Mercurial > repos > galaxyp > openms_assaygeneratormetabo

annotate AssayGeneratorMetabo.xml @ 5:83f5e5c1209c draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 18:57:35 +0000
parents 11ac8ae77fb7
children f3ec820189ca
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cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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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: [Utilities]-->
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4 <tool id="AssayGeneratorMetabo" name="AssayGeneratorMetabo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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5 <description>Assay library generation from DDA data (Metabolomics)</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">AssayGeneratorMetabo</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
5
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17 #if $sirius_executable:
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18 mkdir sirius_executable &&
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19 ln -s '$sirius_executable' 'sirius_executable/${re.sub("[^\w\-_]", "_", $sirius_executable.element_identifier)}.$gxy2omsext($sirius_executable.ext)' &&
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20 #end if
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21 mkdir in_cond.in &&
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22 #if $in_cond.in_select == "no"
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23 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
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24 ${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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25 #else
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26 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
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27 #end if
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28 mkdir in_id_cond.in_id &&
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29 #if $in_id_cond.in_id_select == "no"
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30 mkdir ${' '.join(["'in_id_cond.in_id/%s'" % (i) for i, f in enumerate($in_id_cond.in_id) if f])} &&
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31 ${' '.join(["ln -s '%s' 'in_id_cond.in_id/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_id_cond.in_id) if f])}
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32 #else
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33 ln -s '$in_id_cond.in_id' 'in_id_cond.in_id/${re.sub("[^\w\-_]", "_", $in_id_cond.in_id.element_identifier)}.$gxy2omsext($in_id_cond.in_id.ext)' &&
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34 #end if
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35 mkdir out &&
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36
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37 ## Main program call
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38
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39 set -o pipefail &&
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40 @EXECUTABLE@ -write_ctd ./ &&
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41 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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42 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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43 #if $sirius_executable:
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44 -sirius_executable
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45 'sirius_executable/${re.sub("[^\w\-_]", "_", $sirius_executable.element_identifier)}.$gxy2omsext($sirius_executable.ext)'
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46 #end if
0
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47 -in
5
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48 #if $in_cond.in_select == "no"
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49 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
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50 #else
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51 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
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52 #end if
0
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53 -in_id
5
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54 #if $in_id_cond.in_id_select == "no"
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55 ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_id_cond.in_id) if f])}
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56 #else
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57 'in_id_cond.in_id/${re.sub("[^\w\-_]", "_", $in_id_cond.in_id.element_identifier)}.$gxy2omsext($in_id_cond.in_id.ext)'
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58 #end if
0
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59 -out
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60 'out/output.${out_type}'
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61
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62 ## Postprocessing
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63 && mv 'out/output.${out_type}' '$out'
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64 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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65 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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66 #end if]]></command>
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67 <configfiles>
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68 <inputs name="args_json" data_style="paths"/>
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69 <configfile name="hardcoded_json"><![CDATA[{"out_workspace_directory": "__SIRIUS_WORKSPACE__", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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70 </configfiles>
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71 <inputs>
5
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72 <param argument="-sirius_executable" type="data" format="txt" optional="true" label="The Sirius executable" help="Provide a full or relative path, or make sure it can be found in your PATH environment select txt data sets(s)"/>
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73 <conditional name="in_cond">
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74 <param name="in_select" type="select" label="Run tool in batch mode for -in">
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75 <option value="no">No: process all datasets jointly</option>
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76 <option value="yes">Yes: process each dataset in an independent job</option>
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77 </param>
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78 <when value="no">
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79 <param argument="-in" type="data" format="mzml" multiple="true" optional="false" label="MzML input file(s) used for assay library generation" help=" select mzml data sets(s)"/>
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80 </when>
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81 <when value="yes">
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82 <param argument="-in" type="data" format="mzml" multiple="false" optional="false" label="MzML input file(s) used for assay library generation" help=" select mzml data sets(s)"/>
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83 </when>
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84 </conditional>
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85 <conditional name="in_id_cond">
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86 <param name="in_id_select" type="select" label="Run tool in batch mode for -in_id">
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87 <option value="no">No: process all datasets jointly</option>
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88 <option value="yes">Yes: process each dataset in an independent job</option>
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89 </param>
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90 <when value="no">
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91 <param argument="-in_id" type="data" format="featurexml" multiple="true" optional="false" label="FeatureXML input file(s) containing identification information" help="(e.g. AccurateMassSearch) select featurexml data sets(s)"/>
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92 </when>
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93 <when value="yes">
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94 <param argument="-in_id" type="data" format="featurexml" multiple="false" optional="false" label="FeatureXML input file(s) containing identification information" help="(e.g. AccurateMassSearch) select featurexml data sets(s)"/>
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95 </when>
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96 </conditional>
0
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97 <param name="out_type" type="select" optional="false" label="File type of output out (Assay library output file)">
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98 <option value="tsv">tabular (tsv)</option>
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99 <option value="traML">traml</option>
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100 <option value="pqp">pqp</option>
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101 </param>
5
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102 <param argument="-fragment_annotation" type="select" optional="true" label="Fragment annotation method" help="">
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103 <option value="none">none</option>
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104 <option value="sirius" selected="true">sirius</option>
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105 <expand macro="list_string_san" name="fragment_annotation"/>
0
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106 </param>
5
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107 <param argument="-ambiguity_resolution_mz_tolerance" type="float" optional="true" value="10.0" label="Mz tolerance for the resolution of identification ambiguity over multiple files" help=""/>
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108 <param argument="-ambiguity_resolution_rt_tolerance" type="float" optional="true" value="10.0" label="RT tolerance in seconds for the resolution of identification ambiguity over multiple files" help=""/>
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109 <param argument="-total_occurrence_filter" type="float" optional="true" min="0.0" max="1.0" value="0.1" label="Filter compound based on total occurrence in analysed samples" help=""/>
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110 <param argument="-fragment_annotation_score_threshold" type="float" optional="true" min="0.0" max="1.0" value="0.8" label="Filters annotations based on the explained intensity of the peaks in a spectrum" help=""/>
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111 <param argument="-decoy_generation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Decoys will be generated using the fragmentation tree re-rooting approach" help="This option does only work in combination with the fragment annotation via Sirius"/>
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112 <param argument="-decoy_generation_method" type="select" optional="true" label="Uses different methods for decoy generation" help="Basis for the method is the fragmentation-tree re-rooting approach ('original'). This approach can be extended by using 'resolve_overlap', which will resolve overlapping fragments of the highest intensity fragments chosen, by adding -CH2 mass to the overlapping fragments. 'Add_shift' will add a -CH2 mass shift to the target fragments and use them as additional decoys if fragmentation-tree re-rooting failed. 'Both' combines the extended methods (resolve_overlap, add_shift)">
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113 <option value="original" selected="true">original</option>
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114 <option value="resolve_overlap">resolve_overlap</option>
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115 <option value="add_shift">add_shift</option>
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116 <option value="both">both</option>
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117 <expand macro="list_string_san" name="decoy_generation_method"/>
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118 </param>
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119 <param argument="-method" type="select" optional="true" label="Spectrum with the highest precursor intensity or a consensus spectrum is used for assay library construction (if no fragment annotation is used)" help="">
0
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120 <option value="highest_intensity" selected="true">highest_intensity</option>
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121 <option value="consensus_spectrum">consensus_spectrum</option>
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122 <expand macro="list_string_san" name="method"/>
0
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123 </param>
5
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124 <param argument="-use_exact_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use exact mass for precursor and fragment annotations" help=""/>
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125 <param argument="-exclude_ms2_precursor" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Excludes precursor in ms2 from transition list" help=""/>
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126 <param argument="-precursor_mz_distance" type="float" optional="true" value="0.0001" label="Max m/z distance of the precursor entries of two spectra to be merged in [Da]" help=""/>
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127 <param argument="-consensus_spectrum_precursor_rt_tolerance" type="float" optional="true" value="5.0" label="Tolerance window (left and right) for precursor selection [seconds], for consensus spectrum generation (only available without fragment annotation)" help=""/>
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128 <param argument="-use_known_unknowns" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use features without identification information" help=""/>
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129 <param argument="-min_transitions" type="integer" optional="true" value="3" label="Minimal number of transitions" help=""/>
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130 <param argument="-max_transitions" type="integer" optional="true" value="6" label="Maximal number of transitions" help=""/>
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131 <param argument="-cosine_similarity_threshold" type="float" optional="true" value="0.98" label="Threshold for cosine similarity of MS2 spectra from the same precursor used in consensus spectrum creation" help=""/>
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132 <param argument="-transition_threshold" type="float" optional="true" value="5.0" label="Further transitions need at least x% of the maximum intensity (default 5%)" help=""/>
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133 <section name="deisotoping" title="deisotoping" help="" expanded="false">
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134 <param name="use_deisotoper" argument="-deisotoping:use_deisotoper" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use Deisotoper (if no fragment annotation is used)" help=""/>
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135 <param name="fragment_tolerance" argument="-deisotoping:fragment_tolerance" type="float" optional="true" value="1.0" label="Tolerance used to match isotopic peaks" help=""/>
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136 <param name="fragment_unit" argument="-deisotoping:fragment_unit" type="select" optional="true" label="Unit of the fragment tolerance" help="">
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137 <option value="ppm" selected="true">ppm</option>
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138 <option value="Da">Da</option>
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139 <expand macro="list_string_san" name="fragment_unit"/>
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140 </param>
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141 <param name="min_charge" argument="-deisotoping:min_charge" type="integer" optional="true" min="1" value="1" label="The minimum charge considered" help=""/>
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142 <param name="max_charge" argument="-deisotoping:max_charge" type="integer" optional="true" min="1" value="1" label="The maximum charge considered" help=""/>
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143 <param name="min_isopeaks" argument="-deisotoping:min_isopeaks" type="integer" optional="true" min="2" value="2" label="The minimum number of isotopic peaks (at least 2) required for an isotopic cluste" help=""/>
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144 <param name="max_isopeaks" argument="-deisotoping:max_isopeaks" type="integer" optional="true" min="3" value="3" label="The maximum number of isotopic peaks (at least 2) considered for an isotopic cluste" help=""/>
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145 <param name="keep_only_deisotoped" argument="-deisotoping:keep_only_deisotoped" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only monoisotopic peaks of fragments with isotopic pattern are retained" help=""/>
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146 <param name="annotate_charge" argument="-deisotoping:annotate_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Annotate the charge to the peaks" help=""/>
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147 </section>
5
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148 <section name="preprocessing" title="" help="" expanded="false">
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149 <param name="filter_by_num_masstraces" argument="-preprocessing:filter_by_num_masstraces" type="integer" optional="true" min="1" value="1" label="Number of mass traces each feature has to have to be included" help="To use this parameter, setting the feature_only flag is necessary"/>
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150 <param name="precursor_mz_tolerance" argument="-preprocessing:precursor_mz_tolerance" type="float" optional="true" value="10.0" label="Tolerance window for precursor selection (Feature selection in regard to the precursor)" help=""/>
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151 <param name="precursor_mz_tolerance_unit" argument="-preprocessing:precursor_mz_tolerance_unit" type="select" optional="true" label="Unit of the precursor_mz_tolerance" help="">
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152 <option value="Da">Da</option>
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153 <option value="ppm" selected="true">ppm</option>
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154 <expand macro="list_string_san" name="precursor_mz_tolerance_unit"/>
0
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155 </param>
5
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156 <param name="precursor_rt_tolerance" argument="-preprocessing:precursor_rt_tolerance" type="float" optional="true" value="5.0" label="Tolerance window (left and right) for precursor selection [seconds]" help=""/>
0
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157 <param name="isotope_pattern_iterations" argument="-preprocessing:isotope_pattern_iterations" type="integer" optional="true" value="3" label="Number of iterations that should be performed to extract the C13 isotope pattern" help="If no peak is found (C13 distance) the function will abort. Be careful with noisy data - since this can lead to wrong isotope patterns"/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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158 <param name="feature_only" argument="-preprocessing:feature_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Uses the feature information from in_featureinfo to reduce the search space to MS2 associated with a feature" help=""/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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159 <param name="no_masstrace_info_isotope_pattern" argument="-preprocessing:no_masstrace_info_isotope_pattern" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag if the masstrace information from a feature should be discarded and the isotope_pattern_iterations should be used instead" help=""/>
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160 </section>
5
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161 <section name="project" title="" help="" expanded="false">
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162 <param name="processors" argument="-project:processors" type="integer" optional="true" value="1" label="Number of cpu cores to use" help="If not specified SIRIUS uses all available cores"/>
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163 <param name="ignore_formula" argument="-project:ignore_formula" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Ignore given molecular formula in internal .ms format, while processing" help=""/>
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164 <param name="q" argument="-project:q" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress shell output" help=""/>
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165 </section>
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166 <section name="sirius" title="" help="" expanded="false">
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167 <param name="ppm_max" argument="-sirius:ppm_max" type="float" optional="true" value="10.0" label="Maximum allowed mass deviation in ppm for decomposing masses [ppm]" help=""/>
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168 <param name="ppm_max_ms2" argument="-sirius:ppm_max_ms2" type="float" optional="true" value="10.0" label="Maximum allowed mass deviation in ppm for decomposing masses in MS2 [ppm].If not specified, the same value as for the MS1 is used" help=""/>
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169 <param name="tree_timeout" argument="-sirius:tree_timeout" type="integer" optional="true" min="0" value="0" label="Time out in seconds per fragmentation tree computations" help="0 for an infinite amount of time"/>
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170 <param name="compound_timeout" argument="-sirius:compound_timeout" type="integer" optional="true" min="0" value="100" label="Maximal computation time in seconds for a single compound" help="0 for an infinite amount of time"/>
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171 <param name="no_recalibration" argument="-sirius:no_recalibration" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable recalibration of input spectra" help=""/>
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172 <param name="profile" argument="-sirius:profile" type="select" optional="true" label="Name of the configuration profile" help="">
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173 <option value="default">default</option>
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174 <option value="qtof" selected="true">qtof</option>
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175 <option value="orbitrap">orbitrap</option>
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176 <option value="fticr">fticr</option>
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177 <expand macro="list_string_san" name="profile"/>
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178 </param>
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179 <param name="formula" argument="-sirius:formula" type="text" optional="true" value="" label="Specify the neutral molecular formula of the measured compound to compute its tree or a list of candidate formulas the method should discriminate" help="Omit this option if you want to consider all possible molecular formulas">
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180 <expand macro="list_string_san" name="formula"/>
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181 </param>
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182 <param name="ions_enforced" argument="-sirius:ions_enforced" type="text" optional="true" value="" label="The iontype/adduct of the MS/MS data" help="Example: [M+H]+, . [M-H]-, [M+Cl]-, [M+Na]+, [M]+. You can also provide a . comma separated list of adducts">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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183 <expand macro="list_string_san" name="ions_enforced"/>
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184 </param>
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185 <param name="candidates" argument="-sirius:candidates" type="integer" optional="true" min="1" value="5" label="The number of formula candidates in the SIRIUS output" help=""/>
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186 <param name="candidates_per_ion" argument="-sirius:candidates_per_ion" type="integer" optional="true" value="-1" label="Minimum number of candidates in the output for each ionization" help="Set to force output of results for each possible ionization, even if not part of highest ranked results. -1 omits parameter in Sirius"/>
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187 <param name="elements_considered" argument="-sirius:elements_considered" type="text" optional="true" value="" label="Set the allowed elements for rare element detection" help="Write SBrClBSe to allow the elements S,Br,Cl,B and Se">
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188 <expand macro="list_string_san" name="elements_considered"/>
0
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189 </param>
5
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190 <param name="elements_enforced" argument="-sirius:elements_enforced" type="text" optional="true" value="" label="Enforce elements for molecular formula determination" help="Write CHNOPSCl to allow the elements C, H, N, O, P, S and Cl. Add numbers in brackets to restrict the minimal and maximal allowed occurrence of these elements: CHNOP[5]S[8]Cl[1-2]. When one number is given then it is interpreted as upper bound. Default is CHNOP">
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191 <expand macro="list_string_san" name="elements_enforced"/>
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192 </param>
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193 <param name="no_isotope_score" argument="-sirius:no_isotope_score" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable isotope pattern score" help=""/>
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194 <param name="no_isotope_filter" argument="-sirius:no_isotope_filter" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disable molecular formula filte" help="When filtering is enabled, molecular formulas are excluded if their theoretical isotope pattern does not match the theoretical one, even if their MS/MS pattern has high score"/>
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195 <param name="ions_considered" argument="-sirius:ions_considered" type="text" optional="true" value="" label="the iontype/adduct of the MS/MS data" help="Example: [M+H]+, [M-H]-, [M+Cl]-, [M+Na]+, [M]+. You can also provide a comma separated list of adducts">
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196 <expand macro="list_string_san" name="ions_considered"/>
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197 </param>
5
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198 <param name="db" argument="-sirius:db" type="text" optional="true" value="" label="Search formulas in the Union of the given databases db-name1,db-name2,db-name3" help="If no database is given all possible molecular formulas will be respected (no database is used). Example: possible DBs: ALL,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE">
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199 <expand macro="list_string_san" name="db"/>
0
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200 </param>
5
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201 </section>
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202 <section name="fingerid" title="" help="" expanded="false">
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203 <param name="candidates" argument="-fingerid:candidates" type="integer" optional="true" min="1" value="10" label="Number of molecular structure candidates in the output" help=""/>
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204 <param name="db" argument="-fingerid:db" type="text" optional="true" value="BIO" label="Search formulas in the Union of the given databases db-name1,db-name2,db-name3" help="If no database is given all possible molecular formulas will be respected (no database is used). Example: possible DBs: ALL,BIO,PUBCHEM,MESH,HMDB,KNAPSACK,CHEBI,PUBMED,KEGG,HSDB,MACONDA,METACYC,GNPS,ZINCBIO,UNDP,YMDB,PLANTCYC,NORMAN,ADDITIONAL,PUBCHEMANNOTATIONBIO,PUBCHEMANNOTATIONDRUG,PUBCHEMANNOTATIONSAFETYANDTOXIC,PUBCHEMANNOTATIONFOOD,KEGGMINE,ECOCYCMINE,YMDBMINE">
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205 <expand macro="list_string_san" name="db"/>
0
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206 </param>
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207 </section>
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208 <expand macro="adv_opts_macro">
5
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209 <param argument="-ambiguity_resolution_mz_tolerance_unit" type="select" optional="true" label="Unit of the ambiguity_resolution_mz_tolerance" help="">
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210 <option value="ppm" selected="true">ppm</option>
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211 <option value="Da">Da</option>
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212 <expand macro="list_string_san" name="ambiguity_resolution_mz_tolerance_unit"/>
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213 </param>
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214 <param argument="-precursor_recalibration_window" type="float" optional="true" value="0.01" label="Tolerance window for precursor selection (Annotation of precursor mz and intensity)" help=""/>
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215 <param argument="-precursor_recalibration_window_unit" type="select" optional="true" label="Unit of the precursor_mz_tolerance_annotation" help="">
0
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216 <option value="Da" selected="true">Da</option>
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217 <option value="ppm">ppm</option>
5
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218 <expand macro="list_string_san" name="precursor_recalibration_window_unit"/>
0
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219 </param>
5
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220 <param argument="-min_fragment_mz" type="float" optional="true" value="0.0" label="Minimal m/z of a fragment ion choosen as a transition" help=""/>
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221 <param argument="-max_fragment_mz" type="float" optional="true" value="2000.0" label="Maximal m/z of a fragment ion choosen as a transition" help=""/>
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222 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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223 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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224 <expand macro="list_string_san" name="test"/>
0
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225 </param>
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226 </expand>
2
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227 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
0
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228 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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229 </param>
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230 </inputs>
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231 <outputs>
5
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232 <data name="out" label="${tool.name} on ${on_string}: out" format="pqp">
0
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233 <change_format>
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234 <when input="out_type" value="traML" format="traml"/>
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235 <when input="out_type" value="tsv" format="tabular"/>
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236 </change_format>
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237 </data>
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238 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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239 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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240 </data>
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241 </outputs>
5
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242 <tests><!-- UTILS_AssayGeneratorMetabo_1 -->
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243 <test expect_num_outputs="2">
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244 <section name="adv_opts">
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245 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
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246 <param name="precursor_recalibration_window" value="0.01"/>
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247 <param name="precursor_recalibration_window_unit" value="Da"/>
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248 <param name="min_fragment_mz" value="0.0"/>
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249 <param name="max_fragment_mz" value="2000.0"/>
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250 <param name="force" value="false"/>
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251 <param name="test" value="true"/>
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252 </section>
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253 <conditional name="in_cond">
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254 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
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255 </conditional>
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256 <conditional name="in_id_cond">
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257 <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/>
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258 </conditional>
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259 <param name="out_type" value="tsv"/>
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260 <output name="out" file="AssayGeneratorMetabo_ffm_output.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
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261 <param name="fragment_annotation" value="none"/>
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262 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
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263 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
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264 <param name="total_occurrence_filter" value="0.1"/>
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265 <param name="fragment_annotation_score_threshold" value="0.8"/>
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266 <param name="decoy_generation" value="false"/>
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267 <param name="decoy_generation_method" value="original"/>
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268 <param name="method" value="highest_intensity"/>
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269 <param name="use_exact_mass" value="false"/>
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270 <param name="exclude_ms2_precursor" value="false"/>
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271 <param name="precursor_mz_distance" value="0.0001"/>
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272 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
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273 <param name="use_known_unknowns" value="false"/>
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274 <param name="min_transitions" value="1"/>
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275 <param name="max_transitions" value="3"/>
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276 <param name="cosine_similarity_threshold" value="0.98"/>
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277 <param name="transition_threshold" value="5.0"/>
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278 <section name="deisotoping">
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279 <param name="use_deisotoper" value="false"/>
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280 <param name="fragment_tolerance" value="1.0"/>
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281 <param name="fragment_unit" value="ppm"/>
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282 <param name="min_charge" value="1"/>
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283 <param name="max_charge" value="1"/>
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284 <param name="min_isopeaks" value="2"/>
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285 <param name="max_isopeaks" value="3"/>
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286 <param name="keep_only_deisotoped" value="false"/>
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287 <param name="annotate_charge" value="false"/>
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288 </section>
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289 <section name="preprocessing">
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290 <param name="filter_by_num_masstraces" value="1"/>
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291 <param name="precursor_mz_tolerance" value="10.0"/>
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292 <param name="precursor_mz_tolerance_unit" value="ppm"/>
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293 <param name="precursor_rt_tolerance" value="5.0"/>
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294 <param name="isotope_pattern_iterations" value="3"/>
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295 <param name="feature_only" value="false"/>
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296 <param name="no_masstrace_info_isotope_pattern" value="false"/>
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297 </section>
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298 <section name="project">
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299 <param name="processors" value="1"/>
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300 <param name="ignore_formula" value="false"/>
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301 <param name="q" value="false"/>
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302 </section>
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303 <section name="sirius">
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304 <param name="ppm_max" value="10.0"/>
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305 <param name="ppm_max_ms2" value="10.0"/>
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306 <param name="tree_timeout" value="0"/>
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307 <param name="compound_timeout" value="100"/>
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308 <param name="no_recalibration" value="false"/>
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309 <param name="profile" value="qtof"/>
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310 <param name="formula" value=""/>
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311 <param name="ions_enforced" value=""/>
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312 <param name="candidates" value="5"/>
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313 <param name="candidates_per_ion" value="-1"/>
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314 <param name="elements_considered" value=""/>
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315 <param name="elements_enforced" value=""/>
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316 <param name="no_isotope_score" value="false"/>
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317 <param name="no_isotope_filter" value="false"/>
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318 <param name="ions_considered" value=""/>
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319 <param name="db" value=""/>
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320 </section>
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321 <section name="fingerid">
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322 <param name="candidates" value="10"/>
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323 <param name="db" value="BIO"/>
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324 </section>
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325 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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326 <output name="ctd_out" ftype="xml">
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327 <assert_contents>
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328 <is_valid_xml/>
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329 </assert_contents>
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330 </output>
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331 </test>
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332 <!-- UTILS_AssayGeneratorMetabo_2 -->
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333 <test expect_num_outputs="2">
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334 <section name="adv_opts">
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335 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
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336 <param name="precursor_recalibration_window" value="0.01"/>
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337 <param name="precursor_recalibration_window_unit" value="Da"/>
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338 <param name="min_fragment_mz" value="0.0"/>
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339 <param name="max_fragment_mz" value="2000.0"/>
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340 <param name="force" value="false"/>
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341 <param name="test" value="true"/>
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342 </section>
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343 <conditional name="in_cond">
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344 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
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345 </conditional>
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346 <conditional name="in_id_cond">
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347 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
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348 </conditional>
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349 <param name="out_type" value="tsv"/>
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350 <output name="out" file="AssayGeneratorMetabo_ams_output.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
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351 <param name="fragment_annotation" value="none"/>
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352 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
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353 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
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354 <param name="total_occurrence_filter" value="0.1"/>
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355 <param name="fragment_annotation_score_threshold" value="0.8"/>
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356 <param name="decoy_generation" value="false"/>
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357 <param name="decoy_generation_method" value="original"/>
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358 <param name="method" value="highest_intensity"/>
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359 <param name="use_exact_mass" value="false"/>
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360 <param name="exclude_ms2_precursor" value="false"/>
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361 <param name="precursor_mz_distance" value="0.0001"/>
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362 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
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363 <param name="use_known_unknowns" value="false"/>
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364 <param name="min_transitions" value="1"/>
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365 <param name="max_transitions" value="3"/>
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366 <param name="cosine_similarity_threshold" value="0.98"/>
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367 <param name="transition_threshold" value="5.0"/>
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368 <section name="deisotoping">
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369 <param name="use_deisotoper" value="false"/>
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370 <param name="fragment_tolerance" value="1.0"/>
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371 <param name="fragment_unit" value="ppm"/>
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372 <param name="min_charge" value="1"/>
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373 <param name="max_charge" value="1"/>
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374 <param name="min_isopeaks" value="2"/>
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375 <param name="max_isopeaks" value="3"/>
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376 <param name="keep_only_deisotoped" value="false"/>
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377 <param name="annotate_charge" value="false"/>
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378 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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379 <section name="preprocessing">
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380 <param name="filter_by_num_masstraces" value="1"/>
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381 <param name="precursor_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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382 <param name="precursor_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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383 <param name="precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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384 <param name="isotope_pattern_iterations" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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385 <param name="feature_only" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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386 <param name="no_masstrace_info_isotope_pattern" value="false"/>
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387 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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388 <section name="project">
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389 <param name="processors" value="1"/>
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390 <param name="ignore_formula" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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391 <param name="q" value="false"/>
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392 </section>
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393 <section name="sirius">
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394 <param name="ppm_max" value="10.0"/>
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395 <param name="ppm_max_ms2" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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396 <param name="tree_timeout" value="0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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397 <param name="compound_timeout" value="100"/>
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398 <param name="no_recalibration" value="false"/>
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399 <param name="profile" value="qtof"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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400 <param name="formula" value=""/>
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401 <param name="ions_enforced" value=""/>
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402 <param name="candidates" value="5"/>
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403 <param name="candidates_per_ion" value="-1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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404 <param name="elements_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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405 <param name="elements_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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406 <param name="no_isotope_score" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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407 <param name="no_isotope_filter" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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408 <param name="ions_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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409 <param name="db" value=""/>
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410 </section>
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411 <section name="fingerid">
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412 <param name="candidates" value="10"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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413 <param name="db" value="BIO"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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414 </section>
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415 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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416 <output name="ctd_out" ftype="xml">
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417 <assert_contents>
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418 <is_valid_xml/>
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419 </assert_contents>
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420 </output>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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421 </test>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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422 <!-- UTILS_AssayGeneratorMetabo_3 -->
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423 <test expect_num_outputs="2">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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424 <section name="adv_opts">
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425 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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426 <param name="precursor_recalibration_window" value="0.01"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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427 <param name="precursor_recalibration_window_unit" value="Da"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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428 <param name="min_fragment_mz" value="0.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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429 <param name="max_fragment_mz" value="2000.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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430 <param name="force" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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431 <param name="test" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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432 </section>
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diff changeset
433 <conditional name="in_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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434 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
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435 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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436 <conditional name="in_id_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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437 <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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438 </conditional>
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439 <param name="out_type" value="tsv"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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440 <output name="out" file="AssayGeneratorMetabo_ffm_output_consensus.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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441 <param name="fragment_annotation" value="none"/>
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442 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
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443 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
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444 <param name="total_occurrence_filter" value="0.1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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445 <param name="fragment_annotation_score_threshold" value="0.8"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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446 <param name="decoy_generation" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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447 <param name="decoy_generation_method" value="original"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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448 <param name="method" value="consensus_spectrum"/>
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449 <param name="use_exact_mass" value="false"/>
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450 <param name="exclude_ms2_precursor" value="false"/>
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451 <param name="precursor_mz_distance" value="0.0001"/>
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452 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
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453 <param name="use_known_unknowns" value="false"/>
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454 <param name="min_transitions" value="1"/>
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455 <param name="max_transitions" value="3"/>
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456 <param name="cosine_similarity_threshold" value="0.98"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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457 <param name="transition_threshold" value="5.0"/>
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diff changeset
458 <section name="deisotoping">
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459 <param name="use_deisotoper" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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460 <param name="fragment_tolerance" value="1.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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461 <param name="fragment_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
462 <param name="min_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
463 <param name="max_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
464 <param name="min_isopeaks" value="2"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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465 <param name="max_isopeaks" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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466 <param name="keep_only_deisotoped" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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467 <param name="annotate_charge" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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468 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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469 <section name="preprocessing">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
470 <param name="filter_by_num_masstraces" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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471 <param name="precursor_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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472 <param name="precursor_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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473 <param name="precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
474 <param name="isotope_pattern_iterations" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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475 <param name="feature_only" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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476 <param name="no_masstrace_info_isotope_pattern" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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477 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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478 <section name="project">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
479 <param name="processors" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
480 <param name="ignore_formula" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
481 <param name="q" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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482 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
483 <section name="sirius">
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484 <param name="ppm_max" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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485 <param name="ppm_max_ms2" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
486 <param name="tree_timeout" value="0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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487 <param name="compound_timeout" value="100"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
488 <param name="no_recalibration" value="false"/>
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diff changeset
489 <param name="profile" value="qtof"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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490 <param name="formula" value=""/>
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diff changeset
491 <param name="ions_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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492 <param name="candidates" value="5"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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493 <param name="candidates_per_ion" value="-1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
494 <param name="elements_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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495 <param name="elements_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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496 <param name="no_isotope_score" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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497 <param name="no_isotope_filter" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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498 <param name="ions_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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499 <param name="db" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
500 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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501 <section name="fingerid">
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502 <param name="candidates" value="10"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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503 <param name="db" value="BIO"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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504 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
505 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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506 <output name="ctd_out" ftype="xml">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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507 <assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
508 <is_valid_xml/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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509 </assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
510 </output>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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511 </test>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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512 <!-- UTILS_AssayGeneratorMetabo_4 -->
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513 <test expect_num_outputs="2">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
514 <section name="adv_opts">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
515 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c 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="precursor_recalibration_window" value="0.01"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
517 <param name="precursor_recalibration_window_unit" value="Da"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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518 <param name="min_fragment_mz" value="0.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
519 <param name="max_fragment_mz" value="2000.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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520 <param name="force" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
521 <param name="test" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
522 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
523 <conditional name="in_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
524 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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525 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
526 <conditional name="in_id_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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527 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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528 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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529 <param name="out_type" value="tsv"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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530 <output name="out" file="AssayGeneratorMetabo_ams_output_consensus.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
531 <param name="fragment_annotation" value="none"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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532 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
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533 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
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534 <param name="total_occurrence_filter" value="0.1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
535 <param name="fragment_annotation_score_threshold" value="0.8"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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536 <param name="decoy_generation" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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537 <param name="decoy_generation_method" value="original"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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538 <param name="method" value="consensus_spectrum"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
539 <param name="use_exact_mass" value="false"/>
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540 <param name="exclude_ms2_precursor" value="false"/>
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galaxyp
parents: 4
diff changeset
541 <param name="precursor_mz_distance" value="0.0001"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
542 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
543 <param name="use_known_unknowns" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
544 <param name="min_transitions" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
545 <param name="max_transitions" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
546 <param name="cosine_similarity_threshold" value="0.98"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
547 <param name="transition_threshold" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
548 <section name="deisotoping">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
549 <param name="use_deisotoper" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
550 <param name="fragment_tolerance" value="1.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
551 <param name="fragment_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
552 <param name="min_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
553 <param name="max_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
554 <param name="min_isopeaks" value="2"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
555 <param name="max_isopeaks" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
556 <param name="keep_only_deisotoped" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
557 <param name="annotate_charge" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
558 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
559 <section name="preprocessing">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
560 <param name="filter_by_num_masstraces" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
561 <param name="precursor_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
562 <param name="precursor_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
563 <param name="precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
564 <param name="isotope_pattern_iterations" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
565 <param name="feature_only" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
566 <param name="no_masstrace_info_isotope_pattern" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
567 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
568 <section name="project">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
569 <param name="processors" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
570 <param name="ignore_formula" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
571 <param name="q" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
572 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
573 <section name="sirius">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
574 <param name="ppm_max" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
575 <param name="ppm_max_ms2" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
576 <param name="tree_timeout" value="0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
577 <param name="compound_timeout" value="100"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
578 <param name="no_recalibration" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
579 <param name="profile" value="qtof"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
580 <param name="formula" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
581 <param name="ions_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
582 <param name="candidates" value="5"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
583 <param name="candidates_per_ion" value="-1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
584 <param name="elements_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
585 <param name="elements_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
586 <param name="no_isotope_score" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
587 <param name="no_isotope_filter" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
588 <param name="ions_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
589 <param name="db" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
590 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
591 <section name="fingerid">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
592 <param name="candidates" value="10"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
593 <param name="db" value="BIO"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
594 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
595 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
596 <output name="ctd_out" ftype="xml">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
597 <assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
598 <is_valid_xml/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
599 </assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
600 </output>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
601 </test>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
602 <!-- UTILS_AssayGeneratorMetabo_5 -->
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
603 <test expect_num_outputs="2">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
604 <section name="adv_opts">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
605 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
606 <param name="precursor_recalibration_window" value="0.01"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
607 <param name="precursor_recalibration_window_unit" value="Da"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
608 <param name="min_fragment_mz" value="0.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
609 <param name="max_fragment_mz" value="2000.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
610 <param name="force" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
611 <param name="test" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
612 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
613 <conditional name="in_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
614 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
615 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
616 <conditional name="in_id_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
617 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
618 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
619 <param name="out_type" value="tsv"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
620 <output name="out" file="AssayGeneratorMetabo_ams_uku_output_consensus.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
621 <param name="fragment_annotation" value="none"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
622 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
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diff changeset
623 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
624 <param name="total_occurrence_filter" value="0.1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
625 <param name="fragment_annotation_score_threshold" value="0.8"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
626 <param name="decoy_generation" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
627 <param name="decoy_generation_method" value="original"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
628 <param name="method" value="consensus_spectrum"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
629 <param name="use_exact_mass" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
630 <param name="exclude_ms2_precursor" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
631 <param name="precursor_mz_distance" value="0.0001"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
632 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
633 <param name="use_known_unknowns" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
634 <param name="min_transitions" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
635 <param name="max_transitions" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
636 <param name="cosine_similarity_threshold" value="0.98"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
637 <param name="transition_threshold" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
638 <section name="deisotoping">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
639 <param name="use_deisotoper" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
640 <param name="fragment_tolerance" value="1.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
641 <param name="fragment_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
642 <param name="min_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
643 <param name="max_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
644 <param name="min_isopeaks" value="2"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
645 <param name="max_isopeaks" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
646 <param name="keep_only_deisotoped" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
647 <param name="annotate_charge" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
648 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
649 <section name="preprocessing">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
650 <param name="filter_by_num_masstraces" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
651 <param name="precursor_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
652 <param name="precursor_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
653 <param name="precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
654 <param name="isotope_pattern_iterations" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
655 <param name="feature_only" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
656 <param name="no_masstrace_info_isotope_pattern" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
657 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
658 <section name="project">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
659 <param name="processors" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
660 <param name="ignore_formula" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
661 <param name="q" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
662 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
663 <section name="sirius">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
664 <param name="ppm_max" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
665 <param name="ppm_max_ms2" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
666 <param name="tree_timeout" value="0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
667 <param name="compound_timeout" value="100"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
668 <param name="no_recalibration" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
669 <param name="profile" value="qtof"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
670 <param name="formula" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
671 <param name="ions_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
672 <param name="candidates" value="5"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
673 <param name="candidates_per_ion" value="-1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
674 <param name="elements_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
675 <param name="elements_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
676 <param name="no_isotope_score" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
677 <param name="no_isotope_filter" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
678 <param name="ions_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
679 <param name="db" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
680 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
681 <section name="fingerid">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
682 <param name="candidates" value="10"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
683 <param name="db" value="BIO"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
684 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
685 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
686 <output name="ctd_out" ftype="xml">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
687 <assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
688 <is_valid_xml/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
689 </assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
690 </output>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
691 </test>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
692 <!-- UTILS_AssayGeneratorMetabo_7 -->
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
693 <test expect_num_outputs="2">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
694 <section name="adv_opts">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
695 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
696 <param name="precursor_recalibration_window" value="0.01"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
697 <param name="precursor_recalibration_window_unit" value="Da"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
698 <param name="min_fragment_mz" value="0.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
699 <param name="max_fragment_mz" value="2000.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
700 <param name="force" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
701 <param name="test" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
702 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
703 <conditional name="in_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
704 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
705 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
706 <conditional name="in_id_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
707 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
708 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
709 <param name="out_type" value="tsv"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
710 <output name="out" file="AssayGeneratorMetabo_ams_sirius_output.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
711 <param name="fragment_annotation" value="sirius"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
712 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
713 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
714 <param name="total_occurrence_filter" value="0.1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
715 <param name="fragment_annotation_score_threshold" value="0.8"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
716 <param name="decoy_generation" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
717 <param name="decoy_generation_method" value="original"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
718 <param name="method" value="highest_intensity"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
719 <param name="use_exact_mass" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
720 <param name="exclude_ms2_precursor" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
721 <param name="precursor_mz_distance" value="0.0001"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
722 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
723 <param name="use_known_unknowns" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
724 <param name="min_transitions" value="2"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
725 <param name="max_transitions" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
726 <param name="cosine_similarity_threshold" value="0.98"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
727 <param name="transition_threshold" value="3.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
728 <section name="deisotoping">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
729 <param name="use_deisotoper" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
730 <param name="fragment_tolerance" value="1.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
731 <param name="fragment_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
732 <param name="min_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
733 <param name="max_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
734 <param name="min_isopeaks" value="2"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
735 <param name="max_isopeaks" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
736 <param name="keep_only_deisotoped" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
737 <param name="annotate_charge" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
738 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
739 <section name="preprocessing">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
740 <param name="filter_by_num_masstraces" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
741 <param name="precursor_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
742 <param name="precursor_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
743 <param name="precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
744 <param name="isotope_pattern_iterations" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
745 <param name="feature_only" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
746 <param name="no_masstrace_info_isotope_pattern" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
747 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
748 <section name="project">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
749 <param name="processors" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
750 <param name="ignore_formula" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
751 <param name="q" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
752 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
753 <section name="sirius">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
754 <param name="ppm_max" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
755 <param name="ppm_max_ms2" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
756 <param name="tree_timeout" value="0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
757 <param name="compound_timeout" value="100"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
758 <param name="no_recalibration" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
759 <param name="profile" value="qtof"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
760 <param name="formula" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
761 <param name="ions_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
762 <param name="candidates" value="5"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
763 <param name="candidates_per_ion" value="-1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
764 <param name="elements_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
765 <param name="elements_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
766 <param name="no_isotope_score" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
767 <param name="no_isotope_filter" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
768 <param name="ions_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
769 <param name="db" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
770 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
771 <section name="fingerid">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
772 <param name="candidates" value="10"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
773 <param name="db" value="BIO"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
774 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
775 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
776 <output name="ctd_out" ftype="xml">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
777 <assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
778 <is_valid_xml/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
779 </assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
780 </output>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
781 </test>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
782 <!-- UTILS_AssayGeneratorMetabo_8 -->
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
783 <test expect_num_outputs="2">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
784 <section name="adv_opts">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
785 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
786 <param name="precursor_recalibration_window" value="0.01"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
787 <param name="precursor_recalibration_window_unit" value="Da"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
788 <param name="min_fragment_mz" value="0.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
789 <param name="max_fragment_mz" value="2000.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
790 <param name="force" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
791 <param name="test" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
792 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
793 <conditional name="in_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
794 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
795 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
796 <conditional name="in_id_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
797 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
798 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
799 <param name="out_type" value="tsv"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
800 <output name="out" file="AssayGeneratorMetabo_ams_sirius_ukn_output.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
801 <param name="fragment_annotation" value="sirius"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
802 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
803 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
804 <param name="total_occurrence_filter" value="0.1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
805 <param name="fragment_annotation_score_threshold" value="0.8"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
806 <param name="decoy_generation" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
807 <param name="decoy_generation_method" value="original"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
808 <param name="method" value="highest_intensity"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
809 <param name="use_exact_mass" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
810 <param name="exclude_ms2_precursor" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
811 <param name="precursor_mz_distance" value="0.0001"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
812 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
813 <param name="use_known_unknowns" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
814 <param name="min_transitions" value="2"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
815 <param name="max_transitions" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
816 <param name="cosine_similarity_threshold" value="0.98"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
817 <param name="transition_threshold" value="3.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
818 <section name="deisotoping">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
819 <param name="use_deisotoper" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
820 <param name="fragment_tolerance" value="1.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
821 <param name="fragment_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
822 <param name="min_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
823 <param name="max_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
824 <param name="min_isopeaks" value="2"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
825 <param name="max_isopeaks" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
826 <param name="keep_only_deisotoped" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
827 <param name="annotate_charge" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
828 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
829 <section name="preprocessing">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
830 <param name="filter_by_num_masstraces" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
831 <param name="precursor_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
832 <param name="precursor_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
833 <param name="precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
834 <param name="isotope_pattern_iterations" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
835 <param name="feature_only" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
836 <param name="no_masstrace_info_isotope_pattern" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
837 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
838 <section name="project">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
839 <param name="processors" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
840 <param name="ignore_formula" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
841 <param name="q" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
842 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
843 <section name="sirius">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
844 <param name="ppm_max" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
845 <param name="ppm_max_ms2" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
846 <param name="tree_timeout" value="0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
847 <param name="compound_timeout" value="100"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
848 <param name="no_recalibration" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
849 <param name="profile" value="qtof"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
850 <param name="formula" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
851 <param name="ions_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
852 <param name="candidates" value="5"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
853 <param name="candidates_per_ion" value="-1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
854 <param name="elements_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
855 <param name="elements_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
856 <param name="no_isotope_score" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
857 <param name="no_isotope_filter" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
858 <param name="ions_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
859 <param name="db" value="ALL"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
860 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
861 <section name="fingerid">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
862 <param name="candidates" value="10"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
863 <param name="db" value="BIO"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
864 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
865 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
866 <output name="ctd_out" ftype="xml">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
867 <assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
868 <is_valid_xml/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
869 </assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
870 </output>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
871 </test>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
872 <!-- UTILS_AssayGeneratorMetabo_9 -->
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
873 <test expect_num_outputs="2">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
874 <section name="adv_opts">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
875 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
876 <param name="precursor_recalibration_window" value="0.01"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
877 <param name="precursor_recalibration_window_unit" value="Da"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
878 <param name="min_fragment_mz" value="0.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
879 <param name="max_fragment_mz" value="2000.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
880 <param name="force" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
881 <param name="test" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
882 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
883 <conditional name="in_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
884 <param name="in" value="AssayGeneratorMetabo_intsort_input.mzML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
885 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
886 <conditional name="in_id_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
887 <param name="in_id" value="AssayGeneratorMetabo_intsort_input.featureXML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
888 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
889 <param name="out_type" value="tsv"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
890 <output name="out" file="AssayGeneratorMetabo_ams_sirius_intsort_output.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
891 <param name="fragment_annotation" value="sirius"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
892 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
893 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
894 <param name="total_occurrence_filter" value="0.1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
895 <param name="fragment_annotation_score_threshold" value="0.8"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
896 <param name="decoy_generation" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
897 <param name="decoy_generation_method" value="original"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
898 <param name="method" value="highest_intensity"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
899 <param name="use_exact_mass" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
900 <param name="exclude_ms2_precursor" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
901 <param name="precursor_mz_distance" value="0.0001"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
902 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
903 <param name="use_known_unknowns" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
904 <param name="min_transitions" value="2"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
905 <param name="max_transitions" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
906 <param name="cosine_similarity_threshold" value="0.98"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
907 <param name="transition_threshold" value="3.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
908 <section name="deisotoping">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
909 <param name="use_deisotoper" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
910 <param name="fragment_tolerance" value="1.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
911 <param name="fragment_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
912 <param name="min_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
913 <param name="max_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
914 <param name="min_isopeaks" value="2"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
915 <param name="max_isopeaks" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
916 <param name="keep_only_deisotoped" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
917 <param name="annotate_charge" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
918 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
919 <section name="preprocessing">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
920 <param name="filter_by_num_masstraces" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
921 <param name="precursor_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
922 <param name="precursor_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
923 <param name="precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
924 <param name="isotope_pattern_iterations" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
925 <param name="feature_only" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
926 <param name="no_masstrace_info_isotope_pattern" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
927 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
928 <section name="project">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
929 <param name="processors" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
930 <param name="ignore_formula" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
931 <param name="q" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
932 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
933 <section name="sirius">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
934 <param name="ppm_max" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
935 <param name="ppm_max_ms2" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
936 <param name="tree_timeout" value="0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
937 <param name="compound_timeout" value="100"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
938 <param name="no_recalibration" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
939 <param name="profile" value="qtof"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
940 <param name="formula" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
941 <param name="ions_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
942 <param name="candidates" value="5"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
943 <param name="candidates_per_ion" value="-1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
944 <param name="elements_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
945 <param name="elements_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
946 <param name="no_isotope_score" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
947 <param name="no_isotope_filter" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
948 <param name="ions_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
949 <param name="db" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
950 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
951 <section name="fingerid">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
952 <param name="candidates" value="10"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
953 <param name="db" value="BIO"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
954 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
955 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
956 <output name="ctd_out" ftype="xml">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
957 <assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
958 <is_valid_xml/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
959 </assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
960 </output>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
961 </test>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
962 <!-- UTILS_AssayGeneratorMetabo_10 -->
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
963 <test expect_num_outputs="2">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
964 <section name="adv_opts">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
965 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
966 <param name="precursor_recalibration_window" value="0.01"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
967 <param name="precursor_recalibration_window_unit" value="Da"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
968 <param name="min_fragment_mz" value="100.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
969 <param name="max_fragment_mz" value="900.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
970 <param name="force" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
971 <param name="test" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
972 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
973 <conditional name="in_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
974 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
975 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
976 <conditional name="in_id_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
977 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
978 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
979 <param name="out_type" value="tsv"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
980 <output name="out" file="AssayGeneratorMetabo_ams_sirius_restrict_output.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
981 <param name="fragment_annotation" value="sirius"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
982 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
983 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
984 <param name="total_occurrence_filter" value="0.1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
985 <param name="fragment_annotation_score_threshold" value="0.8"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
986 <param name="decoy_generation" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
987 <param name="decoy_generation_method" value="original"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
988 <param name="method" value="highest_intensity"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
989 <param name="use_exact_mass" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
990 <param name="exclude_ms2_precursor" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
991 <param name="precursor_mz_distance" value="0.0001"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
992 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
993 <param name="use_known_unknowns" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
994 <param name="min_transitions" value="2"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
995 <param name="max_transitions" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
996 <param name="cosine_similarity_threshold" value="0.98"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
997 <param name="transition_threshold" value="3.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
998 <section name="deisotoping">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
999 <param name="use_deisotoper" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 4
diff changeset
1000 <param name="fragment_tolerance" value="1.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1001 <param name="fragment_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1002 <param name="min_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1003 <param name="max_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1004 <param name="min_isopeaks" value="2"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1005 <param name="max_isopeaks" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1006 <param name="keep_only_deisotoped" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
1007 <param name="annotate_charge" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1008 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1009 <section name="preprocessing">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1010 <param name="filter_by_num_masstraces" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1011 <param name="precursor_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1012 <param name="precursor_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1013 <param name="precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1014 <param name="isotope_pattern_iterations" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1015 <param name="feature_only" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1016 <param name="no_masstrace_info_isotope_pattern" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 4
diff changeset
1017 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1018 <section name="project">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1019 <param name="processors" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1020 <param name="ignore_formula" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1021 <param name="q" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1022 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1023 <section name="sirius">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
1024 <param name="ppm_max" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1025 <param name="ppm_max_ms2" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1026 <param name="tree_timeout" value="0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1027 <param name="compound_timeout" value="100"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 4
diff changeset
1028 <param name="no_recalibration" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 4
diff changeset
1029 <param name="profile" value="qtof"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1030 <param name="formula" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 4
diff changeset
1031 <param name="ions_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1032 <param name="candidates" value="5"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 4
diff changeset
1033 <param name="candidates_per_ion" value="-1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 4
diff changeset
1034 <param name="elements_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1035 <param name="elements_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1036 <param name="no_isotope_score" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1037 <param name="no_isotope_filter" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1038 <param name="ions_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1039 <param name="db" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1040 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1041 <section name="fingerid">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1042 <param name="candidates" value="10"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1043 <param name="db" value="BIO"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1044 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1045 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1046 <output name="ctd_out" ftype="xml">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1047 <assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1048 <is_valid_xml/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1049 </assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1050 </output>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1051 </test>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1052 <!-- UTILS_AssayGeneratorMetabo_11 -->
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1053 <test expect_num_outputs="2">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1054 <section name="adv_opts">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1055 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1056 <param name="precursor_recalibration_window" value="0.01"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1057 <param name="precursor_recalibration_window_unit" value="Da"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1058 <param name="min_fragment_mz" value="100.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1059 <param name="max_fragment_mz" value="900.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1060 <param name="force" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1061 <param name="test" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1062 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1063 <conditional name="in_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1064 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1065 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1066 <conditional name="in_id_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1067 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1068 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1069 <param name="out_type" value="tsv"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1070 <output name="out" file="AssayGeneratorMetabo_ams_sirius_restrict_decoy_output.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1071 <param name="fragment_annotation" value="sirius"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1072 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1073 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1074 <param name="total_occurrence_filter" value="0.1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1075 <param name="fragment_annotation_score_threshold" value="0.8"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1076 <param name="decoy_generation" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1077 <param name="decoy_generation_method" value="original"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1078 <param name="method" value="highest_intensity"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1079 <param name="use_exact_mass" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1080 <param name="exclude_ms2_precursor" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1081 <param name="precursor_mz_distance" value="0.0001"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1082 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1083 <param name="use_known_unknowns" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1084 <param name="min_transitions" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1085 <param name="max_transitions" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1086 <param name="cosine_similarity_threshold" value="0.98"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1087 <param name="transition_threshold" value="3.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1088 <section name="deisotoping">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1089 <param name="use_deisotoper" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1090 <param name="fragment_tolerance" value="1.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1091 <param name="fragment_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1092 <param name="min_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1093 <param name="max_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1094 <param name="min_isopeaks" value="2"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1095 <param name="max_isopeaks" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1096 <param name="keep_only_deisotoped" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1097 <param name="annotate_charge" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1098 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1099 <section name="preprocessing">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 4
diff changeset
1100 <param name="filter_by_num_masstraces" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1101 <param name="precursor_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1102 <param name="precursor_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 4
diff changeset
1103 <param name="precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 4
diff changeset
1104 <param name="isotope_pattern_iterations" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1105 <param name="feature_only" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1106 <param name="no_masstrace_info_isotope_pattern" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 4
diff changeset
1107 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1108 <section name="project">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1109 <param name="processors" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 4
diff changeset
1110 <param name="ignore_formula" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 4
diff changeset
1111 <param name="q" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 4
diff changeset
1112 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1113 <section name="sirius">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1114 <param name="ppm_max" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 4
diff changeset
1115 <param name="ppm_max_ms2" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1116 <param name="tree_timeout" value="0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1117 <param name="compound_timeout" value="100"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1118 <param name="no_recalibration" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1119 <param name="profile" value="qtof"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1120 <param name="formula" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1121 <param name="ions_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1122 <param name="candidates" value="5"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1123 <param name="candidates_per_ion" value="-1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1124 <param name="elements_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1125 <param name="elements_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1126 <param name="no_isotope_score" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1127 <param name="no_isotope_filter" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1128 <param name="ions_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1129 <param name="db" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1130 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1131 <section name="fingerid">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1132 <param name="candidates" value="10"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1133 <param name="db" value="BIO"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1134 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1135 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1136 <output name="ctd_out" ftype="xml">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1137 <assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1138 <is_valid_xml/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1139 </assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1140 </output>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1141 </test>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1142 <!-- UTILS_AssayGeneratorMetabo_12 -->
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1143 <test expect_num_outputs="2">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1144 <section name="adv_opts">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1145 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1146 <param name="precursor_recalibration_window" value="0.01"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1147 <param name="precursor_recalibration_window_unit" value="Da"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1148 <param name="min_fragment_mz" value="100.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1149 <param name="max_fragment_mz" value="900.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1150 <param name="force" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1151 <param name="test" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1152 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1153 <conditional name="in_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1154 <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1155 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1156 <conditional name="in_id_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1157 <param name="in_id" value="AssayGeneratorMetabo_decoy_generation_input.featureXML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1158 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1159 <param name="out_type" value="tsv"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1160 <output name="out" file="AssayGeneratorMetabo_decoy_generation_output_original.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1161 <param name="fragment_annotation" value="sirius"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1162 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1163 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1164 <param name="total_occurrence_filter" value="0.1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1165 <param name="fragment_annotation_score_threshold" value="0.8"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1166 <param name="decoy_generation" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1167 <param name="decoy_generation_method" value="original"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1168 <param name="method" value="highest_intensity"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1169 <param name="use_exact_mass" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1170 <param name="exclude_ms2_precursor" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1171 <param name="precursor_mz_distance" value="0.0001"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1172 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1173 <param name="use_known_unknowns" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1174 <param name="min_transitions" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1175 <param name="max_transitions" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1176 <param name="cosine_similarity_threshold" value="0.98"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1177 <param name="transition_threshold" value="3.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1178 <section name="deisotoping">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1179 <param name="use_deisotoper" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1180 <param name="fragment_tolerance" value="1.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1181 <param name="fragment_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1182 <param name="min_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1183 <param name="max_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1184 <param name="min_isopeaks" value="2"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1185 <param name="max_isopeaks" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1186 <param name="keep_only_deisotoped" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1187 <param name="annotate_charge" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1188 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1189 <section name="preprocessing">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1190 <param name="filter_by_num_masstraces" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1191 <param name="precursor_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1192 <param name="precursor_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1193 <param name="precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1194 <param name="isotope_pattern_iterations" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1195 <param name="feature_only" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1196 <param name="no_masstrace_info_isotope_pattern" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1197 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1198 <section name="project">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1199 <param name="processors" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1200 <param name="ignore_formula" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1201 <param name="q" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1202 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1203 <section name="sirius">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1204 <param name="ppm_max" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1205 <param name="ppm_max_ms2" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1206 <param name="tree_timeout" value="0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1207 <param name="compound_timeout" value="100"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1208 <param name="no_recalibration" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1209 <param name="profile" value="qtof"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1210 <param name="formula" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1211 <param name="ions_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1212 <param name="candidates" value="5"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1213 <param name="candidates_per_ion" value="-1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1214 <param name="elements_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1215 <param name="elements_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1216 <param name="no_isotope_score" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1217 <param name="no_isotope_filter" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1218 <param name="ions_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1219 <param name="db" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1220 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1221 <section name="fingerid">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1222 <param name="candidates" value="10"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1223 <param name="db" value="BIO"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1224 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1225 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1226 <output name="ctd_out" ftype="xml">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1227 <assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1228 <is_valid_xml/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1229 </assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1230 </output>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1231 </test>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1232 <!-- UTILS_AssayGeneratorMetabo_13 -->
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1233 <test expect_num_outputs="2">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1234 <section name="adv_opts">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1235 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1236 <param name="precursor_recalibration_window" value="0.01"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1237 <param name="precursor_recalibration_window_unit" value="Da"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1238 <param name="min_fragment_mz" value="100.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1239 <param name="max_fragment_mz" value="900.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1240 <param name="force" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1241 <param name="test" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1242 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1243 <conditional name="in_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1244 <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1245 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1246 <conditional name="in_id_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1247 <param name="in_id" value="AssayGeneratorMetabo_decoy_generation_input.featureXML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1248 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1249 <param name="out_type" value="tsv"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1250 <output name="out" file="AssayGeneratorMetabo_decoy_generation_output_resolve_overlap.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1251 <param name="fragment_annotation" value="sirius"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1252 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1253 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1254 <param name="total_occurrence_filter" value="0.1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1255 <param name="fragment_annotation_score_threshold" value="0.8"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1256 <param name="decoy_generation" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1257 <param name="decoy_generation_method" value="resolve_overlap"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1258 <param name="method" value="highest_intensity"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1259 <param name="use_exact_mass" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1260 <param name="exclude_ms2_precursor" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1261 <param name="precursor_mz_distance" value="0.0001"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1262 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1263 <param name="use_known_unknowns" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1264 <param name="min_transitions" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1265 <param name="max_transitions" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1266 <param name="cosine_similarity_threshold" value="0.98"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1267 <param name="transition_threshold" value="3.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1268 <section name="deisotoping">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1269 <param name="use_deisotoper" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1270 <param name="fragment_tolerance" value="1.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1271 <param name="fragment_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1272 <param name="min_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1273 <param name="max_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1274 <param name="min_isopeaks" value="2"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1275 <param name="max_isopeaks" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1276 <param name="keep_only_deisotoped" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1277 <param name="annotate_charge" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1278 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1279 <section name="preprocessing">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1280 <param name="filter_by_num_masstraces" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1281 <param name="precursor_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1282 <param name="precursor_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1283 <param name="precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1284 <param name="isotope_pattern_iterations" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1285 <param name="feature_only" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1286 <param name="no_masstrace_info_isotope_pattern" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1287 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1288 <section name="project">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1289 <param name="processors" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1290 <param name="ignore_formula" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1291 <param name="q" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1292 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1293 <section name="sirius">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1294 <param name="ppm_max" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1295 <param name="ppm_max_ms2" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1296 <param name="tree_timeout" value="0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1297 <param name="compound_timeout" value="100"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1298 <param name="no_recalibration" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1299 <param name="profile" value="qtof"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1300 <param name="formula" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1301 <param name="ions_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1302 <param name="candidates" value="5"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1303 <param name="candidates_per_ion" value="-1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1304 <param name="elements_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1305 <param name="elements_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1306 <param name="no_isotope_score" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1307 <param name="no_isotope_filter" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1308 <param name="ions_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1309 <param name="db" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1310 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1311 <section name="fingerid">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1312 <param name="candidates" value="10"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1313 <param name="db" value="BIO"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1314 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1315 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1316 <output name="ctd_out" ftype="xml">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1317 <assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1318 <is_valid_xml/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1319 </assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1320 </output>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1321 </test>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1322 <!-- UTILS_AssayGeneratorMetabo_14 -->
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1323 <test expect_num_outputs="2">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1324 <section name="adv_opts">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1325 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1326 <param name="precursor_recalibration_window" value="0.01"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1327 <param name="precursor_recalibration_window_unit" value="Da"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1328 <param name="min_fragment_mz" value="100.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1329 <param name="max_fragment_mz" value="900.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1330 <param name="force" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1331 <param name="test" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1332 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1333 <conditional name="in_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1334 <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1335 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1336 <conditional name="in_id_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1337 <param name="in_id" value="AssayGeneratorMetabo_decoy_generation_input.featureXML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1338 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1339 <param name="out_type" value="tsv"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1340 <output name="out" file="AssayGeneratorMetabo_decoy_generation_output_add_shift.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1341 <param name="fragment_annotation" value="sirius"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1342 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1343 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1344 <param name="total_occurrence_filter" value="0.1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1345 <param name="fragment_annotation_score_threshold" value="0.8"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1346 <param name="decoy_generation" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1347 <param name="decoy_generation_method" value="add_shift"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1348 <param name="method" value="highest_intensity"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1349 <param name="use_exact_mass" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1350 <param name="exclude_ms2_precursor" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1351 <param name="precursor_mz_distance" value="0.0001"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1352 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 4
diff changeset
1353 <param name="use_known_unknowns" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 4
diff changeset
1354 <param name="min_transitions" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1355 <param name="max_transitions" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1356 <param name="cosine_similarity_threshold" value="0.98"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1357 <param name="transition_threshold" value="3.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1358 <section name="deisotoping">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 4
diff changeset
1359 <param name="use_deisotoper" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1360 <param name="fragment_tolerance" value="1.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1361 <param name="fragment_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1362 <param name="min_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1363 <param name="max_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1364 <param name="min_isopeaks" value="2"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1365 <param name="max_isopeaks" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1366 <param name="keep_only_deisotoped" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1367 <param name="annotate_charge" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1368 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1369 <section name="preprocessing">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1370 <param name="filter_by_num_masstraces" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1371 <param name="precursor_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1372 <param name="precursor_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1373 <param name="precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1374 <param name="isotope_pattern_iterations" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1375 <param name="feature_only" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1376 <param name="no_masstrace_info_isotope_pattern" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1377 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1378 <section name="project">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1379 <param name="processors" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1380 <param name="ignore_formula" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1381 <param name="q" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1382 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1383 <section name="sirius">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1384 <param name="ppm_max" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1385 <param name="ppm_max_ms2" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1386 <param name="tree_timeout" value="0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1387 <param name="compound_timeout" value="100"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1388 <param name="no_recalibration" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1389 <param name="profile" value="qtof"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1390 <param name="formula" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1391 <param name="ions_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1392 <param name="candidates" value="5"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1393 <param name="candidates_per_ion" value="-1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1394 <param name="elements_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1395 <param name="elements_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1396 <param name="no_isotope_score" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1397 <param name="no_isotope_filter" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1398 <param name="ions_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1399 <param name="db" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1400 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1401 <section name="fingerid">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1402 <param name="candidates" value="10"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1403 <param name="db" value="BIO"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1404 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1405 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1406 <output name="ctd_out" ftype="xml">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1407 <assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1408 <is_valid_xml/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1409 </assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1410 </output>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1411 </test>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1412 <!-- UTILS_AssayGeneratorMetabo_15 -->
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1413 <test expect_num_outputs="2">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1414 <section name="adv_opts">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1415 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1416 <param name="precursor_recalibration_window" value="0.01"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1417 <param name="precursor_recalibration_window_unit" value="Da"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1418 <param name="min_fragment_mz" value="100.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1419 <param name="max_fragment_mz" value="900.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1420 <param name="force" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1421 <param name="test" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1422 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1423 <conditional name="in_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1424 <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1425 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1426 <conditional name="in_id_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1427 <param name="in_id" value="AssayGeneratorMetabo_decoy_generation_input.featureXML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1428 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1429 <param name="out_type" value="tsv"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1430 <output name="out" file="AssayGeneratorMetabo_decoy_generation_output_both.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1431 <param name="fragment_annotation" value="sirius"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1432 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1433 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 4
diff changeset
1434 <param name="total_occurrence_filter" value="0.1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1435 <param name="fragment_annotation_score_threshold" value="0.8"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1436 <param name="decoy_generation" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1437 <param name="decoy_generation_method" value="both"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1438 <param name="method" value="highest_intensity"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1439 <param name="use_exact_mass" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1440 <param name="exclude_ms2_precursor" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 4
diff changeset
1441 <param name="precursor_mz_distance" value="0.0001"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1442 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1443 <param name="use_known_unknowns" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1444 <param name="min_transitions" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1445 <param name="max_transitions" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1446 <param name="cosine_similarity_threshold" value="0.98"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1447 <param name="transition_threshold" value="3.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1448 <section name="deisotoping">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1449 <param name="use_deisotoper" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1450 <param name="fragment_tolerance" value="1.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1451 <param name="fragment_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1452 <param name="min_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1453 <param name="max_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1454 <param name="min_isopeaks" value="2"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1455 <param name="max_isopeaks" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1456 <param name="keep_only_deisotoped" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1457 <param name="annotate_charge" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1458 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1459 <section name="preprocessing">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1460 <param name="filter_by_num_masstraces" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1461 <param name="precursor_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1462 <param name="precursor_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1463 <param name="precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1464 <param name="isotope_pattern_iterations" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1465 <param name="feature_only" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1466 <param name="no_masstrace_info_isotope_pattern" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1467 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1468 <section name="project">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1469 <param name="processors" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1470 <param name="ignore_formula" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1471 <param name="q" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1472 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1473 <section name="sirius">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1474 <param name="ppm_max" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1475 <param name="ppm_max_ms2" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1476 <param name="tree_timeout" value="0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1477 <param name="compound_timeout" value="100"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1478 <param name="no_recalibration" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1479 <param name="profile" value="qtof"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1480 <param name="formula" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1481 <param name="ions_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1482 <param name="candidates" value="5"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1483 <param name="candidates_per_ion" value="-1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1484 <param name="elements_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1485 <param name="elements_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1486 <param name="no_isotope_score" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1487 <param name="no_isotope_filter" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1488 <param name="ions_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1489 <param name="db" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1490 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1491 <section name="fingerid">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1492 <param name="candidates" value="10"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1493 <param name="db" value="BIO"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1494 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1495 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1496 <output name="ctd_out" ftype="xml">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1497 <assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1498 <is_valid_xml/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1499 </assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1500 </output>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1501 </test>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1502 <!-- UTILS_AssayGeneratorMetabo_16 -->
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1503 <test expect_num_outputs="2">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1504 <section name="adv_opts">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1505 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1506 <param name="precursor_recalibration_window" value="0.01"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1507 <param name="precursor_recalibration_window_unit" value="Da"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1508 <param name="min_fragment_mz" value="100.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1509 <param name="max_fragment_mz" value="900.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1510 <param name="force" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1511 <param name="test" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1512 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1513 <conditional name="in_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1514 <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1515 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1516 <conditional name="in_id_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1517 <param name="in_id" value="AssayGeneratorMetabo_decoy_generation_input_multids.featureXML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1518 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1519 <param name="out_type" value="tsv"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1520 <output name="out" file="AssayGeneratorMetabo_decoy_generation_output_both_multids.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1521 <param name="fragment_annotation" value="sirius"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1522 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1523 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1524 <param name="total_occurrence_filter" value="0.1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1525 <param name="fragment_annotation_score_threshold" value="0.8"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1526 <param name="decoy_generation" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1527 <param name="decoy_generation_method" value="both"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1528 <param name="method" value="highest_intensity"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1529 <param name="use_exact_mass" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1530 <param name="exclude_ms2_precursor" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1531 <param name="precursor_mz_distance" value="0.0001"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1532 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1533 <param name="use_known_unknowns" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1534 <param name="min_transitions" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1535 <param name="max_transitions" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1536 <param name="cosine_similarity_threshold" value="0.98"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1537 <param name="transition_threshold" value="3.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1538 <section name="deisotoping">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1539 <param name="use_deisotoper" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1540 <param name="fragment_tolerance" value="1.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1541 <param name="fragment_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1542 <param name="min_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1543 <param name="max_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1544 <param name="min_isopeaks" value="2"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1545 <param name="max_isopeaks" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1546 <param name="keep_only_deisotoped" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1547 <param name="annotate_charge" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1548 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1549 <section name="preprocessing">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1550 <param name="filter_by_num_masstraces" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1551 <param name="precursor_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1552 <param name="precursor_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1553 <param name="precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1554 <param name="isotope_pattern_iterations" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1555 <param name="feature_only" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1556 <param name="no_masstrace_info_isotope_pattern" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1557 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1558 <section name="project">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1559 <param name="processors" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1560 <param name="ignore_formula" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1561 <param name="q" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1562 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1563 <section name="sirius">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1564 <param name="ppm_max" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1565 <param name="ppm_max_ms2" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1566 <param name="tree_timeout" value="0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1567 <param name="compound_timeout" value="100"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1568 <param name="no_recalibration" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1569 <param name="profile" value="qtof"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1570 <param name="formula" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1571 <param name="ions_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1572 <param name="candidates" value="5"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1573 <param name="candidates_per_ion" value="-1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1574 <param name="elements_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1575 <param name="elements_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1576 <param name="no_isotope_score" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1577 <param name="no_isotope_filter" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1578 <param name="ions_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1579 <param name="db" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1580 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1581 <section name="fingerid">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1582 <param name="candidates" value="10"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1583 <param name="db" value="BIO"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1584 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1585 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1586 <output name="ctd_out" ftype="xml">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1587 <assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1588 <is_valid_xml/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1589 </assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1590 </output>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1591 </test>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1592 <!-- UTILS_AssayGeneratorMetabo_17 -->
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1593 <test expect_num_outputs="2">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1594 <section name="adv_opts">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1595 <param name="ambiguity_resolution_mz_tolerance_unit" value="Da"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1596 <param name="precursor_recalibration_window" value="0.01"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1597 <param name="precursor_recalibration_window_unit" value="Da"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1598 <param name="min_fragment_mz" value="0.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1599 <param name="max_fragment_mz" value="2000.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1600 <param name="force" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1601 <param name="test" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1602 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1603 <conditional name="in_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1604 <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML,AssayGeneratorMetabo_decoy_generation_input_2.mzML,AssayGeneratorMetabo_decoy_generation_input_3.mzML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1605 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1606 <conditional name="in_id_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1607 <param name="in_id" value="AssayGeneratorMetabo_decoy_generation_input.featureXML,AssayGeneratorMetabo_decoy_generation_input_1.featureXML,AssayGeneratorMetabo_decoy_generation_input_2.featureXML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1608 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1609 <param name="out_type" value="tsv"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1610 <output name="out" file="AssayGeneratorMetabo_decoy_generation_linking_output_both.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1611 <param name="fragment_annotation" value="sirius"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1612 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1613 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1614 <param name="total_occurrence_filter" value="0.8"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1615 <param name="fragment_annotation_score_threshold" value="0.8"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1616 <param name="decoy_generation" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1617 <param name="decoy_generation_method" value="both"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1618 <param name="method" value="highest_intensity"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1619 <param name="use_exact_mass" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1620 <param name="exclude_ms2_precursor" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1621 <param name="precursor_mz_distance" value="0.0001"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1622 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1623 <param name="use_known_unknowns" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1624 <param name="min_transitions" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1625 <param name="max_transitions" value="6"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1626 <param name="cosine_similarity_threshold" value="0.98"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1627 <param name="transition_threshold" value="3.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1628 <section name="deisotoping">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1629 <param name="use_deisotoper" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1630 <param name="fragment_tolerance" value="1.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1631 <param name="fragment_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1632 <param name="min_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1633 <param name="max_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1634 <param name="min_isopeaks" value="2"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1635 <param name="max_isopeaks" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1636 <param name="keep_only_deisotoped" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1637 <param name="annotate_charge" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1638 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1639 <section name="preprocessing">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1640 <param name="filter_by_num_masstraces" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1641 <param name="precursor_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1642 <param name="precursor_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1643 <param name="precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1644 <param name="isotope_pattern_iterations" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1645 <param name="feature_only" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1646 <param name="no_masstrace_info_isotope_pattern" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1647 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1648 <section name="project">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1649 <param name="processors" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1650 <param name="ignore_formula" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1651 <param name="q" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1652 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1653 <section name="sirius">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1654 <param name="ppm_max" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1655 <param name="ppm_max_ms2" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1656 <param name="tree_timeout" value="0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1657 <param name="compound_timeout" value="100"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1658 <param name="no_recalibration" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1659 <param name="profile" value="qtof"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1660 <param name="formula" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1661 <param name="ions_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1662 <param name="candidates" value="5"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1663 <param name="candidates_per_ion" value="-1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1664 <param name="elements_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1665 <param name="elements_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1666 <param name="no_isotope_score" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1667 <param name="no_isotope_filter" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1668 <param name="ions_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1669 <param name="db" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1670 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1671 <section name="fingerid">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1672 <param name="candidates" value="10"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1673 <param name="db" value="BIO"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1674 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1675 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1676 <output name="ctd_out" ftype="xml">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1677 <assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1678 <is_valid_xml/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1679 </assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1680 </output>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1681 </test>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1682 <!-- UTILS_AssayGeneratorMetabo_18 -->
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1683 <test expect_num_outputs="2">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1684 <section name="adv_opts">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1685 <param name="ambiguity_resolution_mz_tolerance_unit" value="Da"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1686 <param name="precursor_recalibration_window" value="0.01"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1687 <param name="precursor_recalibration_window_unit" value="Da"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1688 <param name="min_fragment_mz" value="0.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1689 <param name="max_fragment_mz" value="2000.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1690 <param name="force" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1691 <param name="test" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1692 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1693 <conditional name="in_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1694 <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML,AssayGeneratorMetabo_decoy_generation_input_2.mzML,AssayGeneratorMetabo_decoy_generation_input_3.mzML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1695 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1696 <conditional name="in_id_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1697 <param name="in_id" value="AssayGeneratorMetabo_decoy_generation_input.featureXML,AssayGeneratorMetabo_decoy_generation_input_1.featureXML,AssayGeneratorMetabo_decoy_generation_input_2.featureXML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1698 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1699 <param name="out_type" value="tsv"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1700 <output name="out" file="AssayGeneratorMetabo_decoy_generation_linking_moladd_output_both.tmp.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1701 <param name="fragment_annotation" value="sirius"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1702 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1703 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1704 <param name="total_occurrence_filter" value="0.1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1705 <param name="fragment_annotation_score_threshold" value="0.8"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1706 <param name="decoy_generation" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1707 <param name="decoy_generation_method" value="both"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1708 <param name="method" value="highest_intensity"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1709 <param name="use_exact_mass" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1710 <param name="exclude_ms2_precursor" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1711 <param name="precursor_mz_distance" value="0.0001"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1712 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1713 <param name="use_known_unknowns" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1714 <param name="min_transitions" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1715 <param name="max_transitions" value="6"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1716 <param name="cosine_similarity_threshold" value="0.98"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1717 <param name="transition_threshold" value="3.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1718 <section name="deisotoping">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1719 <param name="use_deisotoper" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1720 <param name="fragment_tolerance" value="1.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1721 <param name="fragment_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1722 <param name="min_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1723 <param name="max_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1724 <param name="min_isopeaks" value="2"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1725 <param name="max_isopeaks" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1726 <param name="keep_only_deisotoped" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1727 <param name="annotate_charge" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1728 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1729 <section name="preprocessing">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1730 <param name="filter_by_num_masstraces" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1731 <param name="precursor_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1732 <param name="precursor_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1733 <param name="precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1734 <param name="isotope_pattern_iterations" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1735 <param name="feature_only" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1736 <param name="no_masstrace_info_isotope_pattern" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1737 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1738 <section name="project">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1739 <param name="processors" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1740 <param name="ignore_formula" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1741 <param name="q" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1742 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1743 <section name="sirius">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1744 <param name="ppm_max" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1745 <param name="ppm_max_ms2" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1746 <param name="tree_timeout" value="0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1747 <param name="compound_timeout" value="100"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1748 <param name="no_recalibration" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1749 <param name="profile" value="qtof"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1750 <param name="formula" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1751 <param name="ions_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1752 <param name="candidates" value="5"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1753 <param name="candidates_per_ion" value="-1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1754 <param name="elements_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1755 <param name="elements_enforced" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1756 <param name="no_isotope_score" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1757 <param name="no_isotope_filter" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1758 <param name="ions_considered" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1759 <param name="db" value=""/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1760 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1761 <section name="fingerid">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1762 <param name="candidates" value="10"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1763 <param name="db" value="BIO"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1764 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
1765 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1766 <output name="ctd_out" ftype="xml">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1767 <assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1768 <is_valid_xml/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1769 </assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1770 </output>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1771 </test>
0
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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1772 </tests>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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1773 <help><![CDATA[Assay library generation from DDA data (Metabolomics)
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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1774
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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1775
5
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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1776 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_AssayGeneratorMetabo.html]]></help>
0
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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1777 <expand macro="references"/>
cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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1778 </tool>