Mercurial > repos > galaxyp > openms_assaygeneratormetabo

annotate AssayGeneratorMetabo.xml @ 6:f3ec820189ca draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:29:08 +0000
parents 83f5e5c1209c
children
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cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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1 <!--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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2 <!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
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3 <tool id="AssayGeneratorMetabo" name="AssayGeneratorMetabo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Assay library generation from DDA data (Metabolomics)</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">AssayGeneratorMetabo</token>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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12 @EXT_FOO@
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13 #import re
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cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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15 ## Preprocessing
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16 mkdir in_cond.in &&
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17 #if $in_cond.in_select == "no"
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18 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
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19 ${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
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20 #else
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21 cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
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22 #end if
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23 mkdir in_id_cond.in_id &&
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24 #if $in_id_cond.in_id_select == "no"
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25 mkdir ${' '.join(["'in_id_cond.in_id/%s'" % (i) for i, f in enumerate($in_id_cond.in_id) if f])} &&
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26 ${' '.join(["cp '%s' 'in_id_cond.in_id/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_id_cond.in_id) if f])}
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27 #else
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28 cp '$in_id_cond.in_id' 'in_id_cond.in_id/${re.sub("[^\w\-_]", "_", $in_id_cond.in_id.element_identifier)}.$gxy2omsext($in_id_cond.in_id.ext)' &&
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29 #end if
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30 mkdir out &&
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32 ## Main program call
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cb9d2162b340 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
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34 set -o pipefail &&
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35 @EXECUTABLE@ -write_ctd ./ &&
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36 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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37 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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38 -in
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39 #if $in_cond.in_select == "no"
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40 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
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41 #else
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42 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
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43 #end if
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44 -in_id
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45 #if $in_id_cond.in_id_select == "no"
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46 ${' '.join(["'in_id_cond.in_id/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_id_cond.in_id) if f])}
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47 #else
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48 'in_id_cond.in_id/${re.sub("[^\w\-_]", "_", $in_id_cond.in_id.element_identifier)}.$gxy2omsext($in_id_cond.in_id.ext)'
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49 #end if
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50 -out
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51 'out/output.${out_type}'
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52
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53 ## Postprocessing
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54 && mv 'out/output.${out_type}' '$out'
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55 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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56 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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57 #end if]]></command>
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58 <configfiles>
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59 <inputs name="args_json" data_style="paths"/>
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60 <configfile name="hardcoded_json"><![CDATA[{"sirius_executable": "\$(which sirius)", "out_workspace_directory": "__SIRIUS_WORKSPACE__", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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61 </configfiles>
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62 <inputs>
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63 <conditional name="in_cond">
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64 <param name="in_select" type="select" label="Run tool in batch mode for -in">
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65 <option value="no">No: process all datasets jointly</option>
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66 <option value="yes">Yes: process each dataset in an independent job</option>
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67 </param>
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68 <when value="no">
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69 <param argument="-in" type="data" format="mzml" multiple="true" label="MzML input file(s) used for assay library generation" help=" select mzml data sets(s)"/>
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70 </when>
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71 <when value="yes">
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72 <param argument="-in" type="data" format="mzml" label="MzML input file(s) used for assay library generation" help=" select mzml data sets(s)"/>
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73 </when>
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74 </conditional>
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75 <conditional name="in_id_cond">
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76 <param name="in_id_select" type="select" label="Run tool in batch mode for -in_id">
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77 <option value="no">No: process all datasets jointly</option>
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78 <option value="yes">Yes: process each dataset in an independent job</option>
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79 </param>
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80 <when value="no">
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81 <param argument="-in_id" type="data" format="featurexml" multiple="true" label="FeatureXML input file(s) containing identification information" help="(e.g. AccurateMassSearch) select featurexml data sets(s)"/>
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82 </when>
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83 <when value="yes">
6
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84 <param argument="-in_id" type="data" format="featurexml" label="FeatureXML input file(s) containing identification information" help="(e.g. AccurateMassSearch) select featurexml data sets(s)"/>
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85 </when>
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86 </conditional>
6
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87 <param name="out_type" type="select" label="File type of output out (Assay library output file)">
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88 <option value="tsv">tabular (tsv)</option>
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89 <option value="traML">traml</option>
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90 <option value="pqp">pqp</option>
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91 </param>
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92 <param argument="-fragment_annotation" type="select" label="Fragment annotation method" help="">
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93 <option value="none">none</option>
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94 <option value="sirius" selected="true">sirius</option>
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95 <expand macro="list_string_san" name="fragment_annotation"/>
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96 </param>
6
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97 <param argument="-ambiguity_resolution_mz_tolerance" type="float" value="10.0" label="Mz tolerance for the resolution of identification ambiguity over multiple files" help=""/>
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98 <param argument="-ambiguity_resolution_rt_tolerance" type="float" value="10.0" label="RT tolerance in seconds for the resolution of identification ambiguity over multiple files" help=""/>
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99 <param argument="-total_occurrence_filter" type="float" min="0.0" max="1.0" value="0.1" label="Filter compound based on total occurrence in analysed samples" help=""/>
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100 <param argument="-fragment_annotation_score_threshold" type="float" min="0.0" max="1.0" value="0.8" label="Filters annotations based on the explained intensity of the peaks in a spectrum" help=""/>
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101 <param argument="-decoy_generation" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Decoys will be generated using the fragmentation tree re-rooting approach" help="This option does only work in combination with the fragment annotation via Sirius"/>
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102 <param argument="-decoy_generation_method" type="select" label="Uses different methods for decoy generation" help="Basis for the method is the fragmentation-tree re-rooting approach ('original'). This approach can be extended by using 'resolve_overlap', which will resolve overlapping fragments of the highest intensity fragments chosen, by adding -CH2 mass to the overlapping fragments. 'Add_shift' will add a -CH2 mass shift to the target fragments and use them as additional decoys if fragmentation-tree re-rooting failed. 'Both' combines the extended methods (resolve_overlap, add_shift)">
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103 <option value="original" selected="true">original</option>
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104 <option value="resolve_overlap">resolve_overlap</option>
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105 <option value="add_shift">add_shift</option>
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106 <option value="both">both</option>
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107 <expand macro="list_string_san" name="decoy_generation_method"/>
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108 </param>
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109 <param argument="-method" type="select" label="Spectrum with the highest precursor intensity or a consensus spectrum is used for assay library construction (if no fragment annotation is used)" help="">
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110 <option value="highest_intensity" selected="true">highest_intensity</option>
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111 <option value="consensus_spectrum">consensus_spectrum</option>
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112 <expand macro="list_string_san" name="method"/>
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113 </param>
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114 <param argument="-use_exact_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use exact mass for precursor and fragment annotations" help=""/>
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115 <param argument="-exclude_ms2_precursor" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Excludes precursor in ms2 from transition list" help=""/>
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116 <param argument="-precursor_mz_distance" type="float" value="0.0001" label="Max m/z distance of the precursor entries of two spectra to be merged in [Da]" help=""/>
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117 <param argument="-consensus_spectrum_precursor_rt_tolerance" type="float" value="5.0" label="Tolerance window (left and right) for precursor selection [seconds], for consensus spectrum generation (only available without fragment annotation)" help=""/>
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118 <param argument="-use_known_unknowns" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use features without identification information" help=""/>
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119 <param argument="-min_transitions" type="integer" value="3" label="Minimal number of transitions" help=""/>
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120 <param argument="-max_transitions" type="integer" value="6" label="Maximal number of transitions" help=""/>
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121 <param argument="-cosine_similarity_threshold" type="float" value="0.98" label="Threshold for cosine similarity of MS2 spectra from the same precursor used in consensus spectrum creation" help=""/>
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122 <param argument="-transition_threshold" type="float" value="5.0" label="Further transitions need at least x% of the maximum intensity (default 5%)" help=""/>
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123 <section name="deisotoping" title="deisotoping" help="" expanded="false">
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124 <param name="use_deisotoper" argument="-deisotoping:use_deisotoper" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use Deisotoper (if no fragment annotation is used)" help=""/>
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125 <param name="fragment_tolerance" argument="-deisotoping:fragment_tolerance" type="float" value="1.0" label="Tolerance used to match isotopic peaks" help=""/>
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126 <param name="fragment_unit" argument="-deisotoping:fragment_unit" type="select" label="Unit of the fragment tolerance" help="">
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127 <option value="ppm" selected="true">ppm</option>
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128 <option value="Da">Da</option>
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129 <expand macro="list_string_san" name="fragment_unit"/>
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130 </param>
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131 <param name="min_charge" argument="-deisotoping:min_charge" type="integer" min="1" value="1" label="The minimum charge considered" help=""/>
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132 <param name="max_charge" argument="-deisotoping:max_charge" type="integer" min="1" value="1" label="The maximum charge considered" help=""/>
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133 <param name="min_isopeaks" argument="-deisotoping:min_isopeaks" type="integer" min="2" value="2" label="The minimum number of isotopic peaks (at least 2) required for an isotopic cluste" help=""/>
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134 <param name="max_isopeaks" argument="-deisotoping:max_isopeaks" type="integer" min="3" value="3" label="The maximum number of isotopic peaks (at least 2) considered for an isotopic cluste" help=""/>
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135 <param name="keep_only_deisotoped" argument="-deisotoping:keep_only_deisotoped" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only monoisotopic peaks of fragments with isotopic pattern are retained" help=""/>
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136 <param name="annotate_charge" argument="-deisotoping:annotate_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Annotate the charge to the peaks" help=""/>
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137 </section>
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138 <section name="preprocessing" title="" help="" expanded="false">
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139 <param name="filter_by_num_masstraces" argument="-preprocessing:filter_by_num_masstraces" type="integer" 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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140 <param name="precursor_mz_tolerance" argument="-preprocessing:precursor_mz_tolerance" type="float" value="10.0" label="Tolerance window for precursor selection (Feature selection in regard to the precursor)" help=""/>
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141 <param name="precursor_mz_tolerance_unit" argument="-preprocessing:precursor_mz_tolerance_unit" type="select" label="Unit of the precursor_mz_tolerance" help="">
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142 <option value="Da">Da</option>
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143 <option value="ppm" selected="true">ppm</option>
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144 <expand macro="list_string_san" name="precursor_mz_tolerance_unit"/>
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145 </param>
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146 <param name="precursor_rt_tolerance" argument="-preprocessing:precursor_rt_tolerance" type="float" value="5.0" label="Tolerance window (left and right) for precursor selection [seconds]" help=""/>
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147 <param name="isotope_pattern_iterations" argument="-preprocessing:isotope_pattern_iterations" type="integer" 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"/>
0
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148 <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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149 <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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150 </section>
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151 <section name="project" title="" help="" expanded="false">
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152 <param name="maxmz" argument="-project:maxmz" type="integer" value="-1" label="Just consider compounds with a precursor mz lower or equal" help="this maximum mz. All other compounds in the input file. are ignored"/>
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153 <param name="processors" argument="-project:processors" type="integer" value="1" label="Number of cpu cores to use" help="If not specified SIRIUS uses all available cores"/>
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154 <param name="loglevel" argument="-project:loglevel" type="text" optional="true" value="" label="Set logging level of the Jobs SIRIUS will execute" help="Valid values: SEVERE, WARNING, INFO, FINER, ALL. Default: WARNING">
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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155 <expand macro="list_string_san" name="loglevel"/>
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156 </param>
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157 <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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158 <param name="q" argument="-project:q" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppress shell output" help=""/>
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159 </section>
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160 <section name="sirius" title="" help="" expanded="false">
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161 <param name="ppm_max" argument="-sirius:ppm_max" type="float" value="10.0" label="Maximum allowed mass deviation in ppm for decomposing masses [ppm]" help=""/>
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162 <param name="ppm_max_ms2" argument="-sirius:ppm_max_ms2" type="float" 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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163 <param name="tree_timeout" argument="-sirius:tree_timeout" type="integer" min="0" value="100" label="Time out in seconds per fragmentation tree computations" help="0 for an infinite amount of time"/>
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164 <param name="compound_timeout" argument="-sirius:compound_timeout" type="integer" 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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165 <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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166 <param name="profile" argument="-sirius:profile" type="select" label="Name of the configuration profile" help="">
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167 <option value="default" selected="true">default</option>
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168 <option value="qtof">qtof</option>
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169 <option value="orbitrap">orbitrap</option>
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170 <option value="fticr">fticr</option>
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171 <expand macro="list_string_san" name="profile"/>
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172 </param>
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173 <param name="formulas" argument="-sirius:formulas" 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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174 <expand macro="list_string_san" name="formulas"/>
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175 </param>
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176 <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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177 <expand macro="list_string_san" name="ions_enforced"/>
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178 </param>
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179 <param name="candidates" argument="-sirius:candidates" type="integer" min="0" value="10" label="The number of formula candidates in the SIRIUS output" help=""/>
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180 <param name="candidates_per_ion" argument="-sirius:candidates_per_ion" type="integer" 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"/>
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181 <param name="elements_considered" argument="-sirius:elements_considered" type="text" value="SBrClBSe" 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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182 <expand macro="list_string_san" name="elements_considered"/>
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183 </param>
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184 <param name="elements_enforced" argument="-sirius:elements_enforced" type="text" value="CHNOP" 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">
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185 <expand macro="list_string_san" name="elements_enforced"/>
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186 </param>
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187 <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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188 <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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189 <param name="ions_considered" argument="-sirius:ions_considered" type="text" value="[M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]-" 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">
5
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190 <expand macro="list_string_san" name="ions_considered"/>
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191 </param>
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192 <param name="db" argument="-sirius:db" type="text" value="none" 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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193 <expand macro="list_string_san" name="db"/>
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194 </param>
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195 <param name="solver" argument="-sirius:solver" type="text" value="CLP" label="For GUROBI and CPLEX environment variables need to be configured" help="(see SIRIUS manual: https://boecker-lab.github.io/docs.sirius.github.io/install/)">
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196 <expand macro="list_string_san" name="solver"/>
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197 </param>
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198 </section>
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199 <section name="fingerid" title="" help="" expanded="false">
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200 <param name="db" argument="-fingerid:db" type="text" optional="true" value="" label="Search structures 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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201 <expand macro="list_string_san" name="db"/>
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202 </param>
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203 </section>
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204 <expand macro="adv_opts_macro">
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205 <param argument="-ambiguity_resolution_mz_tolerance_unit" type="select" label="Unit of the ambiguity_resolution_mz_tolerance" help="">
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206 <option value="ppm" selected="true">ppm</option>
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207 <option value="Da">Da</option>
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208 <expand macro="list_string_san" name="ambiguity_resolution_mz_tolerance_unit"/>
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209 </param>
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210 <param argument="-precursor_recalibration_window" type="float" value="0.01" label="Tolerance window for precursor selection (Annotation of precursor mz and intensity)" help=""/>
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211 <param argument="-precursor_recalibration_window_unit" type="select" label="Unit of the precursor_mz_tolerance_annotation" help="">
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212 <option value="Da" selected="true">Da</option>
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213 <option value="ppm">ppm</option>
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214 <expand macro="list_string_san" name="precursor_recalibration_window_unit"/>
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215 </param>
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216 <param argument="-min_fragment_mz" type="float" value="0.0" label="Minimal m/z of a fragment ion choosen as a transition" help=""/>
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217 <param argument="-max_fragment_mz" type="float" value="2000.0" label="Maximal m/z of a fragment ion choosen as a transition" help=""/>
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218 <param argument="-read_sirius_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Read and print the standard output and error of the Sirius executable, even if it succeeds" help=""/>
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219 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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220 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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221 <expand macro="list_string_san" name="test"/>
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222 </param>
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223 </expand>
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224 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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225 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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226 </param>
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227 </inputs>
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228 <outputs>
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229 <data name="out" label="${tool.name} on ${on_string}: out" format="pqp">
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230 <change_format>
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231 <when input="out_type" value="traML" format="traml"/>
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232 <when input="out_type" value="tsv" format="tabular"/>
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233 </change_format>
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234 </data>
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235 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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236 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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237 </data>
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238 </outputs>
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239 <tests>
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240 <!-- TOPP_AssayGeneratorMetabo_1 -->
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241 <test expect_num_outputs="2">
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242 <section name="adv_opts">
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243 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
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244 <param name="precursor_recalibration_window" value="0.01"/>
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245 <param name="precursor_recalibration_window_unit" value="Da"/>
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246 <param name="min_fragment_mz" value="0.0"/>
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247 <param name="max_fragment_mz" value="2000.0"/>
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248 <param name="read_sirius_stdout" value="false"/>
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249 <param name="force" value="false"/>
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250 <param name="test" value="true"/>
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251 </section>
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252 <conditional name="in_cond">
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253 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
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254 </conditional>
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255 <conditional name="in_id_cond">
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256 <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/>
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257 </conditional>
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258 <param name="out_type" value="tsv"/>
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259 <output name="out" value="AssayGeneratorMetabo_ffm_output.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
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260 <param name="fragment_annotation" value="none"/>
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261 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
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262 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
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263 <param name="total_occurrence_filter" value="0.1"/>
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264 <param name="fragment_annotation_score_threshold" value="0.8"/>
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265 <param name="decoy_generation" value="false"/>
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266 <param name="decoy_generation_method" value="original"/>
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267 <param name="method" value="highest_intensity"/>
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268 <param name="use_exact_mass" value="false"/>
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269 <param name="exclude_ms2_precursor" value="false"/>
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270 <param name="precursor_mz_distance" value="0.0001"/>
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271 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
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272 <param name="use_known_unknowns" value="false"/>
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273 <param name="min_transitions" value="1"/>
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274 <param name="max_transitions" value="3"/>
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275 <param name="cosine_similarity_threshold" value="0.98"/>
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276 <param name="transition_threshold" value="5.0"/>
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277 <section name="deisotoping">
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278 <param name="use_deisotoper" value="false"/>
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279 <param name="fragment_tolerance" value="1.0"/>
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280 <param name="fragment_unit" value="ppm"/>
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281 <param name="min_charge" value="1"/>
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282 <param name="max_charge" value="1"/>
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283 <param name="min_isopeaks" value="2"/>
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284 <param name="max_isopeaks" value="3"/>
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285 <param name="keep_only_deisotoped" value="false"/>
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286 <param name="annotate_charge" value="false"/>
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287 </section>
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288 <section name="preprocessing">
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289 <param name="filter_by_num_masstraces" value="1"/>
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290 <param name="precursor_mz_tolerance" value="10.0"/>
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291 <param name="precursor_mz_tolerance_unit" value="ppm"/>
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292 <param name="precursor_rt_tolerance" value="5.0"/>
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293 <param name="isotope_pattern_iterations" value="3"/>
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294 <param name="feature_only" value="false"/>
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295 <param name="no_masstrace_info_isotope_pattern" value="false"/>
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296 </section>
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297 <section name="project">
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298 <param name="maxmz" value="-1"/>
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299 <param name="processors" value="1"/>
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300 <param name="loglevel" value=""/>
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301 <param name="ignore_formula" value="false"/>
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302 <param name="q" value="false"/>
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303 </section>
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304 <section name="sirius">
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305 <param name="ppm_max" value="10.0"/>
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306 <param name="ppm_max_ms2" value="10.0"/>
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307 <param name="tree_timeout" value="100"/>
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308 <param name="compound_timeout" value="100"/>
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309 <param name="no_recalibration" value="false"/>
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310 <param name="profile" value="default"/>
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311 <param name="formulas" value=""/>
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312 <param name="ions_enforced" value=""/>
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313 <param name="candidates" value="10"/>
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314 <param name="candidates_per_ion" value="1"/>
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315 <param name="elements_considered" value="SBrClBSe"/>
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316 <param name="elements_enforced" value="CHNOP"/>
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317 <param name="no_isotope_score" value="false"/>
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318 <param name="no_isotope_filter" value="false"/>
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319 <param name="ions_considered" value="[M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]-"/>
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320 <param name="db" value="none"/>
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321 <param name="solver" value="CLP"/>
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322 </section>
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323 <section name="fingerid">
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324 <param name="db" value=""/>
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325 </section>
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326 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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327 <output name="ctd_out" ftype="xml">
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328 <assert_contents>
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329 <is_valid_xml/>
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330 </assert_contents>
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331 </output>
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332 <assert_stdout>
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333 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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334 </assert_stdout>
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335 </test>
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336 <!-- TOPP_AssayGeneratorMetabo_2 -->
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337 <test expect_num_outputs="2">
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338 <section name="adv_opts">
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339 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
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340 <param name="precursor_recalibration_window" value="0.01"/>
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341 <param name="precursor_recalibration_window_unit" value="Da"/>
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342 <param name="min_fragment_mz" value="0.0"/>
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343 <param name="max_fragment_mz" value="2000.0"/>
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344 <param name="read_sirius_stdout" value="false"/>
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345 <param name="force" value="false"/>
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346 <param name="test" value="true"/>
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347 </section>
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348 <conditional name="in_cond">
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349 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
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350 </conditional>
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351 <conditional name="in_id_cond">
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352 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
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353 </conditional>
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354 <param name="out_type" value="tsv"/>
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355 <output name="out" value="AssayGeneratorMetabo_ams_output.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
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356 <param name="fragment_annotation" value="none"/>
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357 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
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358 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
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359 <param name="total_occurrence_filter" value="0.1"/>
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360 <param name="fragment_annotation_score_threshold" value="0.8"/>
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361 <param name="decoy_generation" value="false"/>
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362 <param name="decoy_generation_method" value="original"/>
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363 <param name="method" value="highest_intensity"/>
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364 <param name="use_exact_mass" value="false"/>
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365 <param name="exclude_ms2_precursor" value="false"/>
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366 <param name="precursor_mz_distance" value="0.0001"/>
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367 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
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368 <param name="use_known_unknowns" value="false"/>
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369 <param name="min_transitions" value="1"/>
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370 <param name="max_transitions" value="3"/>
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371 <param name="cosine_similarity_threshold" value="0.98"/>
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372 <param name="transition_threshold" value="5.0"/>
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373 <section name="deisotoping">
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374 <param name="use_deisotoper" value="false"/>
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375 <param name="fragment_tolerance" value="1.0"/>
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376 <param name="fragment_unit" value="ppm"/>
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377 <param name="min_charge" value="1"/>
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378 <param name="max_charge" value="1"/>
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379 <param name="min_isopeaks" value="2"/>
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380 <param name="max_isopeaks" value="3"/>
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381 <param name="keep_only_deisotoped" value="false"/>
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382 <param name="annotate_charge" value="false"/>
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383 </section>
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384 <section name="preprocessing">
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385 <param name="filter_by_num_masstraces" value="1"/>
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386 <param name="precursor_mz_tolerance" value="10.0"/>
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387 <param name="precursor_mz_tolerance_unit" value="ppm"/>
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388 <param name="precursor_rt_tolerance" value="5.0"/>
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389 <param name="isotope_pattern_iterations" value="3"/>
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390 <param name="feature_only" value="false"/>
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391 <param name="no_masstrace_info_isotope_pattern" value="false"/>
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392 </section>
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393 <section name="project">
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394 <param name="maxmz" value="-1"/>
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395 <param name="processors" value="1"/>
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396 <param name="loglevel" value=""/>
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397 <param name="ignore_formula" value="false"/>
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398 <param name="q" value="false"/>
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399 </section>
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400 <section name="sirius">
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401 <param name="ppm_max" value="10.0"/>
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402 <param name="ppm_max_ms2" value="10.0"/>
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403 <param name="tree_timeout" value="100"/>
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404 <param name="compound_timeout" value="100"/>
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405 <param name="no_recalibration" value="false"/>
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406 <param name="profile" value="default"/>
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407 <param name="formulas" value=""/>
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408 <param name="ions_enforced" value=""/>
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409 <param name="candidates" value="10"/>
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410 <param name="candidates_per_ion" value="1"/>
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411 <param name="elements_considered" value="SBrClBSe"/>
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412 <param name="elements_enforced" value="CHNOP"/>
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413 <param name="no_isotope_score" value="false"/>
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414 <param name="no_isotope_filter" value="false"/>
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415 <param name="ions_considered" value="[M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]-"/>
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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416 <param name="db" value="none"/>
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417 <param name="solver" value="CLP"/>
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418 </section>
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419 <section name="fingerid">
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420 <param name="db" value=""/>
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421 </section>
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422 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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423 <output name="ctd_out" ftype="xml">
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424 <assert_contents>
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425 <is_valid_xml/>
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426 </assert_contents>
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427 </output>
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428 <assert_stdout>
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429 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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430 </assert_stdout>
5
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431 </test>
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432 <!-- TOPP_AssayGeneratorMetabo_3 -->
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433 <test expect_num_outputs="2">
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434 <section name="adv_opts">
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435 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
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436 <param name="precursor_recalibration_window" value="0.01"/>
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437 <param name="precursor_recalibration_window_unit" value="Da"/>
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438 <param name="min_fragment_mz" value="0.0"/>
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439 <param name="max_fragment_mz" value="2000.0"/>
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440 <param name="read_sirius_stdout" value="false"/>
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441 <param name="force" value="false"/>
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442 <param name="test" value="true"/>
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443 </section>
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diff changeset
444 <conditional name="in_cond">
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445 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
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446 </conditional>
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447 <conditional name="in_id_cond">
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448 <param name="in_id" value="AssayGeneratorMetabo_ffm_input.featureXML"/>
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449 </conditional>
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450 <param name="out_type" value="tsv"/>
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451 <output name="out" value="AssayGeneratorMetabo_ffm_output_consensus.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
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452 <param name="fragment_annotation" value="none"/>
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453 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
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454 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
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455 <param name="total_occurrence_filter" value="0.1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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456 <param name="fragment_annotation_score_threshold" value="0.8"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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457 <param name="decoy_generation" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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458 <param name="decoy_generation_method" value="original"/>
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diff changeset
459 <param name="method" value="consensus_spectrum"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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460 <param name="use_exact_mass" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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461 <param name="exclude_ms2_precursor" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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462 <param name="precursor_mz_distance" value="0.0001"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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463 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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464 <param name="use_known_unknowns" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
465 <param name="min_transitions" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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466 <param name="max_transitions" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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467 <param name="cosine_similarity_threshold" value="0.98"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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468 <param name="transition_threshold" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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469 <section name="deisotoping">
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470 <param name="use_deisotoper" value="false"/>
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diff changeset
471 <param name="fragment_tolerance" value="1.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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472 <param name="fragment_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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473 <param name="min_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
474 <param name="max_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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475 <param name="min_isopeaks" value="2"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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476 <param name="max_isopeaks" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
477 <param name="keep_only_deisotoped" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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478 <param name="annotate_charge" value="false"/>
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479 </section>
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diff changeset
480 <section name="preprocessing">
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diff changeset
481 <param name="filter_by_num_masstraces" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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482 <param name="precursor_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
483 <param name="precursor_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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484 <param name="precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
485 <param name="isotope_pattern_iterations" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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486 <param name="feature_only" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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487 <param name="no_masstrace_info_isotope_pattern" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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488 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
489 <section name="project">
6
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490 <param name="maxmz" value="-1"/>
5
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diff changeset
491 <param name="processors" value="1"/>
6
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492 <param name="loglevel" value=""/>
5
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493 <param name="ignore_formula" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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494 <param name="q" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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495 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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496 <section name="sirius">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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497 <param name="ppm_max" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
498 <param name="ppm_max_ms2" value="10.0"/>
6
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499 <param name="tree_timeout" value="100"/>
5
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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500 <param name="compound_timeout" value="100"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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501 <param name="no_recalibration" value="false"/>
6
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diff changeset
502 <param name="profile" value="default"/>
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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503 <param name="formulas" value=""/>
5
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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504 <param name="ions_enforced" value=""/>
6
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505 <param name="candidates" value="10"/>
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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506 <param name="candidates_per_ion" value="1"/>
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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diff changeset
507 <param name="elements_considered" value="SBrClBSe"/>
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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diff changeset
508 <param name="elements_enforced" value="CHNOP"/>
5
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diff changeset
509 <param name="no_isotope_score" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
510 <param name="no_isotope_filter" value="false"/>
6
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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diff changeset
511 <param name="ions_considered" value="[M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]-"/>
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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diff changeset
512 <param name="db" value="none"/>
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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diff changeset
513 <param name="solver" value="CLP"/>
5
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
514 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
515 <section name="fingerid">
6
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516 <param name="db" value=""/>
5
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517 </section>
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518 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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519 <output name="ctd_out" ftype="xml">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
520 <assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
521 <is_valid_xml/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
522 </assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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523 </output>
6
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diff changeset
524 <assert_stdout>
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525 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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diff changeset
526 </assert_stdout>
5
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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527 </test>
6
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528 <!-- TOPP_AssayGeneratorMetabo_4 -->
5
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diff changeset
529 <test expect_num_outputs="2">
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530 <section name="adv_opts">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
531 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
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diff changeset
532 <param name="precursor_recalibration_window" value="0.01"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
533 <param name="precursor_recalibration_window_unit" value="Da"/>
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diff changeset
534 <param name="min_fragment_mz" value="0.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
535 <param name="max_fragment_mz" value="2000.0"/>
6
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 5
diff changeset
536 <param name="read_sirius_stdout" value="false"/>
5
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
537 <param name="force" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
538 <param name="test" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
539 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
540 <conditional name="in_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
541 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
542 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
543 <conditional name="in_id_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
544 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
545 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
546 <param name="out_type" value="tsv"/>
6
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 5
diff changeset
547 <output name="out" value="AssayGeneratorMetabo_ams_output_consensus.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
5
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
548 <param name="fragment_annotation" value="none"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
549 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
550 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
551 <param name="total_occurrence_filter" value="0.1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
552 <param name="fragment_annotation_score_threshold" value="0.8"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
553 <param name="decoy_generation" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
554 <param name="decoy_generation_method" value="original"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
555 <param name="method" value="consensus_spectrum"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
556 <param name="use_exact_mass" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
557 <param name="exclude_ms2_precursor" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
558 <param name="precursor_mz_distance" value="0.0001"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
559 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
560 <param name="use_known_unknowns" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
561 <param name="min_transitions" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
562 <param name="max_transitions" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
563 <param name="cosine_similarity_threshold" value="0.98"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
564 <param name="transition_threshold" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
565 <section name="deisotoping">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
566 <param name="use_deisotoper" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
567 <param name="fragment_tolerance" value="1.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
568 <param name="fragment_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
569 <param name="min_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
570 <param name="max_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
571 <param name="min_isopeaks" value="2"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
572 <param name="max_isopeaks" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
573 <param name="keep_only_deisotoped" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
574 <param name="annotate_charge" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
575 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
576 <section name="preprocessing">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
577 <param name="filter_by_num_masstraces" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
578 <param name="precursor_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
579 <param name="precursor_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
580 <param name="precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
581 <param name="isotope_pattern_iterations" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
582 <param name="feature_only" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
583 <param name="no_masstrace_info_isotope_pattern" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
584 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
585 <section name="project">
6
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 5
diff changeset
586 <param name="maxmz" value="-1"/>
5
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
587 <param name="processors" value="1"/>
6
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 5
diff changeset
588 <param name="loglevel" value=""/>
5
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
589 <param name="ignore_formula" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
590 <param name="q" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
591 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
592 <section name="sirius">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
593 <param name="ppm_max" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
594 <param name="ppm_max_ms2" value="10.0"/>
6
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 5
diff changeset
595 <param name="tree_timeout" value="100"/>
5
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
596 <param name="compound_timeout" value="100"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
597 <param name="no_recalibration" value="false"/>
6
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 5
diff changeset
598 <param name="profile" value="default"/>
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 5
diff changeset
599 <param name="formulas" value=""/>
5
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
600 <param name="ions_enforced" value=""/>
6
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 5
diff changeset
601 <param name="candidates" value="10"/>
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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parents: 5
diff changeset
602 <param name="candidates_per_ion" value="1"/>
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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diff changeset
603 <param name="elements_considered" value="SBrClBSe"/>
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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diff changeset
604 <param name="elements_enforced" value="CHNOP"/>
5
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
605 <param name="no_isotope_score" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
606 <param name="no_isotope_filter" value="false"/>
6
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
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diff changeset
607 <param name="ions_considered" value="[M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]-"/>
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 5
diff changeset
608 <param name="db" value="none"/>
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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diff changeset
609 <param name="solver" value="CLP"/>
5
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
610 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
611 <section name="fingerid">
6
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diff changeset
612 <param name="db" value=""/>
5
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diff changeset
613 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
614 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
615 <output name="ctd_out" ftype="xml">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
616 <assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
617 <is_valid_xml/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
618 </assert_contents>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 4
diff changeset
619 </output>
6
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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parents: 5
diff changeset
620 <assert_stdout>
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 5
diff changeset
621 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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parents: 5
diff changeset
622 </assert_stdout>
5
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 4
diff changeset
623 </test>
6
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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parents: 5
diff changeset
624 <!-- TOPP_AssayGeneratorMetabo_5 -->
5
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
625 <test expect_num_outputs="2">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
626 <section name="adv_opts">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
627 <param name="ambiguity_resolution_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
628 <param name="precursor_recalibration_window" value="0.01"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
629 <param name="precursor_recalibration_window_unit" value="Da"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
630 <param name="min_fragment_mz" value="0.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
631 <param name="max_fragment_mz" value="2000.0"/>
6
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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diff changeset
632 <param name="read_sirius_stdout" value="false"/>
5
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
633 <param name="force" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 4
diff changeset
634 <param name="test" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
635 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
636 <conditional name="in_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
637 <param name="in" value="AssayGeneratorMetabo_input.mzML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
638 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
639 <conditional name="in_id_cond">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
640 <param name="in_id" value="AssayGeneratorMetabo_ams_input.featureXML"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
641 </conditional>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
642 <param name="out_type" value="tsv"/>
6
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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diff changeset
643 <output name="out" value="AssayGeneratorMetabo_ams_uku_output_consensus.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
5
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
644 <param name="fragment_annotation" value="none"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
645 <param name="ambiguity_resolution_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
646 <param name="ambiguity_resolution_rt_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
647 <param name="total_occurrence_filter" value="0.1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 4
diff changeset
648 <param name="fragment_annotation_score_threshold" value="0.8"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
649 <param name="decoy_generation" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
650 <param name="decoy_generation_method" value="original"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
651 <param name="method" value="consensus_spectrum"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 4
diff changeset
652 <param name="use_exact_mass" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
653 <param name="exclude_ms2_precursor" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
654 <param name="precursor_mz_distance" value="0.0001"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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655 <param name="consensus_spectrum_precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
656 <param name="use_known_unknowns" value="true"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
657 <param name="min_transitions" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 4
diff changeset
658 <param name="max_transitions" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 4
diff changeset
659 <param name="cosine_similarity_threshold" value="0.98"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
660 <param name="transition_threshold" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
661 <section name="deisotoping">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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662 <param name="use_deisotoper" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
663 <param name="fragment_tolerance" value="1.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
664 <param name="fragment_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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665 <param name="min_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
666 <param name="max_charge" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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667 <param name="min_isopeaks" value="2"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
668 <param name="max_isopeaks" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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669 <param name="keep_only_deisotoped" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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670 <param name="annotate_charge" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
671 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
672 <section name="preprocessing">
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diff changeset
673 <param name="filter_by_num_masstraces" value="1"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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674 <param name="precursor_mz_tolerance" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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675 <param name="precursor_mz_tolerance_unit" value="ppm"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
676 <param name="precursor_rt_tolerance" value="5.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
677 <param name="isotope_pattern_iterations" value="3"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
678 <param name="feature_only" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
679 <param name="no_masstrace_info_isotope_pattern" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
680 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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681 <section name="project">
6
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diff changeset
682 <param name="maxmz" value="-1"/>
5
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683 <param name="processors" value="1"/>
6
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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684 <param name="loglevel" value=""/>
5
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685 <param name="ignore_formula" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
686 <param name="q" value="false"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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687 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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688 <section name="sirius">
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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689 <param name="ppm_max" value="10.0"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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690 <param name="ppm_max_ms2" value="10.0"/>
6
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diff changeset
691 <param name="tree_timeout" value="100"/>
5
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diff changeset
692 <param name="compound_timeout" value="100"/>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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693 <param name="no_recalibration" value="false"/>
6
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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diff changeset
694 <param name="profile" value="default"/>
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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diff changeset
695 <param name="formulas" value=""/>
5
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696 <param name="ions_enforced" value=""/>
6
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697 <param name="candidates" value="10"/>
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698 <param name="candidates_per_ion" value="1"/>
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699 <param name="elements_considered" value="SBrClBSe"/>
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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700 <param name="elements_enforced" value="CHNOP"/>
5
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701 <param name="no_isotope_score" value="false"/>
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702 <param name="no_isotope_filter" value="false"/>
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703 <param name="ions_considered" value="[M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]-"/>
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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704 <param name="db" value="none"/>
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705 <param name="solver" value="CLP"/>
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706 </section>
83f5e5c1209c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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707 <section name="fingerid">
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708 <param name="db" value=""/>
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709 </section>
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710 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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711 <output name="ctd_out" ftype="xml">
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712 <assert_contents>
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713 <is_valid_xml/>
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714 </assert_contents>
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715 </output>
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716 <assert_stdout>
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717 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
f3ec820189ca planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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718 </assert_stdout>
5
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719 </test>
0
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720 </tests>
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721 <help><![CDATA[Assay library generation from DDA data (Metabolomics)
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722
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723
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724 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_AssayGeneratorMetabo.html]]></help>
0
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725 <expand macro="references"/>
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726 </tool>