Mercurial > repos > galaxyp > openms_siriusadapter

annotate SiriusAdapter.xml @ 9:0c27444604dd 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 19:16:56 +0000
parents 2d655933d65f
children b7505ec60b7d
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7c78a40e68d7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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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="SiriusAdapter" name="SiriusAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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5 <description>Tool for metabolite identification using single and tandem mass spectrometry</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">SiriusAdapter</token>
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8 <import>macros.xml</import>
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9 </macros>
4
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10 <expand macro="requirements"/>
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11 <expand macro="stdio"/>
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12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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13 @EXT_FOO@
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14 #import re
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15
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16 ## Preprocessing
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17 #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($sirius_executable.ext)' &&
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20 #end if
4
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21 mkdir in &&
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22 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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23 #if $in_featureinfo:
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24 mkdir in_featureinfo &&
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25 ln -s '$in_featureinfo' 'in_featureinfo/${re.sub("[^\w\-_]", "_", $in_featureinfo.element_identifier)}.$gxy2omsext($in_featureinfo.ext)' &&
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26 #end if
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27 #if "out_sirius_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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28 mkdir out_sirius &&
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29 #end if
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30 #if "out_fingerid_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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31 mkdir out_fingerid &&
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32 #end if
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33 #if "out_ms_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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34 mkdir out_ms &&
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35 #end if
4
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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($sirius_executable.ext)'
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46 #end if
4
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47 -in
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48 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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49 #if $in_featureinfo:
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50 -in_featureinfo
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51 'in_featureinfo/${re.sub("[^\w\-_]", "_", $in_featureinfo.element_identifier)}.$gxy2omsext($in_featureinfo.ext)'
0
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52 #end if
4
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53 #if "out_sirius_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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54 -out_sirius
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55 'out_sirius/output.${gxy2omsext("mztab")}'
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56 #end if
4
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57 #if "out_fingerid_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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58 -out_fingerid
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59 'out_fingerid/output.${gxy2omsext("mztab")}'
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60 #end if
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61 #if "out_ms_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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62 -out_ms
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63 'out_ms/output.${gxy2omsext("sirius.ms")}'
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64 #end if
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65 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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66 | tee '$stdout'
0
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67 #end if
4
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68
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69 ## Postprocessing
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70 #if "out_sirius_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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71 && mv 'out_sirius/output.${gxy2omsext("mztab")}' '$out_sirius'
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72 #end if
4
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73 #if "out_fingerid_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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74 && mv 'out_fingerid/output.${gxy2omsext("mztab")}' '$out_fingerid'
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75 #end if
4
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76 #if "out_ms_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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77 && mv 'out_ms/output.${gxy2omsext("sirius.ms")}' '$out_ms'
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78 #end if
4
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79 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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80 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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81 #end if]]></command>
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82 <configfiles>
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83 <inputs name="args_json" data_style="paths"/>
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84 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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85 </configfiles>
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86 <inputs>
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87 <param argument="-sirius_executable" type="data" format="txt" optional="true" value="sirius" 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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88 <param argument="-in" type="data" format="mzml" optional="false" label="MzML Input file" help=" select mzml data sets(s)"/>
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89 <param argument="-in_featureinfo" type="data" format="featurexml" optional="true" label="FeatureXML input with feature and adduct information" help=" select featurexml data sets(s)"/>
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90 <param argument="-out_project_space" type="text" optional="true" value="" label="Output directory for SIRIUS project space" help="">
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91 <expand macro="list_string_san" name="out_project_space"/>
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92 </param>
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93 <section name="preprocessing" title="" help="" expanded="false">
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94 <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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95 <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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96 <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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97 <option value="Da">Da</option>
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98 <option value="ppm" selected="true">ppm</option>
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99 <expand macro="list_string_san" name="precursor_mz_tolerance_unit"/>
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100 </param>
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101 <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=""/>
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102 <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"/>
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103 <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=""/>
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104 <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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105 </section>
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106 <section name="project" title="" help="" expanded="false">
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107 <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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108 <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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109 <param name="q" argument="-project:q" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress shell output" help=""/>
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110 </section>
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111 <section name="sirius" title="" help="" expanded="false">
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112 <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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113 <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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114 <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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115 <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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116 <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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117 <param name="profile" argument="-sirius:profile" type="select" optional="true" label="Name of the configuration profile" help="">
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118 <option value="default">default</option>
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119 <option value="qtof" selected="true">qtof</option>
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120 <option value="orbitrap">orbitrap</option>
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121 <option value="fticr">fticr</option>
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122 <expand macro="list_string_san" name="profile"/>
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123 </param>
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124 <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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125 <expand macro="list_string_san" name="formula"/>
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126 </param>
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127 <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">
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128 <expand macro="list_string_san" name="ions_enforced"/>
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129 </param>
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130 <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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131 <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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132 <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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133 <expand macro="list_string_san" name="elements_considered"/>
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134 </param>
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135 <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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136 <expand macro="list_string_san" name="elements_enforced"/>
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137 </param>
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138 <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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139 <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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140 <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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141 <expand macro="list_string_san" name="ions_considered"/>
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142 </param>
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143 <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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144 <expand macro="list_string_san" name="db"/>
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145 </param>
9
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146 </section>
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147 <section name="fingerid" title="" help="" expanded="false">
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148 <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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149 <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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150 <expand macro="list_string_san" name="db"/>
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151 </param>
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152 </section>
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153 <expand macro="adv_opts_macro">
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154 <param argument="-converter_mode" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use this flag in combination with the out_ms file to convert the input mzML and featureXML to a .ms file" help="Without further SIRIUS processing"/>
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155 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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156 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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157 <expand macro="list_string_san" name="test"/>
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158 </param>
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159 </expand>
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160 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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161 <option value="out_sirius_FLAG">out_sirius (MzTab output file for SIRIUS results)</option>
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162 <option value="out_fingerid_FLAG">out_fingerid (MzTab output file for CSI:FingerID, if this parameter is given, SIRIUS will search for a molecular structure using CSI:FingerID after determining the sum formula)</option>
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163 <option value="out_ms_FLAG">out_ms (Internal SIRIUS .ms format after OpenMS preprocessing)</option>
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164 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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165 </param>
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166 </inputs>
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167 <outputs>
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168 <data name="out_sirius" label="${tool.name} on ${on_string}: out_sirius" format="mztab">
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169 <filter>OPTIONAL_OUTPUTS is not None and "out_sirius_FLAG" in OPTIONAL_OUTPUTS</filter>
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170 </data>
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171 <data name="out_fingerid" label="${tool.name} on ${on_string}: out_fingerid" format="mztab">
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172 <filter>OPTIONAL_OUTPUTS is not None and "out_fingerid_FLAG" in OPTIONAL_OUTPUTS</filter>
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173 </data>
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174 <data name="out_ms" label="${tool.name} on ${on_string}: out_ms" format="sirius.ms">
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175 <filter>OPTIONAL_OUTPUTS is not None and "out_ms_FLAG" in OPTIONAL_OUTPUTS</filter>
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176 </data>
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177 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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178 <filter>OPTIONAL_OUTPUTS is None</filter>
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179 </data>
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180 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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181 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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182 </data>
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183 </outputs>
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184 <tests><!-- TOPP_SiriusAdapter_1 -->
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185 <test expect_num_outputs="2">
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186 <section name="adv_opts">
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187 <param name="converter_mode" value="false"/>
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188 <param name="force" value="false"/>
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189 <param name="test" value="true"/>
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190 </section>
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191 <param name="in" value="SiriusAdapter_1_input.mzML"/>
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192 <output name="out_sirius" file="SiriusAdapter_1_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
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193 <param name="out_project_space" value=""/>
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194 <section name="preprocessing">
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195 <param name="filter_by_num_masstraces" value="1"/>
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196 <param name="precursor_mz_tolerance" value="10.0"/>
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197 <param name="precursor_mz_tolerance_unit" value="ppm"/>
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198 <param name="precursor_rt_tolerance" value="5.0"/>
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199 <param name="isotope_pattern_iterations" value="3"/>
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200 <param name="feature_only" value="false"/>
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201 <param name="no_masstrace_info_isotope_pattern" value="false"/>
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202 </section>
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203 <section name="project">
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204 <param name="processors" value="1"/>
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205 <param name="ignore_formula" value="false"/>
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206 <param name="q" value="false"/>
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207 </section>
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208 <section name="sirius">
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209 <param name="ppm_max" value="10.0"/>
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210 <param name="ppm_max_ms2" value="10.0"/>
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211 <param name="tree_timeout" value="0"/>
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212 <param name="compound_timeout" value="100"/>
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213 <param name="no_recalibration" value="false"/>
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214 <param name="profile" value="qtof"/>
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215 <param name="formula" value=""/>
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216 <param name="ions_enforced" value=""/>
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217 <param name="candidates" value="5"/>
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218 <param name="candidates_per_ion" value="-1"/>
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219 <param name="elements_considered" value=""/>
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220 <param name="elements_enforced" value=""/>
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221 <param name="no_isotope_score" value="false"/>
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222 <param name="no_isotope_filter" value="false"/>
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223 <param name="ions_considered" value=""/>
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224 <param name="db" value="all"/>
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225 </section>
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226 <section name="fingerid">
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227 <param name="candidates" value="10"/>
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228 <param name="db" value="BIO"/>
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229 </section>
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230 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
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231 <output name="ctd_out" ftype="xml">
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232 <assert_contents>
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233 <is_valid_xml/>
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234 </assert_contents>
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235 </output>
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236 </test>
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237 <!-- TOPP_SiriusAdapter_2 -->
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238 <test expect_num_outputs="2">
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239 <section name="adv_opts">
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240 <param name="converter_mode" value="false"/>
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241 <param name="force" value="false"/>
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242 <param name="test" value="true"/>
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243 </section>
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244 <param name="in" value="SiriusAdapter_2_input.mzML"/>
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245 <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/>
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246 <output name="out_sirius" file="SiriusAdapter_2_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
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247 <param name="out_project_space" value=""/>
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248 <section name="preprocessing">
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249 <param name="filter_by_num_masstraces" value="3"/>
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250 <param name="precursor_mz_tolerance" value="10.0"/>
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251 <param name="precursor_mz_tolerance_unit" value="ppm"/>
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252 <param name="precursor_rt_tolerance" value="5.0"/>
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253 <param name="isotope_pattern_iterations" value="3"/>
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254 <param name="feature_only" value="true"/>
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255 <param name="no_masstrace_info_isotope_pattern" value="false"/>
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256 </section>
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257 <section name="project">
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258 <param name="processors" value="1"/>
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259 <param name="ignore_formula" value="false"/>
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260 <param name="q" value="false"/>
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261 </section>
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262 <section name="sirius">
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263 <param name="ppm_max" value="10.0"/>
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264 <param name="ppm_max_ms2" value="10.0"/>
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265 <param name="tree_timeout" value="0"/>
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266 <param name="compound_timeout" value="100"/>
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267 <param name="no_recalibration" value="false"/>
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268 <param name="profile" value="qtof"/>
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269 <param name="formula" value=""/>
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270 <param name="ions_enforced" value=""/>
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271 <param name="candidates" value="5"/>
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272 <param name="candidates_per_ion" value="-1"/>
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273 <param name="elements_considered" value=""/>
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274 <param name="elements_enforced" value=""/>
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275 <param name="no_isotope_score" value="false"/>
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276 <param name="no_isotope_filter" value="false"/>
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277 <param name="ions_considered" value=""/>
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278 <param name="db" value="all"/>
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279 </section>
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280 <section name="fingerid">
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281 <param name="candidates" value="10"/>
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282 <param name="db" value="BIO"/>
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283 </section>
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284 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
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285 <output name="ctd_out" ftype="xml">
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286 <assert_contents>
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287 <is_valid_xml/>
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288 </assert_contents>
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289 </output>
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290 </test>
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291 <!-- TOPP_SiriusAdapter_3 -->
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292 <test expect_num_outputs="2">
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293 <section name="adv_opts">
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294 <param name="converter_mode" value="false"/>
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295 <param name="force" value="false"/>
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296 <param name="test" value="true"/>
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297 </section>
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298 <param name="in" value="SiriusAdapter_3_input.mzML"/>
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299 <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/>
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300 <output name="out_sirius" file="SiriusAdapter_3_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
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301 <param name="out_project_space" value=""/>
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302 <section name="preprocessing">
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303 <param name="filter_by_num_masstraces" value="3"/>
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304 <param name="precursor_mz_tolerance" value="10.0"/>
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305 <param name="precursor_mz_tolerance_unit" value="ppm"/>
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306 <param name="precursor_rt_tolerance" value="5.0"/>
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307 <param name="isotope_pattern_iterations" value="3"/>
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308 <param name="feature_only" value="false"/>
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309 <param name="no_masstrace_info_isotope_pattern" value="false"/>
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310 </section>
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311 <section name="project">
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312 <param name="processors" value="1"/>
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313 <param name="ignore_formula" value="false"/>
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314 <param name="q" value="false"/>
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315 </section>
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diff changeset
316 <section name="sirius">
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galaxyp
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317 <param name="ppm_max" value="10.0"/>
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galaxyp
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318 <param name="ppm_max_ms2" value="10.0"/>
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319 <param name="tree_timeout" value="0"/>
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galaxyp
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320 <param name="compound_timeout" value="100"/>
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galaxyp
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321 <param name="no_recalibration" value="false"/>
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galaxyp
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322 <param name="profile" value="qtof"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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323 <param name="formula" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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324 <param name="ions_enforced" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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325 <param name="candidates" value="5"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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326 <param name="candidates_per_ion" value="-1"/>
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galaxyp
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327 <param name="elements_considered" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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328 <param name="elements_enforced" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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329 <param name="no_isotope_score" value="false"/>
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330 <param name="no_isotope_filter" value="false"/>
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galaxyp
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331 <param name="ions_considered" value=""/>
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332 <param name="db" value="all"/>
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333 </section>
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334 <section name="fingerid">
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galaxyp
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335 <param name="candidates" value="10"/>
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336 <param name="db" value="BIO"/>
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337 </section>
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338 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
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339 <output name="ctd_out" ftype="xml">
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340 <assert_contents>
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341 <is_valid_xml/>
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342 </assert_contents>
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343 </output>
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344 </test>
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345 <!-- TOPP_SiriusAdapter_5 -->
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346 <test expect_num_outputs="2">
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347 <section name="adv_opts">
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348 <param name="converter_mode" value="true"/>
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349 <param name="force" value="false"/>
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350 <param name="test" value="true"/>
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351 </section>
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352 <param name="in" value="SiriusAdapter_3_input.mzML"/>
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353 <param name="in_featureinfo" value="SiriusAdapter_3_input.featureXML"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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354 <output name="out_ms" file="SiriusAdapter_5_output.ms" compare="sim_size" delta_frac="0.7" ftype="sirius.ms"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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355 <param name="out_project_space" value=""/>
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356 <section name="preprocessing">
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357 <param name="filter_by_num_masstraces" value="1"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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358 <param name="precursor_mz_tolerance" value="10.0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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359 <param name="precursor_mz_tolerance_unit" value="ppm"/>
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360 <param name="precursor_rt_tolerance" value="5.0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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361 <param name="isotope_pattern_iterations" value="3"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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362 <param name="feature_only" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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363 <param name="no_masstrace_info_isotope_pattern" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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364 </section>
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365 <section name="project">
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366 <param name="processors" value="1"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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367 <param name="ignore_formula" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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368 <param name="q" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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369 </section>
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galaxyp
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diff changeset
370 <section name="sirius">
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galaxyp
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diff changeset
371 <param name="ppm_max" value="10.0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
372 <param name="ppm_max_ms2" value="10.0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
373 <param name="tree_timeout" value="0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
374 <param name="compound_timeout" value="100"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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375 <param name="no_recalibration" value="false"/>
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galaxyp
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diff changeset
376 <param name="profile" value="qtof"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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377 <param name="formula" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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378 <param name="ions_enforced" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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379 <param name="candidates" value="5"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
380 <param name="candidates_per_ion" value="-1"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
381 <param name="elements_considered" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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382 <param name="elements_enforced" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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383 <param name="no_isotope_score" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
384 <param name="no_isotope_filter" value="false"/>
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385 <param name="ions_considered" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
386 <param name="db" value=""/>
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387 </section>
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diff changeset
388 <section name="fingerid">
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389 <param name="candidates" value="10"/>
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diff changeset
390 <param name="db" value="BIO"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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391 </section>
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diff changeset
392 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_ms_FLAG"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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393 <output name="ctd_out" ftype="xml">
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394 <assert_contents>
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395 <is_valid_xml/>
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396 </assert_contents>
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397 </output>
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398 </test>
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399 <!-- TOPP_SiriusAdapter_6 -->
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400 <test expect_num_outputs="2">
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diff changeset
401 <section name="adv_opts">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
402 <param name="converter_mode" value="true"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
403 <param name="force" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
404 <param name="test" value="true"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
405 </section>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
406 <param name="in" value="SiriusAdapter_4_input.mzML"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
407 <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
408 <output name="out_ms" file="SiriusAdapter_6_output.ms" compare="sim_size" delta_frac="0.7" ftype="sirius.ms"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
409 <param name="out_project_space" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
410 <section name="preprocessing">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
411 <param name="filter_by_num_masstraces" value="1"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
412 <param name="precursor_mz_tolerance" value="10.0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
413 <param name="precursor_mz_tolerance_unit" value="ppm"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
414 <param name="precursor_rt_tolerance" value="5.0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
415 <param name="isotope_pattern_iterations" value="3"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
416 <param name="feature_only" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
417 <param name="no_masstrace_info_isotope_pattern" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
418 </section>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
419 <section name="project">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
420 <param name="processors" value="1"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
421 <param name="ignore_formula" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
422 <param name="q" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
423 </section>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
424 <section name="sirius">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
425 <param name="ppm_max" value="10.0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
426 <param name="ppm_max_ms2" value="10.0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
427 <param name="tree_timeout" value="0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
428 <param name="compound_timeout" value="100"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
429 <param name="no_recalibration" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
430 <param name="profile" value="qtof"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
431 <param name="formula" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
432 <param name="ions_enforced" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
433 <param name="candidates" value="5"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
434 <param name="candidates_per_ion" value="-1"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
435 <param name="elements_considered" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
436 <param name="elements_enforced" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
437 <param name="no_isotope_score" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
438 <param name="no_isotope_filter" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
439 <param name="ions_considered" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
440 <param name="db" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
441 </section>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
442 <section name="fingerid">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
443 <param name="candidates" value="10"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
444 <param name="db" value="BIO"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
445 </section>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
446 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_ms_FLAG"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
447 <output name="ctd_out" ftype="xml">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
448 <assert_contents>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
449 <is_valid_xml/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
450 </assert_contents>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
451 </output>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
452 </test>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
453 <!-- TOPP_SiriusAdapter_8 -->
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
454 <test expect_num_outputs="2">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
455 <section name="adv_opts">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
456 <param name="converter_mode" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
457 <param name="force" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
458 <param name="test" value="true"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
459 </section>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
460 <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
461 <param name="in_featureinfo" value="AssayGeneratorMetabo_decoy_generation_input_multids.featureXML"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
462 <output name="out_sirius" file="SiriusAdapter_8_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
463 <param name="out_project_space" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
464 <section name="preprocessing">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
465 <param name="filter_by_num_masstraces" value="1"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
466 <param name="precursor_mz_tolerance" value="10.0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
467 <param name="precursor_mz_tolerance_unit" value="ppm"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
468 <param name="precursor_rt_tolerance" value="5.0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
469 <param name="isotope_pattern_iterations" value="3"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
470 <param name="feature_only" value="true"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
471 <param name="no_masstrace_info_isotope_pattern" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
472 </section>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
473 <section name="project">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
474 <param name="processors" value="1"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
475 <param name="ignore_formula" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
476 <param name="q" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
477 </section>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
478 <section name="sirius">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
479 <param name="ppm_max" value="10.0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
480 <param name="ppm_max_ms2" value="10.0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
481 <param name="tree_timeout" value="0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
482 <param name="compound_timeout" value="100"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
483 <param name="no_recalibration" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
484 <param name="profile" value="qtof"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
485 <param name="formula" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
486 <param name="ions_enforced" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
487 <param name="candidates" value="5"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
488 <param name="candidates_per_ion" value="-1"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
489 <param name="elements_considered" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
490 <param name="elements_enforced" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
491 <param name="no_isotope_score" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
492 <param name="no_isotope_filter" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
493 <param name="ions_considered" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
494 <param name="db" value="all"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
495 </section>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
496 <section name="fingerid">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
497 <param name="candidates" value="10"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
498 <param name="db" value="BIO"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
499 </section>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
500 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
501 <output name="ctd_out" ftype="xml">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
502 <assert_contents>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
503 <is_valid_xml/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
504 </assert_contents>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
505 </output>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
506 </test>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
507 <!-- TOPP_SiriusAdapter_9 -->
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
508 <test expect_num_outputs="2">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
509 <section name="adv_opts">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
510 <param name="converter_mode" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
511 <param name="force" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
512 <param name="test" value="true"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
513 </section>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
514 <param name="in" value="AssayGeneratorMetabo_decoy_generation_input.mzML"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
515 <param name="in_featureinfo" value="AssayGeneratorMetabo_decoy_generation_input_multids.featureXML"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
516 <output name="out_sirius" file="SiriusAdapter_9_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
517 <param name="out_project_space" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
518 <section name="preprocessing">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
519 <param name="filter_by_num_masstraces" value="1"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
520 <param name="precursor_mz_tolerance" value="10.0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
521 <param name="precursor_mz_tolerance_unit" value="ppm"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
522 <param name="precursor_rt_tolerance" value="5.0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
523 <param name="isotope_pattern_iterations" value="3"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
524 <param name="feature_only" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
525 <param name="no_masstrace_info_isotope_pattern" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
526 </section>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
527 <section name="project">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
528 <param name="processors" value="1"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
529 <param name="ignore_formula" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
530 <param name="q" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
531 </section>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
532 <section name="sirius">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
533 <param name="ppm_max" value="10.0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
534 <param name="ppm_max_ms2" value="10.0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
535 <param name="tree_timeout" value="0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
536 <param name="compound_timeout" value="100"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
537 <param name="no_recalibration" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
538 <param name="profile" value="qtof"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
539 <param name="formula" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
540 <param name="ions_enforced" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
541 <param name="candidates" value="5"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
542 <param name="candidates_per_ion" value="-1"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
543 <param name="elements_considered" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
544 <param name="elements_enforced" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
545 <param name="no_isotope_score" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
546 <param name="no_isotope_filter" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
547 <param name="ions_considered" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
548 <param name="db" value="all"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
549 </section>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
550 <section name="fingerid">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
551 <param name="candidates" value="10"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
552 <param name="db" value="BIO"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
553 </section>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
554 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
555 <output name="ctd_out" ftype="xml">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
556 <assert_contents>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
557 <is_valid_xml/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
558 </assert_contents>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
559 </output>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
560 </test>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
561 <!-- TOPP_SiriusAdapter_7 -->
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
562 <test expect_num_outputs="2">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
563 <section name="adv_opts">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
564 <param name="converter_mode" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
565 <param name="force" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
566 <param name="test" value="true"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
567 </section>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
568 <param name="in" value="SiriusAdapter_4_input.mzML"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
569 <param name="in_featureinfo" value="SiriusAdapter_4_input.featureXML"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
570 <output name="out_sirius" file="SiriusAdapter_7_output.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
571 <param name="out_project_space" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
572 <section name="preprocessing">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
573 <param name="filter_by_num_masstraces" value="1"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
574 <param name="precursor_mz_tolerance" value="10.0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
575 <param name="precursor_mz_tolerance_unit" value="ppm"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
576 <param name="precursor_rt_tolerance" value="5.0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
577 <param name="isotope_pattern_iterations" value="3"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
578 <param name="feature_only" value="true"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
579 <param name="no_masstrace_info_isotope_pattern" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
580 </section>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
581 <section name="project">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
582 <param name="processors" value="1"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
583 <param name="ignore_formula" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
584 <param name="q" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
585 </section>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
586 <section name="sirius">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
587 <param name="ppm_max" value="10.0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
588 <param name="ppm_max_ms2" value="10.0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
589 <param name="tree_timeout" value="0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
590 <param name="compound_timeout" value="100"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
591 <param name="no_recalibration" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
592 <param name="profile" value="qtof"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
593 <param name="formula" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
594 <param name="ions_enforced" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
595 <param name="candidates" value="5"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
596 <param name="candidates_per_ion" value="-1"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
597 <param name="elements_considered" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
598 <param name="elements_enforced" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
599 <param name="no_isotope_score" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
600 <param name="no_isotope_filter" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
601 <param name="ions_considered" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
602 <param name="db" value="all"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
603 </section>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
604 <section name="fingerid">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
605 <param name="candidates" value="10"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
606 <param name="db" value="BIO"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
607 </section>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
608 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
609 <output name="ctd_out" ftype="xml">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
610 <assert_contents>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
611 <is_valid_xml/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
612 </assert_contents>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
613 </output>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
614 </test>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
615 <!-- TOPP_SiriusAdapter_4 -->
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
616 <test expect_num_outputs="3">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
617 <section name="adv_opts">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
618 <param name="converter_mode" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
619 <param name="force" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
620 <param name="test" value="true"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
621 </section>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
622 <param name="in" value="SiriusAdapter_2_input.mzML"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
623 <param name="in_featureinfo" value="SiriusAdapter_2_input.featureXML"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
624 <output name="out_sirius" file="SiriusAdapter_4_output.tmp" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
625 <output name="out_fingerid" file="SiriusAdapter_4_foutput.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
626 <param name="out_project_space" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
627 <section name="preprocessing">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
628 <param name="filter_by_num_masstraces" value="1"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
629 <param name="precursor_mz_tolerance" value="10.0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
630 <param name="precursor_mz_tolerance_unit" value="ppm"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
631 <param name="precursor_rt_tolerance" value="5.0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
632 <param name="isotope_pattern_iterations" value="3"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
633 <param name="feature_only" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
634 <param name="no_masstrace_info_isotope_pattern" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
635 </section>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
636 <section name="project">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
637 <param name="processors" value="1"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
638 <param name="ignore_formula" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
639 <param name="q" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
640 </section>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
641 <section name="sirius">
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
642 <param name="ppm_max" value="10.0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
643 <param name="ppm_max_ms2" value="10.0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
644 <param name="tree_timeout" value="0"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
645 <param name="compound_timeout" value="100"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
646 <param name="no_recalibration" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
647 <param name="profile" value="qtof"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
648 <param name="formula" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
649 <param name="ions_enforced" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
650 <param name="candidates" value="5"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
651 <param name="candidates_per_ion" value="-1"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
652 <param name="elements_considered" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
653 <param name="elements_enforced" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
654 <param name="no_isotope_score" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
655 <param name="no_isotope_filter" value="false"/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
656 <param name="ions_considered" value=""/>
0c27444604dd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 8
diff changeset
657 <param name="db" value="ALL"/>
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658 </section>
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659 <section name="fingerid">
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660 <param name="candidates" value="10"/>
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661 <param name="db" value="BIO"/>
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662 </section>
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663 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_sirius_FLAG,out_fingerid_FLAG"/>
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664 <output name="ctd_out" ftype="xml">
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665 <assert_contents>
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666 <is_valid_xml/>
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667 </assert_contents>
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668 </output>
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669 </test>
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670 </tests>
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671 <help><![CDATA[Tool for metabolite identification using single and tandem mass spectrometry
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672
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673
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674 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SiriusAdapter.html]]></help>
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675 <expand macro="references"/>
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676 </tool>