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annotate macros.xml @ 8:efd14b326007 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
author computational-metabolomics
date Wed, 12 Jun 2024 16:05:01 +0000
parents 0cc6b67dccb8
children 751b7378a683
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1 <?xml version="1.0"?>
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2 <macros>
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3 <token name="@TOOL_VERSION@">1.16.2</token>
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4 <token name="@GALAXY_TOOL_VERSION@">2</token>
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6 <xml name="requirements">
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@" >bioconductor-mspurity</requirement>
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9 <requirement type="package" version="1.46.0" >bioconductor-camera</requirement>
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10 <requirement type="package" version="3.12.0" >bioconductor-xcms</requirement>
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11 <requirement type="package" version="1.18.0" >bioconductor-mspuritydata</requirement>
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12 <requirement type="package" version="1.6.6">r-optparse</requirement>
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13 <requirement type="package" version="1.3.1">r-rpostgres</requirement>
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14 <requirement type="package" version="0.10.21">r-rmysql</requirement>
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15 <yield />
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16 </requirements>
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17 </xml>
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19 <xml name="text-adduct-regex-validator">
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20 <validator type="regex" message="Value may include alphanumeric characters, white space, commas, +, -, [ or ] ">[A-Za-z0-9,\[\] \+\-]+</validator>
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21 </xml>
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23 <xml name="offsets">
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24 <param argument="--minoffset" type="float" label="minoffset" value="0.5"
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25 help="Offset to the 'left' for the precursor range e.g. if precursor of interest is
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26 100.0 then the range would be from 99.5 to 100.0"/>
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27 <param argument="--maxoffset" type="float" label="maxoffset" value="0.5"
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28 help="Offset to the 'right' for the precursor range e.g. if precursor of interest is
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29 100.0 then the range would be from 100.0 to 100.5"/>
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30 </xml>
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31 <xml name="general_params">
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32 <param argument="--ilim" type="float" value="0.05"
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33 label="Threshold to remove peaks below x % of the relative intensity of
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34 precursor of interest"
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35 help="All peaks less than this percentage of the precursor ion of interest will be
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36 removed from the purity calculation, default is 5\% (0.05).
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37 Essentially a noise filter to remove peaks that are thought to have either none or
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38 very limited impact on the resulting fragmentation spectra."/>
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39 <param argument="--iw_norm" type="select" label="Normalisation for isolation efficiency">
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40 <option value="gauss" >Gaussian</option>
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41 <option value="rcosine" >Raised cosine</option>
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42 <option value="QE5"> Calculated from Q-Exactive for +/- 0.5 Da windows </option>
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43 <option value="none" selected="true" >No normalisation</option>
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44 </param>
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45 <conditional name="isotopes">
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46 <param argument="--isotopes" type="select" label="Handling of isotopic peaks" >
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47 <option value="keep" >Keep isotopes in precursor ion purity calculation</option>
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48 <option value="exclude_default" selected="true" >Exclude C12/C13 isotopes in precursor ion purity calculation</option>
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49 <option value="user" >Exclude a user supplied list of isotopes in purity calculation</option>
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50 </param>
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51 <when value="keep">
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52 </when>
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53 <when value="exclude_default">
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54 </when>
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55 <when value="user">
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56 <param argument="--im" type="data" format="tabular" label="Isotope matrix" help="
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57 tabular file composing of columns:
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58 ['isotope_id', 'mass diff', 'abundance of isotope', 'ppm tol for mz', 'abundance buffer',
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59 'charge', 'relative atomic mass (int)', 'xflag'].
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60 The xflag indicates if the larger (mass) isotope is the most abundant or less abundant.
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61 e.g. for c12 to c13, the c13 is less abundant so we flag as 1 for Li6 to Li7, the Li7 is more abundant
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62 so we would flag as 0.
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63 Example row: For C13 isotope (single charge) the row could be [1, 1.003355, 1.07, 4, 0.1, 1, 12, 1]"/>
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64 </when>
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65 </conditional>
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66 </xml>
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67
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68
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69 <xml name="camera_xcms">
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70 <param argument="--camera_xcms" type="select" label="Use CAMERA object or XCMS object from RData?"
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71 help="Within the RData file there should be either an XCMS object called xset or a CAMERA object called
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72 xa (or both). The XCMS object is nested within the CAMERA object so either can be used">
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73 <option value="xcms" selected="true" >XCMS (xset)</option>
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74 <option value="camera" >CAMERA (xa)</option>
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75 </param>
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76 </xml>
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77
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78
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79 <xml name="fileload">
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80 <conditional name="file_load_conditional">
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81 <param name="file_load_select" type="select" label="Resubmit your dataset"
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82 help="Use only if you get a message which say that your original dataset or
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83 dataset collection can not be found the server." >
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84 <option value="no" >no need</option>
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85 <option value="yes" >yes</option>
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86 </param>
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87 <when value="no">
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88 </when>
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89 <when value="yes">
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90 <param name="input" type="data_collection" collection_type="list" format="mzxml,mzml,mzdata,netcdf"
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91 multiple="true" label="File(s) from your history containing your chromatograms"
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92 help="Select the dataset collection containing the files that were used
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93 for processing" />
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94 </when>
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95 </conditional>
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96 </xml>
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97
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98 <xml name="grp_peaklist">
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99 <conditional name="grp_peaklist_opt">
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100 <param name="grp_peaklist_opt" type="select" label="Add a different grouped peaklist to database?">
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101 <option value="yes" >Provide group peaklist </option>
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102 <option value="no" selected="true">Use default grouped peaklist</option>
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103 </param>
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104 <when value="no">
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105 </when>
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106 <when value="yes">
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107 <param argument="--grp_peaklist" type="data" label="grouped peaklist"
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108 help="User supplied grouped peaklist to add to the database (if additional columns required e.g.
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109 CAMERA annotations" format="tsv,tabular"/>
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110 </when>
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111 </conditional>
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112 </xml>
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113
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114 <xml name="sm_input" token_ql='Query' token_dblabel="SQLite database" token_ql_shrt="Q"
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115 token_user="True" token_mspuritydatalib="False" token_msp="False" token_help="">
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116 <conditional name="@QL_SHRT@_dbPth_con">
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117 <param argument="--@QL_SHRT@_dbPth_select" type="select" label="Input" help="@HELP@" >
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118 <option value="sqlite" selected="@USER@" >SQLite database of (LC)-MS/MS data</option>
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119 <option value="local_config" selected="@USER@" >Locally configured SQLite, MySQL or PostgreSQL database</option>
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120 <option value="msPurityData" selected="@MSPURITYDATALIB@" >Prepared database of MassBank, HMDB, LipidBlast and GNPS</option>
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121 </param>
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122 <when value="sqlite">
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123 <param argument="--@QL_SHRT@_dbPth" type="data" label="@QL@ SQLite database" format="sqlite" help=""/>
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124 </when>
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125 <when value="local_config">
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126 </when>
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127 <when value="msPurityData">
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128 </when>
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129 </conditional>
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130 </xml>
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131
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132
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133 <xml name="filters" token_ql="Query" token_polarity_positive="false" token_ql_shrt="Q"
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134 token_sources_select="false" token_instrument_types_select="false">
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135
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136 <section name="@QL_SHRT@_filters" title="Filters" expanded="False">
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137
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138 <param argument="--@QL_SHRT@_ppmPrec" type="float" value="5" label="ppm error of the precursor for spectra"/>
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139 <param argument="--@QL_SHRT@_ppmProd" type="float" value="10" label="ppm error of the product for spectra"/>
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140
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141 <conditional name="@QL_SHRT@_raThres_cond">
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142 <param name="@QL_SHRT@_raThres_bool" type="boolean" label="Filter on relative abundance threshold?"/>
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143 <when value="true">
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144 <param argument="--@QL_SHRT@_raThres" type="float" value = '2' label="Relative abundance threshold"/>
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145 </when>
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146 <when value="false">
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147 </when>
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148 </conditional>
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149
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150 <conditional name="@QL_SHRT@_polarity_cond">
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151 <param name="@QL_SHRT@_polarity_bool" type="boolean" label="Filter on polarity?" help="" />
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152 <when value="true">
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153 <param argument="--@QL_SHRT@_polarity" type="select" label="Polarity" multiple="true" >
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154 <option value="positive" selected="@POLARITY_POSITIVE@">Positive</option>
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155 <option value="negative" >Negative</option>
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156 <option value="NA" >NA</option>
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157 </param>
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158 </when>
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159 <when value="false">
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160 </when>
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161 </conditional>
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162
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163 <conditional name="@QL_SHRT@_purity_cond">
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164 <param name="@QL_SHRT@_purity_bool" type="boolean" label="Filter on precursor ion purity?"/>
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165 <when value="true">
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166 <param argument="--@QL_SHRT@_purity" type="float" min="0" max="1" value="0.6"
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167 label="Precursor ion purity threshold"/>
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168 </when>
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169 <when value="false">
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170 </when>
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171 </conditional>
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172
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
173 <conditional name="@QL_SHRT@_xcmsGroups_cond">
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
174 <param name="@QL_SHRT@_xcmsGroups_bool" type="boolean" label="Filter on XCMS groups ids?"/>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
175 <when value="true">
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
176 <param argument="--@QL_SHRT@_xcmsGroups" type="text" value=""
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
177 label="XCMS group ids of spectra"
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
178 help="comma seperated list of grpids (correspond to column 'grpid in c_peak_group'))
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
179 e.g '12,27,30'" />
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
180 </when>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
181 <when value="false">
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
182 </when>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
183 </conditional>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
184
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
185
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
186 <conditional name="@QL_SHRT@_pids_cond">
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
187 <param name="@QL_SHRT@_pids_bool" type="boolean" label="Filter on pids?"/>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
188 <when value="true">
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
189 <param argument="--@QL_SHRT@_pids" type="text" value=""
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
190 label="pids of spectra (correspond to column 'pid; in s_peak_meta)"
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
191 help="comma seperated list of pids (correspond to column 'pid; in s_peak_meta))
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
192 e.g '3001,5561'" />
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
193 </when>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
194 <when value="false">
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
195 </when>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
196 </conditional>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
197
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
198
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
199 <conditional name="@QL_SHRT@_rtrange_cond">
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
200 <param name="@QL_SHRT@_rtrange_bool" type="boolean"
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
201 label="Filter on retention time range?"
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
202 help="Filter the spectra between two points of retention time range"/>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
203 <when value="true">
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
204 <param argument="--@QL_SHRT@_rtrangeMin" label="Minimum retention time range (seconds)"
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
205 type="float" value="0" help=""/>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
206 <param argument="--@QL_SHRT@_rtrangeMax" label="Maximum retention time range (seconds)"
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
207 type="float" value="3000" help=""/>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
208 </when>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
209 <when value="false">
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
210 </when>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
211 </conditional>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
212
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
213
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
214
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
215 <conditional name="@QL_SHRT@_accessions_cond">
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
216 <param name="@QL_SHRT@_accessions_bool" type="boolean"
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
217 label="Filter on accessions?"
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
218 help="Filter on unique accessions IDs (e.g. from MassBank and MoNA)"/>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
219 <when value="true">
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
220 <param argument="--@QL_SHRT@_accessions" type="text" value=""
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
221 label="Spectra accessions"
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
222 help="Comma seperated list of accessions))
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
223 e.g 'AC000001,BS001003,LIT00001'" />
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
224 </when>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
225 <when value="false">
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
226 </when>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
227 </conditional>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
228
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
229
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
230 <conditional name="@QL_SHRT@_sources_cond">
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
231 <param name="@QL_SHRT@_sources_bool" type="boolean"
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
232 label="Filter on sources?" help="" value="@SOURCES_SELECT@" />
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
233 <when value="true">
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
234 <param argument="--@QL_SHRT@_sources" type="select" multiple="true"
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
235 help="@QL_SHRT@ The default internal SQLite database of library (reference) spectra
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
236 contains fragmentation spectra from MassBank, LipidBlast and GNPS. A copy is
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
237 available from here:
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
238 https://bioconductor.org/packages/release/data/experiment/html/msPurityData.html" >
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
239 <option value="massbank" selected="true">MassBank from MoNa</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
240 <option value="gnps" selected="true">GNPS</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
241 <option value="hmdb" selected="true">HMDB</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
242 <option value="lipidblast" selected="true">LipidBlast</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
243 </param>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
244 <param name="@QL_SHRT@_sourcesUser" type="text" label="Sources - user specific" value=""
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
245 help="comma seperated list of additional sources (e.g. if the user has other
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
246 sources - like there own personal library)
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
247 e.g 'LIPIDS_03052019,HILIC_03052019'" />
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
248 </when>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
249 <when value="false">
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
250 </when>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
251 </conditional>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
252 <conditional name="@QL_SHRT@_instrumentTypes_cond">
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
253 <param name="@QL_SHRT@_instrumentTypes_bool" type="boolean"
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
254 value="@INSTRUMENT_TYPES_SELECT@"
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
255 label="Filter on instrument type?" help="" />
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
256 <when value="true">
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
257 <param argument="--@QL_SHRT@_instrumentTypes" type="select" multiple="true"
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
258 help="" >
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
259 <option value="APCI-ITFT" selected="true" >APCI-ITFT</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
260 <option value="APCI-ITTOF" selected="true" >APCI-ITTOF</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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261 <option value="CE-ESI-TOF" selected="true" >CE-ESI-TOF</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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262 <option value="CI-B">CI-B</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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263 <option value="EI-B">EI-B</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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264 <option value="EI-EBEB">EI-EBEB</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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265 <option value="ESI-ITFT" selected="true" >ESI-ITFT</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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266 <option value="ESI-ITTOF" selected="true" >ESI-ITTOF</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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267 <option value="ESI-QFT" selected="true" >ESI-QFT</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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268 <option value="ESI-QTOF" selected="true" >ESI-QTOF</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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269 <option value="ESI-TOF" selected="true" >ESI-TOF</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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270 <option value="FAB-B">FAB-B</option>
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computational-metabolomics
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271 <option value="FAB-BE">FAB-BE</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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272 <option value="FAB-EB">FAB-EB</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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273 <option value="FAB-EBEB">FAB-EBEB</option>
7
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274 <option value="FD-B">FD-B</option>
0
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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275 <option value="FI-B">FI-B</option>
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computational-metabolomics
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276 <option value="Flow-injection QqQ/MS">Flow-injection QqQ/MS</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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277 <option value="GC-EI-Q">GC-EI-Q</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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278 <option value="GC-EI-QQ">GC-EI-QQ</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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279 <option value="GC-EI-TOF">GC-EI-TOF</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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280 <option value="GC-MS">GC-MS</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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281 <option value="Hybrid FT">Hybrid FT</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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282 <option value="in source CID" selected="true" >in source CID</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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283 <option value="In-silico QTOF" selected="true" >In-silico QTOF</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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284 <option value="Ion trap" selected="true" >Ion trap</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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285 <option value="LC-APCI-ITFT" selected="true" >LC-APCI-ITFT</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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286 <option value="LC-APCI-QTOF" selected="true" >LC-APCI-QTOF</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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287 <option value="LC-APCI-Q" selected="true">LC-APCI-Q</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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288 <option value="LC-APPI-QQ">LC-APPI-QQ</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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289 <option value="LC-ESI-IT" selected="true">LC-ESI-IT</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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290 <option value="LC-ESI-ITFT" selected="true">LC-ESI-ITFT</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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291 <option value="LC-ESI-ITTOF" selected="true">LC-ESI-ITTOF</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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292 <option value="LC-ESI-Q" selected="true">LC-ESI-Q</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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293 <option value="LC-ESI-QFT" selected="true">LC-ESI-QFT</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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294 <option value="LC-ESI-QIT" selected="true">LC-ESI-QIT</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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295 <option value="LC-ESI-QQ" selected="true">LC-ESI-QQ</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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296 <option value="LC-ESI-QTOF" selected="true">LC-ESI-QTOF</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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297 <option value="LC-ESI-TOF" selected="true">LC-ESI-TOF</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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298 <option value="LC-Q-TOF/MS" selected="true">LC-Q-TOF/MS</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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299 <option value="LC-QTOF" selected="true">LC-QTOF</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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300 <option value="Linear Ion Trap" selected="true">Linear Ion Trap</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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301 <option value="LIT" selected="true">LIT</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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302 <option value="MALDI-QIT" selected="true">MALDI-QIT</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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303 <option value="MALDI-TOF" selected="true">MALDI-TOF</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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304 <option value="MALDI-TOFTOF" selected="true">MALDI-TOFTOF</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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305 <option value="orbitrap" selected="true">orbitrap</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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306 <option value="QIT" selected="true">QIT</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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307 <option value="QIT-FT" selected="true">QIT-FT</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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308 <option value="QIT-TOF" selected="true">QIT-TOF</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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309 <option value="QqQ" selected="true">QqQ</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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310 <option value="Q-TOF" selected="true">Q-TOF</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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311 <option value="Quattro_QQQ" selected="true">Quattro_QQQ</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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312 <option value="none">None</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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313 </param>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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314 <param argument="--@QL_SHRT@_instrumentTypesUser" type="text" value=""
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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315 help="Types of the instruments to be included in the search. Use a comma to
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
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316 separate the instrument types or leave empty to ignore filter."/>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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317 </when>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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318 <when value="false">
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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319 </when>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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320 </conditional>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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321 <conditional name="@QL_SHRT@_instruments_cond">
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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322 <param name="@QL_SHRT@_instruments_bool" type="boolean" label="Filter on instrument name?" help="" />
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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323 <when value="true">
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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324 <param argument="--@QL_SHRT@_instruments" type="text" value=""
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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325 help="Known instrument names to filter on. Use a comma to
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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326 separate the instrument types or leave empty to ignore filter."/>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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327 </when>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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328 <when value="false">
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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329 </when>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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330 </conditional>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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331
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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332
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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333
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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334 <conditional name="@QL_SHRT@_spectraTypes_cond">
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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335 <param name="@QL_SHRT@_spectraTypes_bool" type="boolean" label="Filter on spectral type?"
7
0cc6b67dccb8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e3b17490a958d80ebe78ef1bebebef48948e1240"
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336 help="Note that when using 'scan' spectra types the spectraFilter option may need to be FALSE
0cc6b67dccb8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e3b17490a958d80ebe78ef1bebebef48948e1240"
computational-metabolomics
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diff changeset
337 if 'allfrag' was not selecting when performing filterFragSpectra or if no filtering was performed at all" />
0
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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338 <when value="true">
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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339 <param argument="--@QL_SHRT@_spectraTypes" type="select" multiple="true" label="Spectra type" >
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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340 <option value="av_all" selected="true">Averaged all spectra ignoring inter-intra relationships </option>
6
2f71b3495221 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
computational-metabolomics
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341 <option value="inter">Averaged inter spectra</option>
2f71b3495221 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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342 <option value="intra">Averaged intra spectra </option>
7
0cc6b67dccb8 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e3b17490a958d80ebe78ef1bebebef48948e1240"
computational-metabolomics
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343 <option value="scan">All individual scans (may need to set spectraFilter to false with this option)</option>
0
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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344 <option value="NA">Not applicable/defined</option>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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345 </param>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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346 </when>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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347 <when value="false">
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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348 </when>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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349 </conditional>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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350
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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351 <param argument="--@QL_SHRT@_spectraFilter" type="boolean" checked="true"
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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352 label="Ignore any peaks flagged in the spectra in previous stages?"
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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353 help="" />
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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354
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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355 </section>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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356 </xml>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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357
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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358
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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359
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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360
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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361 <xml name="citations">
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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362 <citations>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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363 <citation type="doi">10.1021/acs.analchem.6b04358</citation>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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364 <yield />
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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365 </citations>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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366 </xml>
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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367
f52287a06c02 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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368 </macros>