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annotate macros.xml @ 10:1ce857d74106 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit b6b8da66a6eef180ca8e333f98fc4b7575bac7b3
author tomnl
date Thu, 27 Jun 2019 12:40:06 -0400
parents c874652f3029
children a90832e6acb2
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1 <?xml version="1.0"?>
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2 <macros>
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3 <token name="@TOOL_VERSION@">1.11.3</token>
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4 <token name="@GALAXY_TOOL_VERSION@">0.2.5</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 <yield />
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10 </requirements>
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11 </xml>
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14 <xml name="offsets">
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15 <param name="minoffset" type="float" label="minoffset" value="0.5" argument='--minoffset'
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16 help="Offset to the 'left' for the precursor range e.g. if precursor of interest is
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17 100.0 then the range would be from 999.5 to 100.0"/>
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18 <param name="maxoffset" type="float" label="maxoffset" value="0.5" argument='--maxoffset'
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19 help="Offset to the 'right' for the precursor range e.g. if precursor of interest is
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20 100.0 then the range would be from 100.0 to 100.5"/>
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21 </xml>
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22 <xml name="general_params">
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23 <param name="ilim" type="float" value="0.05" argument='--ilim'
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24 label="Threshold to remove peaks below x % of the relative intensity of
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25 precursor of interest"
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26 help="All peaks less than this percentage of the precursor ion of interest will be
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27 removed from the purity calculation, default is 5\% (0.05).
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28 Essentially a noise filter to remove peaks that are thought to have either none or
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29 very limited impact on the resulting fragmentation spectra."/>
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30 <param name="iw_norm" type="select" label="Normalisation for isolation efficiency">
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31 <option value="gauss" >Gaussian</option>
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32 <option value="rcosine" >Raised cosine</option>
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33 <option value="QE5"> Calculated from Q-Exactive for +/- 0.5 Da windows </option>
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34 <option value="none" selected="true" >No normalisation</option>
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35 </param>
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36 <conditional name="isotopes">
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37 <param name="isotopes" type="select" label="Handling of isotopic peaks" >
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38 <option value="keep" >Keep isotopes in precursor ion purity calculation</option>
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39 <option value="exclude_default" selected="true" >Exclude C12/C13 isotopes in precursor ion purity calculation</option>
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40 <option value="user" >Exclude a user supplied list of isotopes in purity calculation</option>
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41 </param>
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42 <when value="keep">
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43 </when>
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44 <when value="exclude_default">
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45 </when>
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46 <when value="user">
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47 <param name="im" type="data" format="tabular" label="Isotope matrix" help="
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48 tabular file composing of columns:
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49 ['isotope_id', 'mass diff', 'abundance of isotope', 'ppm tol for mz', 'abundance buffer',
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50 'charge', 'relative atomic mass (int)', 'xflag'].
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51 The xflag indicates if the larger (mass) isotope is the most abundant or less abundant.
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52 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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53 so we would flag as 0.
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54 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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55 </when>
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56 </conditional>
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57 </xml>
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58
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59
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60 <xml name="camera_xcms">
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61 <param name="camera_xcms" type="select" label="Use CAMERA object or XCMS object from RData?"
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62 help="Within the RData file there should be either an XCMS object called xset or a CAMERA object called
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63 xa (or both). The XCMS object is nested within the CAMERA object so either can be used">
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64 <option value="xcms" selected="true" >XCMS (xset)</option>
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65 <option value="camera" >CAMERA (xa)</option>
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66 </param>
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67 </xml>
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68
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69
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70 <xml name="fileload">
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71 <conditional name="file_load_conditional">
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72 <param name="file_load_select" type="select" label="Resubmit your dataset"
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73 help="Use only if you get a message which say that your original dataset or
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74 dataset collection can not be found the server." >
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75 <option value="no" >no need</option>
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76 <option value="yes" >yes</option>
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77 </param>
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78 <when value="no">
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79 </when>
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80 <when value="yes">
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81 <param name="input" type="data_collection" collection_type="list" format="mzxml,mzml,mzdata,netcdf"
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82 multiple="true" label="File(s) from your history containing your chromatograms"
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83 help="Select the dataset collection containing the files that were used
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84 for processing" />
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85 </when>
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86 </conditional>
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87 </xml>
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88
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89 <xml name="grp_peaklist">
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90 <conditional name="grp_peaklist_opt">
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91 <param name="grp_peaklist_opt" type="select" label="Add a different grouped peaklist to database?">
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92 <option value="yes" >Provide group peaklist </option>
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93 <option value="no" selected="true">Use default grouped peaklist</option>
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94 </param>
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95 <when value="no">
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96 </when>
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97 <when value="yes">
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98 <param type="data" name="grp_peaklist" label="grouped peaklist"
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99 help="User supplied grouped peaklist to add to the database (if additional columns required e.g.
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100 CAMERA annotations" format="tsv,tabular"/>
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101 </when>
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102 </conditional>
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103 </xml>
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104
0
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105
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106 <xml name="sm_input" token_ql='Query' token_dblabel="SQLite database" token_ql_shrt="Q"
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107 token_user="True" token_mspuritydatalib="False" token_msp="False" token_help="">
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108 <conditional name="@QL_SHRT@_dbPth_con">
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109 <param name="@QL_SHRT@_dbPth_select" type="select" label="Input" help="@HELP@" >
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110 <option value="userdb" selected="@USER@" >SQLite database of (LC)-MS/MS data</option>
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111 <option value="msPurityData" selected="@MSPURITYDATALIB@" >Prepared database of MassBank, HMDB, LipidBlast and GNPS</option>
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112 <option value="msp" >MSP file (SQLite database will be created using using msp2db)</option>
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113 </param>
0
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114 <when value="userdb">
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115 <param type="data" name="@QL_SHRT@_dbPth" label="@QL@ SQLite database" format="sqlite" help=""/>
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116 </when>
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117 <when value="msp">
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118 <param type="data" name="@QL_SHRT@_msp" label="@QL@ MSP file" format="msp" help=""/>
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119 </when>
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120
0
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121 <when value="msPurityData">
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122 </when>
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123 </conditional>
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124 </xml>
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125
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126
0
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127 <xml name="filters" token_ql="Query" token_polarity_positive="false" token_ql_shrt="Q"
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128 token_sources_select="false" token_instrument_types_select="false">
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129
0
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130 <section name="@QL_SHRT@_filters" title="Filters" expanded="False">
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131
0
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132 <param name="@QL_SHRT@_ppmPrec" type="float" value="5" label="ppm error of the precursor for spectra"/>
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133 <param name="@QL_SHRT@_ppmProd" type="float" value="10" label="ppm error of the product for spectra"/>
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134
0
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135 <conditional name="@QL_SHRT@_raThres_cond">
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136 <param name="@QL_SHRT@_raThres_bool" type="boolean" label="Filter on relative abundance threshold?"/>
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137 <when value="true">
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138 <param name="@QL_SHRT@_raThres" type="float" value = '2' label="Relative abundance threshold"/>
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139 </when>
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140 <when value="false">
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141 </when>
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142 </conditional>
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143
0
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144 <conditional name="@QL_SHRT@_polarity_cond">
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145 <param name="@QL_SHRT@_polarity_bool" type="boolean" label="Filter on polarity?" help="" />
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146 <when value="true">
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147 <param name="@QL_SHRT@_polarity" type="select" label="Polarity" multiple="true" >
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148 <option value="positive" selected="@POLARITY_POSITIVE@">Positive</option>
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149 <option value="negative" >Negative</option>
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150 <option value="NA" >NA</option>
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151 </param>
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152 </when>
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153 <when value="false">
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154 </when>
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155 </conditional>
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156
0
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157 <conditional name="@QL_SHRT@_purity_cond">
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158 <param name="@QL_SHRT@_purity_bool" type="boolean" label="Filter on precursor ion purity?"/>
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159 <when value="true">
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160 <param name="@QL_SHRT@_purity" type="float" min="0" max="1" value="0.6"
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161 label="Precursor ion purity threshold"/>
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162 </when>
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163 <when value="false">
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164 </when>
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165 </conditional>
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166
0
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167 <conditional name="@QL_SHRT@_xcmsGroups_cond">
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168 <param name="@QL_SHRT@_xcmsGroups_bool" type="boolean" label="Filter on XCMS groups ids?"/>
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169 <when value="true">
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170 <param name="@QL_SHRT@_xcmsGroups" type="text" value=""
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171 label="XCMS group ids of spectra"
0
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172 help="comma seperated list of grpids (correspond to column 'grpid in c_peak_group'))
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173 e.g '12,27,30'" />
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174 </when>
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175 <when value="false">
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176 </when>
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177 </conditional>
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178
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179
0
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180 <conditional name="@QL_SHRT@_pids_cond">
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181 <param name="@QL_SHRT@_pids_bool" type="boolean" label="Filter on pids?"/>
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182 <when value="true">
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183 <param name="@QL_SHRT@_pids" type="text" value=""
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184 label="pids of spectra (correspond to column 'pid; in s_peak_meta)"
0
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185 help="comma seperated list of pids (correspond to column 'pid; in s_peak_meta))
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186 e.g '3001,5561'" />
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187 </when>
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188 <when value="false">
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189 </when>
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190 </conditional>
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191
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192
0
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193 <conditional name="@QL_SHRT@_rtrange_cond">
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194 <param name="@QL_SHRT@_rtrange_bool" type="boolean"
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195 label="Filter on retention time range?"
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196 help="Filter the spectra between two points of retention time range"/>
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197 <when value="true">
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198 <param name="@QL_SHRT@_rtrangeMin" label="Minimum retention time range (seconds)"
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199 type="float" value="0" help=""/>
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200 <param name="@QL_SHRT@_rtrangeMax" label="Maximum retention time range (seconds)"
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201 type="float" value="3000" help=""/>
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202 </when>
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203 <when value="false">
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204 </when>
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205 </conditional>
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206
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207
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208
0
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209 <conditional name="@QL_SHRT@_accessions_cond">
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210 <param name="@QL_SHRT@_accessions_bool" type="boolean"
0
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211 label="Filter on accessions?"
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212 help="Filter on unique accessions IDs (e.g. from MassBank and MoNA)"/>
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213 <when value="true">
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214 <param name="@QL_SHRT@_accessions" type="text" value=""
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215 label="Spectra accessions"
0
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216 help="Comma seperated list of accessions))
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217 e.g 'AC000001,BS001003,LIT00001'" />
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218 </when>
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219 <when value="false">
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220 </when>
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221 </conditional>
10
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222
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223
0
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224 <conditional name="@QL_SHRT@_sources_cond">
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225 <param name="@QL_SHRT@_sources_bool" type="boolean"
0
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226 label="Filter on sources?" help="" value="@SOURCES_SELECT@" />
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227 <when value="true">
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228 <param name="@QL_SHRT@_sources" type="select" multiple="true"
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229 help="@QL_SHRT@ The default internal SQLite database of library (reference) spectra
1ce857d74106 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit b6b8da66a6eef180ca8e333f98fc4b7575bac7b3
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230 contains fragmentation spectra from MassBank, LipidBlast and GNPS. A copy is
1ce857d74106 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit b6b8da66a6eef180ca8e333f98fc4b7575bac7b3
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diff changeset
231 available from here:
0
fc9bb7e49a3a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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232 https://bioconductor.org/packages/release/data/experiment/html/msPurityData.html" >
fc9bb7e49a3a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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233 <option value="massbank" selected="true">MassBank from MoNa</option>
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234 <option value="gnps" selected="true">GNPS</option>
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235 <option value="hmdb" selected="true">HMDB</option>
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236 <option value="lipidblast" selected="true">LipidBlast</option>
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237 </param>
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238 <param name="@QL_SHRT@_sourcesUser" type="text" label="Sources - user specific" value=""
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239 help="comma seperated list of additional sources (e.g. if the user has other
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240 sources - like there own personal library)
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241 e.g 'LIPIDS_03052019,HILIC_03052019'" />
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242 </when>
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243 <when value="false">
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244 </when>
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245 </conditional>
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246 <conditional name="@QL_SHRT@_instrumentTypes_cond">
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247 <param name="@QL_SHRT@_instrumentTypes_bool" type="boolean"
0
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248 value="@INSTRUMENT_TYPES_SELECT@"
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249 label="Filter on instrument type?" help="" />
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250 <when value="true">
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251 <param name="@QL_SHRT@_instrumentTypes" type="select" multiple="true"
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252 help="" >
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253 <option value="APCI-ITFT">APCI-ITFT</option>
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254 <option value="CE-ESI-TOF" selected="true">CE-ESI-TOF</option>
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255 <option value="CI-B">CI-B</option>
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256 <option value="EI-B">EI-B</option>
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257 <option value="EI-EBEB">EI-EBEB</option>
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258 <option value="ESI-ITFT" selected="true">ESI-ITFT</option>
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259 <option value="ESI-ITTOF" selected="true">ESI-ITTOF</option>
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260 <option value="ESI-QTOF" selected="true">ESI-QTOF</option>
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261 <option value="FAB-B">FAB-B</option>
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262 <option value="FAB-BE-MS">FAB-BE-MS</option>
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263 <option value="FAB-EB">FAB-EB</option>
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264 <option value="FAB-EBEB">FAB-EBEB</option>
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265 <option value="FI-B">FI-B</option>
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266 <option value="GC-EI-Q">GC-EI-Q</option>
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267 <option value="GC-EI-QQ">GC-EI-QQ</option>
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268 <option value="GC-EI-TOF">GC-EI-TOF</option>
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269 <option value="LC-APCI-QTOF">LC-APCI-QTOF</option>
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270 <option value="LC-APPI-QQ">LC-APPI-QQ</option>
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271 <option value="LC-ESI-IT" selected="true">LC-ESI-IT</option>
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272 <option value="LC-ESI-ITFT" selected="true">LC-ESI-ITFT</option>
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273 <option value="LC-ESI-ITTOF" selected="true">LC-ESI-ITTOF</option>
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274 <option value="LC-ESI-Q">LC-ESI-Q</option>
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275 <option value="LC-ESI-QFT" selected="true" >LC-ESI-QFT</option>
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276 <option value="LC-ESI-QIT" selected="true">LC-ESI-QIT</option>
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277 <option value="LC-ESI-QQ" selected="true">LC-ESI-QQ</option>
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278 <option value="LC-ESI-QTOF" selected="true">LC-ESI-QTOF</option>
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279 <option value="LC-ESI-TOF" selected="true">LC-ESI-TOF</option>
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280 <option value="MALDI-QIT">MALDI-QIT</option>
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281 <option value="MALDI-TOF">MALDI-TOF</option>
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282 <option value="ALDI-TOFTOF">ALDI-TOFTOF</option>
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283 <option value="none">None</option>
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284 </param>
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285 <param name="@QL_SHRT@_instrumentTypesUser" type="text" value=""
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286 help="Types of the instruments to be included in the search. Use a comma to
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287 separate the instrument types or leave empty to ignore filter."/>
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288 </when>
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289 <when value="false">
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290 </when>
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291 </conditional>
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292 <conditional name="@QL_SHRT@_instruments_cond">
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293 <param name="@QL_SHRT@_instruments_bool" type="boolean" label="Filter on instrument name?" help="" />
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294 <when value="true">
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295 <param name="@QL_SHRT@_instruments" type="text" value=""
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296 help="Known instrument names to filter on. Use a comma to
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297 separate the instrument types or leave empty to ignore filter."/>
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298 </when>
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299 <when value="false">
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300 </when>
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301 </conditional>
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302
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303
0
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304
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305 <conditional name="@QL_SHRT@_spectraTypes_cond">
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306 <param name="@QL_SHRT@_spectraTypes_bool" type="boolean" label="Filter on spectral type?"
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307 help="" />
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308 <when value="true">
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309 <param name="@QL_SHRT@_spectraTypes" type="select" multiple="true" label="Spectra type" >
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310 <option value="av_all" selected="true">Averaged all spectra ignoring inter-intra relationships </option>
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311 <option value="av_inter">Averaged inter spectra</option>
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312 <option value="av_intra">Averaged intra spectra </option>
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313 <option value="scans">All individual scans</option>
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314 <option value="NA">Not applicable/defined</option>
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315 </param>
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316 </when>
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317 <when value="false">
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318 </when>
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319 </conditional>
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320
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321 <param name="@QL_SHRT@_spectraFilter" type="boolean" checked="true"
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322 label="Ignore any peaks flagged in the spectra in previous stages?"
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323 help="" />
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324
0
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325 </section>
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326 </xml>
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327
0
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328
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329
0
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330
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331 <xml name="citations">
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332 <citations>
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333 <citation type="doi">10.1021/acs.analchem.6b04358</citation>
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334 <yield />
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335 </citations>
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336 </xml>
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337
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338 </macros>