Mercurial > repos > tomnl > mspurity_createmsp

annotate createMSP.xml @ 0:df2efceff4cd draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
author tomnl
date Fri, 24 May 2019 09:06:56 -0400
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1 <tool id="mspurity_createmsp" name="msPurity.createMSP" version="0.2.0">
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2 <description>Create MSP files from msPurity processed data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 </expand>
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8 <stdio>
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9 <exit_code range="1:" />
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10 </stdio>
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11 <command interpreter="Rscript" ><![CDATA[
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12 createMSP.R
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13 --rdata_input "$rdata_input"
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14 --method "$method"
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16 #if $metadata_cond.metadata_select == "true"
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17 --metadata "$metadata_cond.metadata"
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18 --metadata_cols "$metadata_cond.metadata_cols"
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19 --adduct_split "$metadata_cond.adduct_split"
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20 #end if
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22 #if $xcms_group_cond.xcms_group_select == "true"
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23 --xcms_groupids "$xcms_group_cond.xcms_groupids"
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24 #end if
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26 $filter
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28 --msp_schema "$msp_schema"
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29 --intensity_ra "$intensity_ra"
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31 --out_dir '.'
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32 ]]></command>
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33 <inputs>
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34 <param name="rdata_input" type="data" format="rdata" label="msPurity purityA dataset" argument="--purity_dataset"
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35 help="RData file containing the purityA object following frag4feature and/or averageFragmentation"/>
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36 <param name="method" type="select" label="How to choose fragmentation spectra (if precursor was fragmented in >1 scans per XCMS group feature)"
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37 help="'Average all' will use the averaged MS/MS spectra of the XCMS grouped feature, ignoring inter and intra file relationships,
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38 'Average' (intra)' will use the intra file (within file) averaged MS/MS spectra of the XCMS grouped feature,
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39 'Average (inter)' will use the inter file (across file) MS/MS averaged spectra,
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40 'All scans' will export all matching MS/MS spectra to XCMS grouped features,
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41 'Max intensity' will choose the most MS/MS spectra with the most intense precursor ion for each XCMS grouped feature"
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42 argument="--method">
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43 <option value="av_all" selected="true">Average (all)</option>
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44 <option value="av_intra">Average (intra)</option>
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45 <option value="av_inter">Average (inter)</option>
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46 <option value="all">All scans</option>
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47 <option value="max" >Max intensity</option>
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48 </param>
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49
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50 <conditional name="metadata_cond">
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51 <param name="metadata_select" type="boolean" label="Use additional metadata?" />
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52 <when value="true">
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53 <param type="data" name="metadata" label="Metadata for each feature" format="tsv,tabular"
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54 help="Metadata for each grouped XCMS feature, the data will be added to the MSP metadata.
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55 Using the MassBank format e.g. https://github.com/MassBank/MassBank-data/blob/master/MetaboLights/ML003001.txt "/>
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56
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57 <param name="metadata_cols" type="text" label="Metadata columns for name" value="CH$NAME, MS$FOCUSED_ION: PRECURSOR_TYPE" help="Comma separated string of column names where the corresponding values in the metadata will be used for the MSP spectra name"/>
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58 <param name="adduct_split" type="boolean" checked="true" label="Create MSP spectra for each adduct?" help="If either 'adduct' or 'MS$FOCUSED_ION: PRECURSOR_TYPE'
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59 column is in metadata then each adduct will have it's own MSP spectra.
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60 (Useful, if the MSP file will be used for further annotation)" />
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61 </when>
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62 <when value="false">
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63 </when>
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64 </conditional>
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65
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66 <conditional name="xcms_group_cond">
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67 <param name="xcms_group_select" type="boolean" label="Select XCMS groups?" help="if set to no, all XCMS group features will be used" />
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68 <when value="true">
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69 <param name="xcms_groupids" type="text" label="XCMS peak group ids" value=""
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70 help="Comma separated string of XCMS group ids to export MSP spectra for. If blank all XCMS peak groups will be used"/>
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71 </when>
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72 <when value="false">
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73 </when>
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74 </conditional>
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75
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76 <param name="intensity_ra" type="select" label="Include intensity, relative abundanace or both in the MSP file"
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77 argument="--intensity_ra">
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78 <option value="intensity_ra" selected="true">Both intensity and relative abundance</option>
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79 <option value="intensity">Intensity only</option>
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80 <option value="ra">Relative abundance only</option>
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81 </param>
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82
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83 <param name="msp_schema" type="select" label="MSP schema to use for files"
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84 argument="--msp_schema">
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85 <option value="massbank" selected="true">MassBank (Europe)</option>
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86 <option value="mona">MoNA</option>
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87
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88 </param>
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89
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90 <param name="filter" type="boolean" checked="true" truevalue="--filter" falsevalue="" label="Filter peaks that have been flagged in prior processing steps" help="" />
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91
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92 </inputs>
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93 <outputs>
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94 <data name="createMSP_output" format="msp" from_work_dir="lcmsms_spectra.msp" label="${tool.name} on ${on_string}: msp"/>
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95 </outputs>
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96 <tests>
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97 <test>
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98 <param name="method" value="all"/>
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99 <param name="rdata_input" value="frag4feature_output.RData"/>
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100 <output name="createMSP_output" file="createMSP_output_scans_all.msp"/>
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101 </test>
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102 <test>
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103 <param name="method" value="av_all"/>
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104 <param name="rdata_input" value="averageFragSpectra_output_all.RData"/>
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105 <output name="createMSP_output" file="createMSP_output_av_all.msp"/>
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106 </test>
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107 <test>
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108 <param name="method" value="av_all"/>
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109 <param name="rdata_input" value="averageFragSpectra_output_all.RData"/>
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110 <param name="metadata_cond|metadata_select" value="true"/>
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111 <param name="metadata_cond|metadata" value="createMSP_input_metadata.tsv"/>
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112 <param name="metadata_cond|metadata_cols" value="AC$CHROMATOGRAPHY: COLUMN_NAME, AC$MASS_SPECTROMETRY: ION_MODE, AC$MASS_SPECTROMETRY: MS_TYPE, CH$LINK: INCHIKEY, CH$LINK: PUBCHEM CH$NAME
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113 "/>
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114 <param name="xcms_group_cond|xcms_group_select" value="true"/>
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115 <param name="xcms_group_cond|xcms_groupids" value="8,12"/>
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116 <param name="metadata_cond|adduct_split" value="true"/>
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117 <output name="createMSP_output" file="createMSP_output_av_all_metadata.msp"/>
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118 </test>
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119 <test>
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120 <param name="method" value="av_all"/>
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121 <param name="rdata_input" value="averageFragSpectra_output_all.RData"/>
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122 <param name="xcms_group_cond|xcms_group_select" value="true"/>
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123 <param name="xcms_group_cond|xcms_groupids" value="8,12"/>
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124 <output name="createMSP_output" file="createMSP_output_av_all_and_all_xcms.msp"/>
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125 </test>
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126 <test>
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127 <param name="method" value="av_intra"/>
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128 <param name="rdata_input" value="averageFragSpectra_output_intra.RData"/>
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129 <output name="createMSP_output" file="createMSP_output_av_intra.msp"/>
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130 </test>
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131 <test>
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132 <param name="method" value="av_inter"/>
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133 <param name="rdata_input" value="averageFragSpectra_output_inter.RData"/>
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134 <output name="createMSP_output" file="createMSP_output_av_inter.msp"/>
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135 </test>
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136 <test>
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137 <param name="method" value="max"/>
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138 <param name="rdata_input" value="frag4feature_output.RData"/>
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139 <output name="createMSP_output" file="createMSP_output_max.msp"/>
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140 </test>
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141 </tests>
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142 <help><![CDATA[
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143 ------------------------------
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144 Create MSP Files from msPurity
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145 ------------------------------
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146
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147 Description
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148 -----------
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149
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150 | This tool will extract the MSMS spectra data from an msPurity-frag4feature object into a file with MSP data format.
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151
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152
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153
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154
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155 Developers and contributors
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156 ---------------------------
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157
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158 - **Jordi Capellades (j.capellades.to@gmail.com) - Universitat Rovira i Virgili (SP)**
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159 - **Andris Jankevics (a.jankevics@bham.ac.uk) - University of Birmingham (UK)**
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160 - **Thomas N. Lawson (t.n.lawson@bham.ac.uk) - University of Birmingham (UK)**
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161 - **Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)**
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162
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163 ]]></help>
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164
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165 <expand macro="citations" />
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166
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167 </tool>