" value="Da" label="Unit in which the distance between two peaks is given" help="(-mz_binning_width_unit) ">
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99 <option value="Da">Da</option>
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100 <option value="ppm">ppm</option>
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101 </param>
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102 <param name="param_algorithm_sort_blocks" type="select" optional="True" value="RT_ascending" label="Sort blocks by <?> before merging them (useful for precursor order)" help="(-sort_blocks) ">
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103 <option value="RT_ascending">RT_ascending</option>
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104 <option value=" RT_descending"> RT_descending</option>
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105 </param>
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106 </expand>
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107 </inputs>
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108 <outputs>
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109 <data name="param_out" format="mzml"/>
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110 </outputs>
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111 <help>**What it does**
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112
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113 Merges spectra (each MS level separately), increasing S/N ratios.
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114
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115
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116 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SpectraMerger.html</help>
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117 <expand macro="references"/>
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118 </tool>
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