Mercurial > repos > galaxyp > openms_accuratemasssearch

annotate AccurateMassSearch.xml @ 16:532cf3ddcc91 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:05:06 +0000
parents 2dea459da18e
children 31e674c86840
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9c63c85a3cf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="AccurateMassSearch" name="AccurateMassSearch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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5 <description>Match MS signals to molecules from a database by mass.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">AccurateMassSearch</token>
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8 <import>macros.xml</import>
9c63c85a3cf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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9 </macros>
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10 <expand macro="requirements"/>
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11 <expand macro="stdio"/>
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12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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13 @EXT_FOO@
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14 #import re
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15
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16 ## Preprocessing
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17 mkdir in &&
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18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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19 mkdir out &&
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20 #if "out_annotation_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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21 mkdir out_annotation &&
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22 #end if
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23 #if $positive_adducts:
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24 mkdir positive_adducts &&
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25 ln -s '$positive_adducts' 'positive_adducts/${re.sub("[^\w\-_]", "_", $positive_adducts.element_identifier)}.$gxy2omsext($positive_adducts.ext)' &&
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26 #end if
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27 #if $negative_adducts:
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28 mkdir negative_adducts &&
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29 ln -s '$negative_adducts' 'negative_adducts/${re.sub("[^\w\-_]", "_", $negative_adducts.element_identifier)}.$gxy2omsext($negative_adducts.ext)' &&
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9c63c85a3cf5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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30 #end if
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31 #if $db.mapping_cond.mapping:
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32 mkdir db.mapping_cond.mapping &&
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33 #if $db.mapping_cond.mapping_select == "no"
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34 mkdir ${' '.join(["'db.mapping_cond.mapping/%s'" % (i) for i, f in enumerate($db.mapping_cond.mapping) if f])} &&
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35 ${' '.join(["ln -s '%s' 'db.mapping_cond.mapping/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($db.mapping_cond.mapping) if f])}
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36 #else
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37 ln -s '$db.mapping_cond.mapping' 'db.mapping_cond.mapping/${re.sub("[^\w\-_]", "_", $db.mapping_cond.mapping.element_identifier)}.$gxy2omsext($db.mapping_cond.mapping.ext)' &&
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38 #end if
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39 #end if
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40 #if $db.struct_cond.struct:
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41 mkdir db.struct_cond.struct &&
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42 #if $db.struct_cond.struct_select == "no"
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43 mkdir ${' '.join(["'db.struct_cond.struct/%s'" % (i) for i, f in enumerate($db.struct_cond.struct) if f])} &&
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44 ${' '.join(["ln -s '%s' 'db.struct_cond.struct/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($db.struct_cond.struct) if f])}
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45 #else
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46 ln -s '$db.struct_cond.struct' 'db.struct_cond.struct/${re.sub("[^\w\-_]", "_", $db.struct_cond.struct.element_identifier)}.$gxy2omsext($db.struct_cond.struct.ext)' &&
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47 #end if
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48 #end if
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49
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50 ## Main program call
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51
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52 set -o pipefail &&
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53 @EXECUTABLE@ -write_ctd ./ &&
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54 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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55 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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56 -in
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57 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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58 -out
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59 'out/output.${gxy2omsext("mztab")}'
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60 #if "out_annotation_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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61 -out_annotation
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62 'out_annotation/output.${out_annotation_type}'
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63 #end if
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64 #if $positive_adducts:
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65 -positive_adducts
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66 'positive_adducts/${re.sub("[^\w\-_]", "_", $positive_adducts.element_identifier)}.$gxy2omsext($positive_adducts.ext)'
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67 #end if
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68 #if $negative_adducts:
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69 -negative_adducts
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70 'negative_adducts/${re.sub("[^\w\-_]", "_", $negative_adducts.element_identifier)}.$gxy2omsext($negative_adducts.ext)'
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71 #end if
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72 #if $db.mapping_cond.mapping:
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73 -db:mapping
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74 #if $db.mapping_cond.mapping_select == "no"
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75 ${' '.join(["'db.mapping_cond.mapping/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($db.mapping_cond.mapping) if f])}
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76 #else
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77 'db.mapping_cond.mapping/${re.sub("[^\w\-_]", "_", $db.mapping_cond.mapping.element_identifier)}.$gxy2omsext($db.mapping_cond.mapping.ext)'
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78 #end if
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79 #end if
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80 #if $db.struct_cond.struct:
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81 -db:struct
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82 #if $db.struct_cond.struct_select == "no"
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83 ${' '.join(["'db.struct_cond.struct/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($db.struct_cond.struct) if f])}
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84 #else
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85 'db.struct_cond.struct/${re.sub("[^\w\-_]", "_", $db.struct_cond.struct.element_identifier)}.$gxy2omsext($db.struct_cond.struct.ext)'
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86 #end if
0
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87 #end if
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88 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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89 | tee '$stdout'
0
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90 #end if
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91
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92 ## Postprocessing
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93 && mv 'out/output.${gxy2omsext("mztab")}' '$out'
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94 #if "out_annotation_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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95 && mv 'out_annotation/output.${out_annotation_type}' '$out_annotation'
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96 #end if
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97 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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98 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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99 #end if]]></command>
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100 <configfiles>
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101 <inputs name="args_json" data_style="paths"/>
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102 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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103 </configfiles>
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104 <inputs>
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105 <param argument="-in" type="data" format="consensusxml,featurexml" optional="false" label="featureXML or consensusXML file" help=" select consensusxml,featurexml data sets(s)"/>
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106 <param name="out_annotation_type" type="select" optional="false" label="File type of output out_annotation (A copy of the input file, annotated with matching hits from the database.)">
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107 <option value="featureXML">featurexml</option>
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108 <option value="consensusXML">consensusxml</option>
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109 <option value="oms">sqlite (oms)</option>
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110 </param>
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111 <param argument="-positive_adducts" type="data" format="tabular" optional="true" label="This file contains the list of potential positive adducts that will be looked for in the database" help="Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/PositiveAdducts.tsv in OpenMS/share is used select tabular data sets(s)"/>
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112 <param argument="-negative_adducts" type="data" format="tabular" optional="true" label="This file contains the list of potential negative adducts that will be looked for in the database" help="Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/NegativeAdducts.tsv in OpenMS/share is used select tabular data sets(s)"/>
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113 <section name="db" title="Database files which contain the identifications" help="" expanded="false">
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114 <conditional name="mapping_cond">
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115 <param name="mapping_select" type="select" label="Run tool in batch mode for -mapping">
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116 <option value="no">No: process all datasets jointly</option>
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117 <option value="yes">Yes: process each dataset in an independent job</option>
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118 </param>
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119 <when value="no">
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120 <param name="mapping" argument="-db:mapping" type="data" format="tabular" multiple="true" optional="true" label="Database input file(s), containing three tab-separated columns of mass, formula, identifie" help="If 'mass' is 0, it is re-computed from the molecular sum formula. By default CHEMISTRY/HMDBMappingFile.tsv in OpenMS/share is used! If empty, the default will be used select tabular data sets(s)"/>
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121 </when>
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122 <when value="yes">
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123 <param name="mapping" argument="-db:mapping" type="data" format="tabular" multiple="false" optional="true" label="Database input file(s), containing three tab-separated columns of mass, formula, identifie" help="If 'mass' is 0, it is re-computed from the molecular sum formula. By default CHEMISTRY/HMDBMappingFile.tsv in OpenMS/share is used! If empty, the default will be used select tabular data sets(s)"/>
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124 </when>
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125 </conditional>
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126 <conditional name="struct_cond">
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127 <param name="struct_select" type="select" label="Run tool in batch mode for -struct">
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128 <option value="no">No: process all datasets jointly</option>
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129 <option value="yes">Yes: process each dataset in an independent job</option>
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130 </param>
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131 <when value="no">
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132 <param name="struct" argument="-db:struct" type="data" format="tabular" multiple="true" optional="true" label="Database input file(s), containing four tab-separated columns of identifier, name, SMILES, INCHI.The identifier should match with mapping file" help="SMILES and INCHI are reported in the output, but not used otherwise. By default CHEMISTRY/HMDB2StructMapping.tsv in OpenMS/share is used! If empty, the default will be used select tabular data sets(s)"/>
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133 </when>
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134 <when value="yes">
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135 <param name="struct" argument="-db:struct" type="data" format="tabular" multiple="false" optional="true" label="Database input file(s), containing four tab-separated columns of identifier, name, SMILES, INCHI.The identifier should match with mapping file" help="SMILES and INCHI are reported in the output, but not used otherwise. By default CHEMISTRY/HMDB2StructMapping.tsv in OpenMS/share is used! If empty, the default will be used select tabular data sets(s)"/>
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136 </when>
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137 </conditional>
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138 </section>
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139 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
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140 <param name="mass_error_value" argument="-algorithm:mass_error_value" type="float" optional="true" value="5.0" label="Tolerance allowed for accurate mass search" help=""/>
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141 <param name="mass_error_unit" argument="-algorithm:mass_error_unit" type="select" optional="true" label="Unit of mass error (ppm or Da)" help="">
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142 <option value="ppm" selected="true">ppm</option>
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143 <option value="Da">Da</option>
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144 <expand macro="list_string_san" name="mass_error_unit"/>
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145 </param>
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146 <param name="ionization_mode" argument="-algorithm:ionization_mode" type="select" optional="true" label="Positive or negative ionization mode" help="If 'auto' is used, the first feature of the input map must contain the meta-value 'scan_polarity'. If its missing, the tool will exit with error">
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147 <option value="positive" selected="true">positive</option>
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148 <option value="negative">negative</option>
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149 <option value="auto">auto</option>
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150 <expand macro="list_string_san" name="ionization_mode"/>
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151 </param>
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152 <param name="isotopic_similarity" argument="-algorithm:isotopic_similarity" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a similarity score for each hit (only if the feature exhibits at least two isotopic mass traces)" help=""/>
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153 <param name="use_feature_adducts" argument="-algorithm:use_feature_adducts" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to filter AMS candidates mismatching available feature adduct annotation" help=""/>
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154 <param name="keep_unidentified_masses" argument="-algorithm:keep_unidentified_masses" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Keep features that did not yield any DB hit" help=""/>
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155 <param name="id_format" argument="-algorithm:id_format" type="select" optional="true" label="Use legacy (ProteinID/PeptideID based storage of metabolomics data) with mzTab-v1.0.0 as output format or novel Identification Data (ID) with mzTab-v2.0.0-M as output format (ID and its MzTab-M output is currently only support for featureXML files)" help="">
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156 <option value="legacy" selected="true">legacy</option>
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157 <option value="ID">ID</option>
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158 <expand macro="list_string_san" name="id_format"/>
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159 </param>
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160 <section name="mzTab" title="" help="" expanded="false">
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161 <param name="exportIsotopeIntensities" argument="-algorithm:mzTab:exportIsotopeIntensities" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[featureXML input only] Export column with available isotope trace intensities (opt_global_MTint)" help=""/>
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162 </section>
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163 </section>
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164 <expand macro="adv_opts_macro">
16
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165 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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166 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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167 <expand macro="list_string_san" name="test"/>
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168 </param>
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169 </expand>
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170 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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171 <option value="out_annotation_FLAG">out_annotation (A copy of the input file, annotated with matching hits from the database)</option>
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172 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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173 </param>
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174 </inputs>
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175 <outputs>
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176 <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/>
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177 <data name="out_annotation" label="${tool.name} on ${on_string}: out_annotation" format="consensusxml">
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178 <change_format>
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179 <when input="out_annotation_type" value="featureXML" format="featurexml"/>
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180 <when input="out_annotation_type" value="oms" format="sqlite"/>
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181 </change_format>
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182 <filter>OPTIONAL_OUTPUTS is not None and "out_annotation_FLAG" in OPTIONAL_OUTPUTS</filter>
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183 </data>
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184 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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185 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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186 </data>
0
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187 </outputs>
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188 <tests><!-- UTILS_AccurateMassSearch_1 -->
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189 <test expect_num_outputs="2">
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190 <section name="adv_opts">
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191 <param name="force" value="false"/>
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192 <param name="test" value="true"/>
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193 </section>
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194 <param name="in" value="ConsensusMapNormalizer_input.consensusXML"/>
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195 <output name="out" file="AccurateMassSearch_1_output.tmp.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
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196 <param name="positive_adducts" value="CHEMISTRY/PositiveAdducts.tsv" ftype="tabular"/>
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197 <param name="negative_adducts" value="CHEMISTRY/NegativeAdducts.tsv" ftype="tabular"/>
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198 <section name="db">
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199 <conditional name="mapping_cond">
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200 <param name="mapping" value="CHEMISTRY/HMDBMappingFile.tsv" ftype="tabular"/>
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201 </conditional>
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202 <conditional name="struct_cond">
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203 <param name="struct" value="CHEMISTRY/HMDB2StructMapping.tsv" ftype="tabular"/>
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204 </conditional>
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205 </section>
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206 <section name="algorithm">
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207 <param name="mass_error_value" value="5.0"/>
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208 <param name="mass_error_unit" value="ppm"/>
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209 <param name="ionization_mode" value="positive"/>
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210 <param name="isotopic_similarity" value="false"/>
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211 <param name="use_feature_adducts" value="false"/>
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212 <param name="keep_unidentified_masses" value="true"/>
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213 <param name="id_format" value="legacy"/>
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214 <section name="mzTab">
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215 <param name="exportIsotopeIntensities" value="false"/>
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216 </section>
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217 </section>
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218 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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219 <output name="ctd_out" ftype="xml">
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220 <assert_contents>
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221 <is_valid_xml/>
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222 </assert_contents>
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223 </output>
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224 </test>
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225 <!-- UTILS_AccurateMassSearch_2 -->
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226 <test expect_num_outputs="3">
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227 <section name="adv_opts">
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228 <param name="force" value="false"/>
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229 <param name="test" value="true"/>
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230 </section>
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231 <param name="in" value="AccurateMassSearch_2_input.featureXML"/>
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232 <output name="out" file="AccurateMassSearch_2_output.tmp.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
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233 <param name="out_annotation_type" value="featureXML"/>
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234 <output name="out_annotation" file="AccurateMassSearch_2_output.tmp.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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235 <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/>
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236 <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/>
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237 <section name="db">
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238 <conditional name="mapping_cond">
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239 <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/>
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240 </conditional>
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241 <conditional name="struct_cond">
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242 <param name="struct" value="AMS_test_Struct.tsv" ftype="tabular"/>
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243 </conditional>
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244 </section>
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245 <section name="algorithm">
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246 <param name="mass_error_value" value="5.0"/>
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247 <param name="mass_error_unit" value="ppm"/>
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248 <param name="ionization_mode" value="positive"/>
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249 <param name="isotopic_similarity" value="false"/>
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250 <param name="use_feature_adducts" value="false"/>
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251 <param name="keep_unidentified_masses" value="false"/>
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252 <param name="id_format" value="legacy"/>
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253 <section name="mzTab">
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254 <param name="exportIsotopeIntensities" value="true"/>
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255 </section>
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256 </section>
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257 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_annotation_FLAG"/>
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258 <output name="ctd_out" ftype="xml">
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259 <assert_contents>
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260 <is_valid_xml/>
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261 </assert_contents>
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262 </output>
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263 </test>
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264 <!-- UTILS_AccurateMassSearch_3 -->
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265 <test expect_num_outputs="3">
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266 <section name="adv_opts">
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267 <param name="force" value="false"/>
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268 <param name="test" value="true"/>
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269 </section>
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270 <param name="in" value="AccurateMassSearch_2_input.featureXML"/>
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271 <output name="out" file="AccurateMassSearch_3_output.tmp.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
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272 <param name="out_annotation_type" value="featureXML"/>
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273 <output name="out_annotation" file="AccurateMassSearch_2_output.tmp.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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274 <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/>
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275 <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/>
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276 <section name="db">
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277 <conditional name="mapping_cond">
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278 <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/>
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279 </conditional>
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280 <conditional name="struct_cond">
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281 <param name="struct" value="AMS_test_Struct.tsv" ftype="tabular"/>
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282 </conditional>
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283 </section>
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284 <section name="algorithm">
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285 <param name="mass_error_value" value="5.0"/>
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286 <param name="mass_error_unit" value="ppm"/>
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287 <param name="ionization_mode" value="positive"/>
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288 <param name="isotopic_similarity" value="false"/>
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289 <param name="use_feature_adducts" value="false"/>
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290 <param name="keep_unidentified_masses" value="true"/>
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291 <param name="id_format" value="legacy"/>
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292 <section name="mzTab">
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293 <param name="exportIsotopeIntensities" value="false"/>
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294 </section>
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295 </section>
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296 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_annotation_FLAG"/>
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297 <output name="ctd_out" ftype="xml">
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298 <assert_contents>
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299 <is_valid_xml/>
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300 </assert_contents>
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301 </output>
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302 </test>
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303 <!-- UTILS_AccurateMassSearch_5 -->
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304 <test expect_num_outputs="3">
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305 <section name="adv_opts">
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306 <param name="force" value="false"/>
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307 <param name="test" value="true"/>
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308 </section>
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309 <param name="in" value="AccurateMassSearch_2_input.featureXML"/>
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310 <output name="out" file="AccurateMassSearch_5_output.tmp.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
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311 <param name="out_annotation_type" value="oms"/>
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312 <output name="out_annotation" file="AccurateMassSearch_5_output.tmp.oms" compare="sim_size" delta_frac="0.7" ftype="sqlite"/>
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313 <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/>
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314 <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/>
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315 <section name="db">
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316 <conditional name="mapping_cond">
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317 <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/>
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318 </conditional>
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319 <conditional name="struct_cond">
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320 <param name="struct" value="AMS_test_Struct.tsv" ftype="tabular"/>
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321 </conditional>
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322 </section>
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323 <section name="algorithm">
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324 <param name="mass_error_value" value="5.0"/>
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325 <param name="mass_error_unit" value="ppm"/>
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326 <param name="ionization_mode" value="positive"/>
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327 <param name="isotopic_similarity" value="false"/>
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328 <param name="use_feature_adducts" value="false"/>
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329 <param name="keep_unidentified_masses" value="true"/>
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330 <param name="id_format" value="ID"/>
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331 <section name="mzTab">
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332 <param name="exportIsotopeIntensities" value="false"/>
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333 </section>
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334 </section>
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335 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_annotation_FLAG"/>
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336 <output name="ctd_out" ftype="xml">
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337 <assert_contents>
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338 <is_valid_xml/>
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339 </assert_contents>
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340 </output>
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341 </test>
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342 <!-- UTILS_AccurateMassSearch_6 -->
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343 <test expect_num_outputs="3">
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344 <section name="adv_opts">
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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 <param name="in" value="AccurateMassSearch_2_input.featureXML"/>
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349 <output name="out" file="AccurateMassSearch_6_output.tmp.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
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350 <param name="out_annotation_type" value="featureXML"/>
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351 <output name="out_annotation" file="AccurateMassSearch_6_output.tmp.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
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352 <param name="positive_adducts" value="AMS_PositiveAdducts.tsv" ftype="tabular"/>
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353 <param name="negative_adducts" value="AMS_NegativeAdducts.tsv" ftype="tabular"/>
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354 <section name="db">
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355 <conditional name="mapping_cond">
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356 <param name="mapping" value="AMS_test_Mapping.tsv" ftype="tabular"/>
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357 </conditional>
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358 <conditional name="struct_cond">
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359 <param name="struct" value="AMS_test_Struct.tsv" ftype="tabular"/>
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360 </conditional>
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361 </section>
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362 <section name="algorithm">
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363 <param name="mass_error_value" value="5.0"/>
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364 <param name="mass_error_unit" value="ppm"/>
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365 <param name="ionization_mode" value="positive"/>
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366 <param name="isotopic_similarity" value="false"/>
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367 <param name="use_feature_adducts" value="false"/>
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368 <param name="keep_unidentified_masses" value="true"/>
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369 <param name="id_format" value="ID"/>
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370 <section name="mzTab">
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371 <param name="exportIsotopeIntensities" value="false"/>
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372 </section>
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373 </section>
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374 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_annotation_FLAG"/>
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375 <output name="ctd_out" ftype="xml">
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376 <assert_contents>
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377 <is_valid_xml/>
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378 </assert_contents>
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379 </output>
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380 </test>
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381 </tests>
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382 <help><![CDATA[Match MS signals to molecules from a database by mass.
0
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383
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384
16
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385 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_AccurateMassSearch.html]]></help>
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386 <expand macro="references"/>
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387 </tool>