annotate FeatureFinderMultiplex.xml @ 16:9876bda3ec53 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 18:59:52 +0000
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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3 <!--Proposed Tool Section: [Quantitation]-->
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4 <tool id="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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5 <description>Determination of peak ratios in LC-MS data</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">FeatureFinderMultiplex</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="requirements"/>
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11 <expand macro="stdio"/>
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12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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13 @EXT_FOO@
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14 #import re
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15
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16 ## Preprocessing
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17 mkdir in &&
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18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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19 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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20 mkdir out &&
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21 #end if
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22 #if "out_multiplets_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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23 mkdir out_multiplets &&
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24 #end if
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25 #if "out_blacklist_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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26 mkdir out_blacklist &&
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27 #end if
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28
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29 ## Main program call
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30
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31 set -o pipefail &&
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32 @EXECUTABLE@ -write_ctd ./ &&
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33 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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34 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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35 -in
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36 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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37 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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38 -out
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39 'out/output.${gxy2omsext("featurexml")}'
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40 #end if
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41 #if "out_multiplets_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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42 -out_multiplets
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43 'out_multiplets/output.${gxy2omsext("consensusxml")}'
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44 #end if
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45 #if "out_blacklist_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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46 -out_blacklist
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47 'out_blacklist/output.${gxy2omsext("mzml")}'
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48 #end if
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49 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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50 | tee '$stdout'
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51 #end if
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52
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53 ## Postprocessing
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54 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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55 && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
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56 #end if
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57 #if "out_multiplets_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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58 && mv 'out_multiplets/output.${gxy2omsext("consensusxml")}' '$out_multiplets'
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59 #end if
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60 #if "out_blacklist_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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61 && mv 'out_blacklist/output.${gxy2omsext("mzml")}' '$out_blacklist'
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62 #end if
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63 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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64 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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65 #end if]]></command>
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66 <configfiles>
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67 <inputs name="args_json" data_style="paths"/>
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68 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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69 </configfiles>
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70 <inputs>
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71 <param argument="-in" type="data" format="mzml" optional="false" label="LC-MS dataset in either centroid or profile mode" help=" select mzml data sets(s)"/>
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72 <section name="algorithm" title="algorithmic parameters" help="" expanded="false">
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73 <param name="labels" argument="-algorithm:labels" type="text" optional="true" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="If the sample is unlabelled (i.e. you want to detect only single peptide features) please leave this parameter empty. [...] specifies the labels for a single sample. For example. [][Lys8,Arg10] ... SILAC. [][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC. [Dimethyl0][Dimethyl6] ... Dimethyl. [Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl. [ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL">
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74 <expand macro="list_string_san" name="labels"/>
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75 </param>
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76 <param name="charge" argument="-algorithm:charge" type="text" optional="true" value="1:4" label="Range of charge states in the sample" help="i.e. min charge : max charge">
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77 <expand macro="list_string_san" name="charge"/>
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78 </param>
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79 <param name="isotopes_per_peptide" argument="-algorithm:isotopes_per_peptide" type="text" optional="true" value="3:6" label="Range of isotopes per peptide in the sample" help="For example 3:6, if isotopic peptide patterns in the sample consist of either three, four, five or six isotopic peaks. ">
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80 <expand macro="list_string_san" name="isotopes_per_peptide"/>
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81 </param>
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82 <param name="rt_typical" argument="-algorithm:rt_typical" type="float" optional="true" min="0.0" value="40.0" label="Typical retention time [s] over which a characteristic peptide elutes" help="(This is not an upper bound. Peptides that elute for longer will be reported.)"/>
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83 <param name="rt_band" argument="-algorithm:rt_band" type="float" optional="true" min="0.0" value="0.0" label="The algorithm searches for characteristic isotopic peak patterns, spectrum by spectrum" help="For some low-intensity peptides, an important peak might be missing in one spectrum but be present in one of the neighbouring ones. The algorithm takes a bundle of neighbouring spectra with width rt_band into account. For example with rt_band = 0, all characteristic isotopic peaks have to be present in one and the same spectrum. As rt_band increases, the sensitivity of the algorithm but also the likelihood of false detections increases"/>
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84 <param name="rt_min" argument="-algorithm:rt_min" type="float" optional="true" min="0.0" value="2.0" label="Lower bound for the retention time [s]" help="(Any peptides seen for a shorter time period are not reported.)"/>
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85 <param name="mz_tolerance" argument="-algorithm:mz_tolerance" type="float" optional="true" min="0.0" value="6.0" label="m/z tolerance for search of peak patterns" help=""/>
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86 <param name="mz_unit" argument="-algorithm:mz_unit" type="select" optional="true" label="Unit of the 'mz_tolerance' paramete" help="">
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87 <option value="Da">Da</option>
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88 <option value="ppm" selected="true">ppm</option>
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89 <expand macro="list_string_san" name="mz_unit"/>
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90 </param>
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91 <param name="intensity_cutoff" argument="-algorithm:intensity_cutoff" type="float" optional="true" min="0.0" value="1000.0" label="Lower bound for the intensity of isotopic peaks" help=""/>
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92 <param name="peptide_similarity" argument="-algorithm:peptide_similarity" type="float" optional="true" min="-1.0" max="1.0" value="0.5" label="Two peptides in a multiplet are expected to have the same isotopic pattern" help="This parameter is a lower bound on their similarity"/>
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93 <param name="averagine_similarity" argument="-algorithm:averagine_similarity" type="float" optional="true" min="-1.0" max="1.0" value="0.4" label="The isotopic pattern of a peptide should resemble the averagine model at this m/z position" help="This parameter is a lower bound on similarity between measured isotopic pattern and the averagine model"/>
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94 <param name="averagine_similarity_scaling" argument="-algorithm:averagine_similarity_scaling" type="float" optional="true" min="0.0" max="1.0" value="0.95" label="Let x denote this scaling factor, and p the averagine similarity paramete" help="For the detection of single peptides, the averagine parameter p is replaced by p' = p + x(1-p), i.e. x = 0 -&gt; p' = p and x = 1 -&gt; p' = 1. (For knock_out = true, peptide doublets and singlets are detected simultaneously. For singlets, the peptide similarity filter is irreleavant. In order to compensate for this 'missing filter', the averagine parameter p is replaced by the more restrictive p' when searching for singlets.)"/>
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95 <param name="missed_cleavages" argument="-algorithm:missed_cleavages" type="integer" optional="true" min="0" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/>
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96 <param name="spectrum_type" argument="-algorithm:spectrum_type" type="select" optional="true" label="Type of MS1 spectra in input mzML file" help="'automatic' determines the spectrum type directly from the input mzML file">
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97 <option value="profile">profile</option>
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98 <option value="centroid">centroid</option>
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99 <option value="automatic" selected="true">automatic</option>
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100 <expand macro="list_string_san" name="spectrum_type"/>
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101 </param>
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102 <param name="averagine_type" argument="-algorithm:averagine_type" type="select" optional="true" label="The type of averagine to use, currently RNA, DNA or peptide" help="">
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103 <option value="peptide" selected="true">peptide</option>
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104 <option value="RNA">RNA</option>
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105 <option value="DNA">DNA</option>
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106 <expand macro="list_string_san" name="averagine_type"/>
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107 </param>
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108 <param name="knock_out" argument="-algorithm:knock_out" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Is it likely that knock-outs are present" help="(Supported for doublex, triplex and quadruplex experiments only.)"/>
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109 </section>
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110 <section name="labels" title="mass shifts for all possible labels" help="" expanded="false">
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111 <param name="Arg6" argument="-labels:Arg6" type="float" optional="true" min="0.0" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help=""/>
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112 <param name="Arg10" argument="-labels:Arg10" type="float" optional="true" min="0.0" value="10.0082686" label="Label:13C(6)15N(4) | C(-6) 13C(6) N(-4) 15N(4) | unimod #267" help=""/>
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113 <param name="Lys4" argument="-labels:Lys4" type="float" optional="true" min="0.0" value="4.0251069836" label="Label:2H(4) | H(-4) 2H(4) | unimod #481" help=""/>
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114 <param name="Lys6" argument="-labels:Lys6" type="float" optional="true" min="0.0" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help=""/>
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115 <param name="Lys8" argument="-labels:Lys8" type="float" optional="true" min="0.0" value="8.0141988132" label="Label:13C(6)15N(2) | C(-6) 13C(6) N(-2) 15N(2) | unimod #259" help=""/>
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116 <param name="Leu3" argument="-labels:Leu3" type="float" optional="true" min="0.0" value="3.01883" label="Label:2H(3) | H(-3) 2H(3) | unimod #262" help=""/>
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117 <param name="Dimethyl0" argument="-labels:Dimethyl0" type="float" optional="true" min="0.0" value="28.0313" label="Dimethyl | H(4) C(2) | unimod #36" help=""/>
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118 <param name="Dimethyl4" argument="-labels:Dimethyl4" type="float" optional="true" min="0.0" value="32.056407" label="Dimethyl:2H(4) | 2H(4) C(2) | unimod #199" help=""/>
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119 <param name="Dimethyl6" argument="-labels:Dimethyl6" type="float" optional="true" min="0.0" value="34.063117" label="Dimethyl:2H(4)13C(2) | 2H(4) 13C(2) | unimod #510" help=""/>
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120 <param name="Dimethyl8" argument="-labels:Dimethyl8" type="float" optional="true" min="0.0" value="36.07567" label="Dimethyl:2H(6)13C(2) | H(-2) 2H(6) 13C(2) | unimod #330" help=""/>
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121 <param name="ICPL0" argument="-labels:ICPL0" type="float" optional="true" min="0.0" value="105.021464" label="ICPL | H(3) C(6) N O | unimod #365" help=""/>
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122 <param name="ICPL4" argument="-labels:ICPL4" type="float" optional="true" min="0.0" value="109.046571" label="ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #687" help=""/>
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123 <param name="ICPL6" argument="-labels:ICPL6" type="float" optional="true" min="0.0" value="111.041593" label="ICPL:13C(6) | H(3) 13C(6) N O | unimod #364" help=""/>
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124 <param name="ICPL10" argument="-labels:ICPL10" type="float" optional="true" min="0.0" value="115.0667" label="ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866" help=""/>
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125 </section>
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126 <expand macro="adv_opts_macro">
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127 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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128 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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129 <expand macro="list_string_san" name="test"/>
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130 </param>
0
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131 </expand>
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132 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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133 <option value="out_FLAG">out (Output file containing the individual peptide features)</option>
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134 <option value="out_multiplets_FLAG">out_multiplets (Optional output file containing all detected peptide groups)</option>
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135 <option value="out_blacklist_FLAG">out_blacklist (Optional output file containing all peaks which have been associated with a peptide feature (and subsequently blacklisted))</option>
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136 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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137 </param>
0
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138 </inputs>
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139 <outputs>
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140 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml">
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141 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
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142 </data>
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143 <data name="out_multiplets" label="${tool.name} on ${on_string}: out_multiplets" format="consensusxml">
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144 <filter>OPTIONAL_OUTPUTS is not None and "out_multiplets_FLAG" in OPTIONAL_OUTPUTS</filter>
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145 </data>
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146 <data name="out_blacklist" label="${tool.name} on ${on_string}: out_blacklist" format="mzml">
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147 <filter>OPTIONAL_OUTPUTS is not None and "out_blacklist_FLAG" in OPTIONAL_OUTPUTS</filter>
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148 </data>
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149 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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150 <filter>OPTIONAL_OUTPUTS is None</filter>
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151 </data>
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152 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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153 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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154 </data>
0
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155 </outputs>
16
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156 <tests><!-- TOPP_FeatureFinderMultiplex_1 -->
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157 <test expect_num_outputs="3">
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158 <section name="adv_opts">
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159 <param name="force" value="false"/>
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160 <param name="test" value="true"/>
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161 </section>
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162 <param name="in" value="FeatureFinderMultiplex_1_input.mzML"/>
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163 <output name="out" file="FeatureFinderMultiplex_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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164 <output name="out_multiplets" file="FeatureFinderMultiplex_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
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165 <section name="algorithm">
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166 <param name="labels" value="[Dimethyl0][Dimethyl8]"/>
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167 <param name="charge" value="1:4"/>
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168 <param name="isotopes_per_peptide" value="3:6"/>
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169 <param name="rt_typical" value="90.0"/>
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170 <param name="rt_band" value="10.0"/>
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171 <param name="rt_min" value="5.0"/>
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172 <param name="mz_tolerance" value="40.0"/>
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173 <param name="mz_unit" value="ppm"/>
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174 <param name="intensity_cutoff" value="10.0"/>
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175 <param name="peptide_similarity" value="0.8"/>
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176 <param name="averagine_similarity" value="0.75"/>
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177 <param name="averagine_similarity_scaling" value="0.75"/>
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178 <param name="missed_cleavages" value="1"/>
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179 <param name="spectrum_type" value="automatic"/>
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180 <param name="averagine_type" value="peptide"/>
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181 <param name="knock_out" value="false"/>
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182 </section>
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183 <section name="labels">
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184 <param name="Arg6" value="6.0201290268"/>
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185 <param name="Arg10" value="10.0082686"/>
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186 <param name="Lys4" value="4.0251069836"/>
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187 <param name="Lys6" value="6.0201290268"/>
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188 <param name="Lys8" value="8.0141988132"/>
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189 <param name="Leu3" value="3.01883"/>
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190 <param name="Dimethyl0" value="28.0313"/>
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191 <param name="Dimethyl4" value="32.056407"/>
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192 <param name="Dimethyl6" value="34.063117"/>
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193 <param name="Dimethyl8" value="36.07567"/>
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194 <param name="ICPL0" value="105.021464"/>
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195 <param name="ICPL4" value="109.046571"/>
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196 <param name="ICPL6" value="111.041593"/>
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197 <param name="ICPL10" value="115.0667"/>
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198 </section>
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199 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
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200 <output name="ctd_out" ftype="xml">
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201 <assert_contents>
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202 <is_valid_xml/>
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203 </assert_contents>
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204 </output>
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205 </test>
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206 <!-- TOPP_FeatureFinderMultiplex_2 -->
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207 <test expect_num_outputs="3">
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208 <section name="adv_opts">
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209 <param name="force" value="false"/>
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210 <param name="test" value="true"/>
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211 </section>
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212 <param name="in" value="FeatureFinderMultiplex_2_input.mzML"/>
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213 <output name="out" file="FeatureFinderMultiplex_2_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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214 <output name="out_multiplets" file="FeatureFinderMultiplex_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
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215 <section name="algorithm">
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216 <param name="labels" value="[][Lys8,Arg10]"/>
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217 <param name="charge" value="1:4"/>
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218 <param name="isotopes_per_peptide" value="3:6"/>
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219 <param name="rt_typical" value="40.0"/>
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220 <param name="rt_band" value="5.0"/>
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221 <param name="rt_min" value="2.0"/>
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222 <param name="mz_tolerance" value="6.0"/>
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223 <param name="mz_unit" value="ppm"/>
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224 <param name="intensity_cutoff" value="1000.0"/>
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225 <param name="peptide_similarity" value="0.5"/>
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226 <param name="averagine_similarity" value="0.4"/>
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227 <param name="averagine_similarity_scaling" value="0.75"/>
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228 <param name="missed_cleavages" value="0"/>
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229 <param name="spectrum_type" value="automatic"/>
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230 <param name="averagine_type" value="peptide"/>
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231 <param name="knock_out" value="false"/>
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232 </section>
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233 <section name="labels">
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234 <param name="Arg6" value="6.0201290268"/>
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235 <param name="Arg10" value="10.0082686"/>
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236 <param name="Lys4" value="4.0251069836"/>
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237 <param name="Lys6" value="6.0201290268"/>
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238 <param name="Lys8" value="8.0141988132"/>
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239 <param name="Leu3" value="3.01883"/>
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240 <param name="Dimethyl0" value="28.0313"/>
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241 <param name="Dimethyl4" value="32.056407"/>
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242 <param name="Dimethyl6" value="34.063117"/>
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243 <param name="Dimethyl8" value="36.07567"/>
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244 <param name="ICPL0" value="105.021464"/>
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245 <param name="ICPL4" value="109.046571"/>
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246 <param name="ICPL6" value="111.041593"/>
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247 <param name="ICPL10" value="115.0667"/>
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248 </section>
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249 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
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250 <output name="ctd_out" ftype="xml">
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251 <assert_contents>
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252 <is_valid_xml/>
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253 </assert_contents>
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254 </output>
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255 </test>
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256 <!-- TOPP_FeatureFinderMultiplex_3 -->
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257 <test expect_num_outputs="3">
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258 <section name="adv_opts">
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259 <param name="force" value="false"/>
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260 <param name="test" value="true"/>
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261 </section>
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262 <param name="in" value="FeatureFinderMultiplex_3_input.mzML"/>
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263 <output name="out" file="FeatureFinderMultiplex_3_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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264 <output name="out_multiplets" file="FeatureFinderMultiplex_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
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265 <section name="algorithm">
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266 <param name="labels" value="[]"/>
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267 <param name="charge" value="5:15"/>
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268 <param name="isotopes_per_peptide" value="5:10"/>
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269 <param name="rt_typical" value="45.0"/>
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270 <param name="rt_band" value="5.0"/>
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271 <param name="rt_min" value="2.0"/>
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272 <param name="mz_tolerance" value="6.0"/>
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273 <param name="mz_unit" value="ppm"/>
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274 <param name="intensity_cutoff" value="200.0"/>
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275 <param name="peptide_similarity" value="0.5"/>
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276 <param name="averagine_similarity" value="0.4"/>
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277 <param name="averagine_similarity_scaling" value="0.75"/>
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278 <param name="missed_cleavages" value="0"/>
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279 <param name="spectrum_type" value="automatic"/>
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280 <param name="averagine_type" value="RNA"/>
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281 <param name="knock_out" value="false"/>
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282 </section>
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283 <section name="labels">
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284 <param name="Arg6" value="6.0201290268"/>
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285 <param name="Arg10" value="10.0082686"/>
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286 <param name="Lys4" value="4.0251069836"/>
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287 <param name="Lys6" value="6.0201290268"/>
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288 <param name="Lys8" value="8.0141988132"/>
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289 <param name="Leu3" value="3.01883"/>
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290 <param name="Dimethyl0" value="28.0313"/>
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291 <param name="Dimethyl4" value="32.056407"/>
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292 <param name="Dimethyl6" value="34.063117"/>
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293 <param name="Dimethyl8" value="36.07567"/>
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294 <param name="ICPL0" value="105.021464"/>
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295 <param name="ICPL4" value="109.046571"/>
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296 <param name="ICPL6" value="111.041593"/>
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297 <param name="ICPL10" value="115.0667"/>
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298 </section>
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299 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
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300 <output name="ctd_out" ftype="xml">
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301 <assert_contents>
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302 <is_valid_xml/>
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303 </assert_contents>
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304 </output>
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305 </test>
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306 <!-- TOPP_FeatureFinderMultiplex_4 -->
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307 <test expect_num_outputs="3">
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308 <section name="adv_opts">
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309 <param name="force" value="false"/>
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310 <param name="test" value="true"/>
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311 </section>
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312 <param name="in" value="FeatureFinderMultiplex_4_input.mzML"/>
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313 <output name="out" file="FeatureFinderMultiplex_4_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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314 <output name="out_multiplets" file="FeatureFinderMultiplex_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
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315 <section name="algorithm">
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316 <param name="labels" value="[]"/>
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317 <param name="charge" value="5:15"/>
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318 <param name="isotopes_per_peptide" value="5:10"/>
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319 <param name="rt_typical" value="45.0"/>
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320 <param name="rt_band" value="5.0"/>
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321 <param name="rt_min" value="2.0"/>
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322 <param name="mz_tolerance" value="6.0"/>
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323 <param name="mz_unit" value="ppm"/>
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324 <param name="intensity_cutoff" value="200.0"/>
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325 <param name="peptide_similarity" value="0.5"/>
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326 <param name="averagine_similarity" value="0.4"/>
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327 <param name="averagine_similarity_scaling" value="0.75"/>
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328 <param name="missed_cleavages" value="0"/>
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329 <param name="spectrum_type" value="automatic"/>
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330 <param name="averagine_type" value="DNA"/>
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331 <param name="knock_out" value="false"/>
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332 </section>
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333 <section name="labels">
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334 <param name="Arg6" value="6.0201290268"/>
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335 <param name="Arg10" value="10.0082686"/>
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336 <param name="Lys4" value="4.0251069836"/>
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337 <param name="Lys6" value="6.0201290268"/>
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338 <param name="Lys8" value="8.0141988132"/>
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339 <param name="Leu3" value="3.01883"/>
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340 <param name="Dimethyl0" value="28.0313"/>
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341 <param name="Dimethyl4" value="32.056407"/>
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342 <param name="Dimethyl6" value="34.063117"/>
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343 <param name="Dimethyl8" value="36.07567"/>
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344 <param name="ICPL0" value="105.021464"/>
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345 <param name="ICPL4" value="109.046571"/>
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346 <param name="ICPL6" value="111.041593"/>
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347 <param name="ICPL10" value="115.0667"/>
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348 </section>
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349 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
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350 <output name="ctd_out" ftype="xml">
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351 <assert_contents>
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352 <is_valid_xml/>
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353 </assert_contents>
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354 </output>
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355 </test>
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356 <!-- TOPP_FeatureFinderMultiplex_5 -->
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357 <test expect_num_outputs="3">
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358 <section name="adv_opts">
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359 <param name="force" value="false"/>
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360 <param name="test" value="true"/>
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361 </section>
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362 <param name="in" value="FeatureFinderMultiplex_5_input.mzML"/>
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363 <output name="out" file="FeatureFinderMultiplex_5_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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364 <output name="out_multiplets" file="FeatureFinderMultiplex_5_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
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365 <section name="algorithm">
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366 <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
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367 <param name="charge" value="1:5"/>
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368 <param name="isotopes_per_peptide" value="3:6"/>
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369 <param name="rt_typical" value="50.0"/>
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370 <param name="rt_band" value="3.0"/>
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371 <param name="rt_min" value="8.0"/>
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372 <param name="mz_tolerance" value="10.0"/>
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373 <param name="mz_unit" value="ppm"/>
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374 <param name="intensity_cutoff" value="10000000.0"/>
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375 <param name="peptide_similarity" value="0.95"/>
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376 <param name="averagine_similarity" value="0.8"/>
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377 <param name="averagine_similarity_scaling" value="0.95"/>
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378 <param name="missed_cleavages" value="3"/>
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379 <param name="spectrum_type" value="profile"/>
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380 <param name="averagine_type" value="peptide"/>
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381 <param name="knock_out" value="false"/>
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382 </section>
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383 <section name="labels">
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384 <param name="Arg6" value="6.0201290268"/>
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385 <param name="Arg10" value="10.0082686"/>
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386 <param name="Lys4" value="4.0251069836"/>
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387 <param name="Lys6" value="6.0201290268"/>
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388 <param name="Lys8" value="8.0141988132"/>
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389 <param name="Leu3" value="3.01883"/>
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390 <param name="Dimethyl0" value="28.0313"/>
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391 <param name="Dimethyl4" value="32.056407"/>
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392 <param name="Dimethyl6" value="34.063117"/>
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393 <param name="Dimethyl8" value="36.07567"/>
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394 <param name="ICPL0" value="105.021464"/>
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395 <param name="ICPL4" value="109.046571"/>
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396 <param name="ICPL6" value="111.041593"/>
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397 <param name="ICPL10" value="115.0667"/>
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398 </section>
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399 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
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400 <output name="ctd_out" ftype="xml">
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401 <assert_contents>
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402 <is_valid_xml/>
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403 </assert_contents>
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404 </output>
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405 </test>
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406 <!-- TOPP_FeatureFinderMultiplex_6 -->
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407 <test expect_num_outputs="3">
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408 <section name="adv_opts">
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409 <param name="force" value="false"/>
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410 <param name="test" value="true"/>
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411 </section>
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412 <param name="in" value="FeatureFinderMultiplex_6_input.mzML"/>
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413 <output name="out" file="FeatureFinderMultiplex_6_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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414 <output name="out_multiplets" file="FeatureFinderMultiplex_6_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
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415 <section name="algorithm">
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416 <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
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417 <param name="charge" value="1:5"/>
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418 <param name="isotopes_per_peptide" value="3:6"/>
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419 <param name="rt_typical" value="50.0"/>
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420 <param name="rt_band" value="3.0"/>
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421 <param name="rt_min" value="8.0"/>
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422 <param name="mz_tolerance" value="10.0"/>
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423 <param name="mz_unit" value="ppm"/>
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424 <param name="intensity_cutoff" value="10000000.0"/>
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425 <param name="peptide_similarity" value="0.95"/>
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426 <param name="averagine_similarity" value="0.8"/>
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427 <param name="averagine_similarity_scaling" value="1.0"/>
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428 <param name="missed_cleavages" value="3"/>
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429 <param name="spectrum_type" value="profile"/>
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430 <param name="averagine_type" value="peptide"/>
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431 <param name="knock_out" value="false"/>
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432 </section>
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433 <section name="labels">
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434 <param name="Arg6" value="6.0201290268"/>
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435 <param name="Arg10" value="10.0082686"/>
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436 <param name="Lys4" value="4.0251069836"/>
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437 <param name="Lys6" value="6.0201290268"/>
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438 <param name="Lys8" value="8.0141988132"/>
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439 <param name="Leu3" value="3.01883"/>
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440 <param name="Dimethyl0" value="28.0313"/>
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441 <param name="Dimethyl4" value="32.056407"/>
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442 <param name="Dimethyl6" value="34.063117"/>
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443 <param name="Dimethyl8" value="36.07567"/>
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444 <param name="ICPL0" value="105.021464"/>
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445 <param name="ICPL4" value="109.046571"/>
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446 <param name="ICPL6" value="111.041593"/>
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447 <param name="ICPL10" value="115.0667"/>
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448 </section>
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449 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
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450 <output name="ctd_out" ftype="xml">
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451 <assert_contents>
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452 <is_valid_xml/>
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453 </assert_contents>
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454 </output>
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455 </test>
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456 <!-- TOPP_FeatureFinderMultiplex_7 -->
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457 <test expect_num_outputs="3">
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458 <section name="adv_opts">
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459 <param name="force" value="false"/>
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460 <param name="test" value="true"/>
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461 </section>
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462 <param name="in" value="FeatureFinderMultiplex_7_input.mzML"/>
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463 <output name="out" file="FeatureFinderMultiplex_7_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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464 <output name="out_multiplets" file="FeatureFinderMultiplex_7_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
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465 <section name="algorithm">
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466 <param name="labels" value="[][Dimethyl4]"/>
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467 <param name="charge" value="1:4"/>
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468 <param name="isotopes_per_peptide" value="3:6"/>
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469 <param name="rt_typical" value="40.0"/>
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470 <param name="rt_band" value="5.0"/>
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471 <param name="rt_min" value="2.0"/>
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472 <param name="mz_tolerance" value="6.0"/>
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473 <param name="mz_unit" value="ppm"/>
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474 <param name="intensity_cutoff" value="1000.0"/>
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475 <param name="peptide_similarity" value="0.5"/>
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476 <param name="averagine_similarity" value="0.4"/>
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477 <param name="averagine_similarity_scaling" value="0.75"/>
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diff changeset
478 <param name="missed_cleavages" value="0"/>
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galaxyp
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479 <param name="spectrum_type" value="automatic"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
480 <param name="averagine_type" value="peptide"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
481 <param name="knock_out" value="false"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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482 </section>
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galaxyp
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diff changeset
483 <section name="labels">
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galaxyp
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diff changeset
484 <param name="Arg6" value="6.0201290268"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
485 <param name="Arg10" value="10.0082686"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
486 <param name="Lys4" value="4.0251069836"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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487 <param name="Lys6" value="6.0201290268"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
488 <param name="Lys8" value="8.0141988132"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
489 <param name="Leu3" value="3.01883"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
490 <param name="Dimethyl0" value="28.0313"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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491 <param name="Dimethyl4" value="31.0094"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
492 <param name="Dimethyl6" value="34.063117"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
493 <param name="Dimethyl8" value="36.07567"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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494 <param name="ICPL0" value="105.021464"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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495 <param name="ICPL4" value="109.046571"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
496 <param name="ICPL6" value="111.041593"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
497 <param name="ICPL10" value="115.0667"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
498 </section>
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499 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
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500 <output name="ctd_out" ftype="xml">
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501 <assert_contents>
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diff changeset
502 <is_valid_xml/>
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503 </assert_contents>
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504 </output>
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505 </test>
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diff changeset
506 <!-- TOPP_FeatureFinderMultiplex_8 -->
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galaxyp
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507 <test expect_num_outputs="3">
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
508 <section name="adv_opts">
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galaxyp
parents: 14
diff changeset
509 <param name="force" value="false"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
510 <param name="test" value="true"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
511 </section>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
512 <param name="in" value="FeatureFinderMultiplex_8_input.mzML"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
513 <output name="out" file="FeatureFinderMultiplex_8_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
514 <output name="out_multiplets" file="FeatureFinderMultiplex_8_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
515 <section name="algorithm">
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
516 <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
517 <param name="charge" value="1:7"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
518 <param name="isotopes_per_peptide" value="3:8"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
519 <param name="rt_typical" value="50.0"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
520 <param name="rt_band" value="3.0"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
521 <param name="rt_min" value="8.0"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
522 <param name="mz_tolerance" value="10.0"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
523 <param name="mz_unit" value="ppm"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
524 <param name="intensity_cutoff" value="10.0"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
525 <param name="peptide_similarity" value="0.2"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
526 <param name="averagine_similarity" value="0.25"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
527 <param name="averagine_similarity_scaling" value="0.95"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
528 <param name="missed_cleavages" value="4"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
529 <param name="spectrum_type" value="automatic"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
530 <param name="averagine_type" value="peptide"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
531 <param name="knock_out" value="true"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
532 </section>
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galaxyp
parents: 14
diff changeset
533 <section name="labels">
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
534 <param name="Arg6" value="6.0201290268"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
535 <param name="Arg10" value="10.0082686"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
536 <param name="Lys4" value="4.0251069836"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
537 <param name="Lys6" value="6.0201290268"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
538 <param name="Lys8" value="8.0141988132"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
539 <param name="Leu3" value="3.01883"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
540 <param name="Dimethyl0" value="28.0313"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
541 <param name="Dimethyl4" value="32.056407"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
542 <param name="Dimethyl6" value="34.063117"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
543 <param name="Dimethyl8" value="36.07567"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
544 <param name="ICPL0" value="105.021464"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
545 <param name="ICPL4" value="109.046571"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 14
diff changeset
546 <param name="ICPL6" value="111.041593"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 14
diff changeset
547 <param name="ICPL10" value="115.0667"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
548 </section>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
549 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
550 <output name="ctd_out" ftype="xml">
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
551 <assert_contents>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
552 <is_valid_xml/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
553 </assert_contents>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
554 </output>
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parents: 14
diff changeset
555 </test>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
556 <!-- TOPP_FeatureFinderMultiplex_9 -->
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galaxyp
parents: 14
diff changeset
557 <test expect_num_outputs="3">
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
558 <section name="adv_opts">
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 14
diff changeset
559 <param name="force" value="false"/>
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diff changeset
560 <param name="test" value="true"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
561 </section>
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parents: 14
diff changeset
562 <param name="in" value="FeatureFinderMultiplex_9_input.mzML"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
563 <output name="out" file="FeatureFinderMultiplex_9_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
564 <output name="out_multiplets" file="FeatureFinderMultiplex_9_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
565 <section name="algorithm">
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
566 <param name="labels" value="[0][6.03705]"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
567 <param name="charge" value="2:8"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
568 <param name="isotopes_per_peptide" value="3:8"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
569 <param name="rt_typical" value="40.0"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
570 <param name="rt_band" value="0.0"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
571 <param name="rt_min" value="4.0"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
572 <param name="mz_tolerance" value="10.0"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
573 <param name="mz_unit" value="ppm"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
574 <param name="intensity_cutoff" value="1000.0"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
575 <param name="peptide_similarity" value="0.5"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
576 <param name="averagine_similarity" value="0.4"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
577 <param name="averagine_similarity_scaling" value="0.95"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
578 <param name="missed_cleavages" value="0"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
579 <param name="spectrum_type" value="centroid"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
580 <param name="averagine_type" value="peptide"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
581 <param name="knock_out" value="false"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
582 </section>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
583 <section name="labels">
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
584 <param name="Arg6" value="6.0201290268"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
585 <param name="Arg10" value="10.0082686"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
586 <param name="Lys4" value="4.0251069836"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
587 <param name="Lys6" value="6.0201290268"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
588 <param name="Lys8" value="8.0141988132"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
589 <param name="Leu3" value="3.01883"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
590 <param name="Dimethyl0" value="28.0313"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
591 <param name="Dimethyl4" value="32.056407"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
592 <param name="Dimethyl6" value="34.063117"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
593 <param name="Dimethyl8" value="36.07567"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
594 <param name="ICPL0" value="105.021464"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
595 <param name="ICPL4" value="109.046571"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
596 <param name="ICPL6" value="111.041593"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
597 <param name="ICPL10" value="115.0667"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
598 </section>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
599 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
600 <output name="ctd_out" ftype="xml">
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
601 <assert_contents>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
602 <is_valid_xml/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
603 </assert_contents>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
604 </output>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
605 </test>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
606 <!-- TOPP_FeatureFinderMultiplex_10 -->
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
607 <test expect_num_outputs="3">
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
608 <section name="adv_opts">
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
609 <param name="force" value="false"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
610 <param name="test" value="true"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
611 </section>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
612 <param name="in" value="FeatureFinderMultiplex_10_input.mzML"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
613 <output name="out" file="FeatureFinderMultiplex_10_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
614 <output name="out_multiplets" file="FeatureFinderMultiplex_10_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
615 <section name="algorithm">
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
616 <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
617 <param name="charge" value="1:7"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
618 <param name="isotopes_per_peptide" value="3:6"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
619 <param name="rt_typical" value="50.0"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
620 <param name="rt_band" value="5.0"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
621 <param name="rt_min" value="8.0"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
622 <param name="mz_tolerance" value="6.0"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
623 <param name="mz_unit" value="ppm"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
624 <param name="intensity_cutoff" value="10.0"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
625 <param name="peptide_similarity" value="0.4"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
626 <param name="averagine_similarity" value="0.5"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
627 <param name="averagine_similarity_scaling" value="0.95"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
628 <param name="missed_cleavages" value="3"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
629 <param name="spectrum_type" value="profile"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
630 <param name="averagine_type" value="peptide"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
631 <param name="knock_out" value="true"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
632 </section>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
633 <section name="labels">
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
634 <param name="Arg6" value="6.0201290268"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
635 <param name="Arg10" value="10.0082686"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
636 <param name="Lys4" value="4.0251069836"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
637 <param name="Lys6" value="6.0201290268"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
638 <param name="Lys8" value="8.0141988132"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
639 <param name="Leu3" value="3.01883"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
640 <param name="Dimethyl0" value="28.0313"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
641 <param name="Dimethyl4" value="32.056407"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
642 <param name="Dimethyl6" value="34.063117"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
643 <param name="Dimethyl8" value="36.07567"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
644 <param name="ICPL0" value="105.021464"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 14
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645 <param name="ICPL4" value="109.046571"/>
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galaxyp
parents: 14
diff changeset
646 <param name="ICPL6" value="111.041593"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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647 <param name="ICPL10" value="115.0667"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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648 </section>
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diff changeset
649 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_multiplets_FLAG"/>
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650 <output name="ctd_out" ftype="xml">
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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651 <assert_contents>
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diff changeset
652 <is_valid_xml/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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653 </assert_contents>
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diff changeset
654 </output>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
655 </test>
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656 <!-- TOPP_FeatureFinderMultiplex_11 -->
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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657 <test expect_num_outputs="2">
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galaxyp
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diff changeset
658 <section name="adv_opts">
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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659 <param name="force" value="false"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 14
diff changeset
660 <param name="test" value="true"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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661 </section>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
662 <param name="in" value="FeatureFinderMultiplex_11_input.mzML"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 14
diff changeset
663 <output name="out" file="FeatureFinderMultiplex_11_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
664 <section name="algorithm">
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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665 <param name="labels" value="[]"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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666 <param name="charge" value="1:4"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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667 <param name="isotopes_per_peptide" value="3:6"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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668 <param name="rt_typical" value="1e-05"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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669 <param name="rt_band" value="0.0"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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670 <param name="rt_min" value="0.0"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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671 <param name="mz_tolerance" value="10.0"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 14
diff changeset
672 <param name="mz_unit" value="ppm"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
673 <param name="intensity_cutoff" value="1000.0"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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674 <param name="peptide_similarity" value="0.5"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
675 <param name="averagine_similarity" value="0.7"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 14
diff changeset
676 <param name="averagine_similarity_scaling" value="0.95"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
677 <param name="missed_cleavages" value="0"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 14
diff changeset
678 <param name="spectrum_type" value="automatic"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
679 <param name="averagine_type" value="peptide"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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680 <param name="knock_out" value="false"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
681 </section>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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682 <section name="labels">
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
683 <param name="Arg6" value="6.0201290268"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
684 <param name="Arg10" value="10.0082686"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
685 <param name="Lys4" value="4.0251069836"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
686 <param name="Lys6" value="6.0201290268"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
687 <param name="Lys8" value="8.0141988132"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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688 <param name="Leu3" value="3.01883"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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689 <param name="Dimethyl0" value="28.0313"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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690 <param name="Dimethyl4" value="32.056407"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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691 <param name="Dimethyl6" value="34.063117"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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692 <param name="Dimethyl8" value="36.07567"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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693 <param name="ICPL0" value="105.021464"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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694 <param name="ICPL4" value="109.046571"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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695 <param name="ICPL6" value="111.041593"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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696 <param name="ICPL10" value="115.0667"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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697 </section>
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698 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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699 <output name="ctd_out" ftype="xml">
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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700 <assert_contents>
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701 <is_valid_xml/>
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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702 </assert_contents>
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703 </output>
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704 </test>
12
3098bea02bd8 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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705 </tests>
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706 <help><![CDATA[Determination of peak ratios in LC-MS data
0
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707
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708
16
9876bda3ec53 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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709 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FeatureFinderMultiplex.html]]></help>
12
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710 <expand macro="references"/>
0
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711 </tool>