Mercurial > repos > galaxyp > openms_featurefindermultiplex

annotate FeatureFinderMultiplex.xml @ 16:94fa01499b7f draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 2adf8edc3de4e1cd3b299b26abb14544d17d0636"
author galaxyp
date Fri, 06 Nov 2020 18:11:20 +0000
parents 16ad734997d9
children
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8abd89528480 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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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@GALAXY_VERSION@" profile="20.05">
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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 <import>macros_autotest.xml</import>
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10 <import>macros_test.xml</import>
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11 </macros>
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12 <expand macro="requirements"/>
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13 <expand macro="stdio"/>
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14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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15 @EXT_FOO@
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16 #import re
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17
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18 ## Preprocessing
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19 mkdir in &&
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20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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21 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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22 mkdir out &&
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23 #end if
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24 #if "out_multiplets_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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25 mkdir out_multiplets &&
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26 #end if
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27 #if "out_blacklist_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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28 mkdir out_blacklist &&
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29 #end if
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30
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31 ## Main program call
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32
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33 set -o pipefail &&
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34 @EXECUTABLE@ -write_ctd ./ &&
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35 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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36 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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37 -in
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38 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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39 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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40 -out
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41 'out/output.${gxy2omsext("featurexml")}'
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42 #end if
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43 #if "out_multiplets_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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44 -out_multiplets
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45 'out_multiplets/output.${gxy2omsext("consensusxml")}'
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46 #end if
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47 #if "out_blacklist_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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48 -out_blacklist
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49 'out_blacklist/output.${gxy2omsext("mzml")}'
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50 #end if
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51 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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52 | tee '$stdout'
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53 #end if
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54
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55 ## Postprocessing
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56 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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57 && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
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58 #end if
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59 #if "out_multiplets_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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60 && mv 'out_multiplets/output.${gxy2omsext("consensusxml")}' '$out_multiplets'
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61 #end if
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62 #if "out_blacklist_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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63 && mv 'out_blacklist/output.${gxy2omsext("mzml")}' '$out_blacklist'
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64 #end if
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65 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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66 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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67 #end if]]></command>
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68 <configfiles>
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69 <inputs name="args_json" data_style="paths"/>
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70 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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71 </configfiles>
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72 <inputs>
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73 <param name="in" 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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74 <section name="algorithm" title="algorithmic parameters" help="" expanded="false">
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75 <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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76 <expand macro="list_string_san"/>
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77 </param>
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78 <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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79 <expand macro="list_string_san"/>
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80 </param>
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81 <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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82 <expand macro="list_string_san"/>
0
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83 </param>
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84 <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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85 <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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86 <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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87 <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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88 <param name="mz_unit" argument="-algorithm:mz_unit" display="radio" type="select" optional="false" label="Unit of the 'mz_tolerance' paramete" help="">
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89 <option value="Da">Da</option>
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90 <option value="ppm" selected="true">ppm</option>
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91 <expand macro="list_string_san"/>
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92 </param>
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93 <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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94 <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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95 <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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96 <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 simulataneously. 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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97 <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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98 <param name="spectrum_type" argument="-algorithm:spectrum_type" display="radio" type="select" optional="false" 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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99 <option value="profile">profile</option>
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100 <option value="centroid">centroid</option>
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101 <option value="automatic" selected="true">automatic</option>
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102 <expand macro="list_string_san"/>
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103 </param>
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104 <param name="averagine_type" argument="-algorithm:averagine_type" display="radio" type="select" optional="false" label="The type of averagine to use, currently RNA, DNA or peptide" help="">
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105 <option value="peptide" selected="true">peptide</option>
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106 <option value="RNA">RNA</option>
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107 <option value="DNA">DNA</option>
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108 <expand macro="list_string_san"/>
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109 </param>
13
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110 <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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111 </section>
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112 <section name="labels" title="mass shifts for all possible labels" help="" expanded="false">
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113 <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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114 <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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115 <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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116 <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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117 <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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118 <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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119 <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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120 <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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121 <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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122 <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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123 <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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124 <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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125 <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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126 <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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127 </section>
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128 <expand macro="adv_opts_macro">
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129 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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130 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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131 <expand macro="list_string_san"/>
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132 </param>
0
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133 </expand>
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134 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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135 <option value="out_FLAG">out (Output file containing the individual peptide features)</option>
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136 <option value="out_multiplets_FLAG">out_multiplets (Optional output file containing all detected peptide groups)</option>
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137 <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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138 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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139 </param>
0
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140 </inputs>
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141 <outputs>
13
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142 <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml">
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143 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
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144 </data>
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145 <data name="out_multiplets" label="${tool.name} on ${on_string}: out_multiplets" format="consensusxml">
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146 <filter>OPTIONAL_OUTPUTS is not None and "out_multiplets_FLAG" in OPTIONAL_OUTPUTS</filter>
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147 </data>
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148 <data name="out_blacklist" label="${tool.name} on ${on_string}: out_blacklist" format="mzml">
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149 <filter>OPTIONAL_OUTPUTS is not None and "out_blacklist_FLAG" in OPTIONAL_OUTPUTS</filter>
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150 </data>
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151 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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152 <filter>OPTIONAL_OUTPUTS is None</filter>
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153 </data>
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154 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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155 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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156 </data>
0
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157 </outputs>
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158 <tests>
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159 <expand macro="autotest_FeatureFinderMultiplex"/>
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160 <expand macro="manutest_FeatureFinderMultiplex"/>
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161 </tests>
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162 <help><![CDATA[Determination of peak ratios in LC-MS data
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163
8abd89528480 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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164
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165 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_FeatureFinderMultiplex.html]]></help>
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166 <expand macro="references"/>
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167 </tool>