Mercurial > repos > tomnl > mspurity_createmsp

annotate createMSP.xml @ 12:5dd61e94d70d draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
author tomnl
date Fri, 13 Sep 2019 11:53:46 -0400
parents 4b3b0f5a55d9
children 70257c77ea04
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1 <tool id="mspurity_createmsp" name="msPurity.createMSP" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
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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 "$metadata_cond.metadata_cols"
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19 --metadata_cols_filter "$metadata_cond.metadata_cols_filter"
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20
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21 #end if
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23 #if $xcms_group_cond.xcms_group_select == "true"
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24 --xcms_groupids "$xcms_group_cond.xcms_groupids"
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25 #end if
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27 $filter
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28 $adduct_split
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30 --msp_schema "$msp_schema"
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31 --intensity_ra "$intensity_ra"
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32 --include_adducts "$include_adducts"
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34 --out_dir '.'
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35 ]]></command>
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36 <inputs>
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37 <param name="rdata_input" type="data" format="rdata" label="msPurity purityA dataset" argument="--purity_dataset"
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38 help="RData file containing the purityA object following frag4feature and/or averageFragmentation"/>
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39 <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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40 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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41 'Average' (intra)' will use the intra file (within file) averaged MS/MS spectra of the XCMS grouped feature,
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42 'Average (inter)' will use the inter file (across file) MS/MS averaged spectra,
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43 'All scans' will export all matching MS/MS spectra to XCMS grouped features,
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44 'Max intensity' will choose the most MS/MS spectra with the most intense precursor ion for each XCMS grouped feature"
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45 argument="--method">
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46 <option value="av_all" selected="true">Average (all)</option>
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47 <option value="av_intra">Average (intra)</option>
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48 <option value="av_inter">Average (inter)</option>
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49 <option value="all">All scans</option>
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50 <option value="max" >Max intensity</option>
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51 </param>
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52
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53 <conditional name="metadata_cond">
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54 <param name="metadata_select" type="boolean" label="Use additional metadata?" />
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55 <when value="true">
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56 <param type="data" name="metadata" label="Metadata for each feature" format="tsv,tabular"
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57 help="Metadata for each grouped XCMS feature, e.g. could be the adduct calculated from CAMERA "/>
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58
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59 <param name="metadata_cols_filter" type="text" label="Metadata columns to use" value=""
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60 help="Comma separated string of column names where the corresponding values in the metadata will be used"/>
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61
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62 <param name="metadata_cols" type="text" label="Metadata columns for MSP spectra name" value=""
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63 help="Comma separated string of column names where the corresponding values in the metadata will be used
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64 for MSP spectra name"/>
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66 </when>
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67 <when value="false">
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68 </when>
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69 </conditional>
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71 <conditional name="xcms_group_cond">
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72 <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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73 <when value="true">
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74 <param name="xcms_groupids" type="text" label="XCMS peak group ids" value=""
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75 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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76 </when>
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77 <when value="false">
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78 </when>
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79 </conditional>
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81 <param name="intensity_ra" type="select" label="Include intensity, relative abundanace or both in the MSP file"
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82 argument="--intensity_ra">
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83 <option value="intensity_ra" selected="true">Both intensity and relative abundance</option>
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84 <option value="intensity">Intensity only</option>
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85 <option value="ra">Relative abundance only</option>
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86 </param>
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87
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88 <param name="msp_schema" type="select" label="MSP schema to use for files"
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89 argument="--msp_schema">
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90 <option value="massbank" selected="true">MassBank (Europe)</option>
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91 <option value="mona">MoNA</option>
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92
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93 </param>
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94
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95 <param name="filter" type="boolean" checked="true" truevalue="--filter" falsevalue=""
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96 label="Filter peaks that have been flagged in prior processing steps" help="" />
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97
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98
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99 <param name="include_adducts" type="select" label="Always include the following adduct descriptions in the MSP file"
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100 help="Additional adducts to include, can be useful for downstream processing" multiple="true"
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101 argument="--include_adducts">
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102 <option value="[M+H]+">[M+H]+</option>
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103 <option value="[M+Na]+">[M+Na]+</option>
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104 <option value="[M+NH4]+">[M+NH4]+</option>
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105 <option value="[M+K]+" >[M+K]+</option>
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106 <option value="[M+CH3OH+H]+">[M+CH3OH+H]+</option>
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107 <option value="[M+ACN+H]+">[M+ACN+H]+</option>
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108 <option value="[M+ACN+Na]+">[M+ACN+Na]+</option>
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109 <option value="[M+2ACN+H]+">[M+2ACN+H]+</option>
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110 <option value="[M-H]-">[M-H]-</option>
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111 <option value="[M+HCOO]-" >[M+HCOO]-</option>
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112 <option value="[M+CH3COO]-" >[M+CH3COO]-</option>
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113 <option value="[M-H+CH3COOH]-" >[M-H+CH3COOH]-</option>
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114 </param>
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115 <param name="adduct_split" type="boolean" checked="true" label="Create MSP spectra for each adduct?"
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116 help="Useful if the MSP file will be used for further annotation" truevalue="--adduct_split" falsevalue="" />
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117
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118 </inputs>
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119 <outputs>
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120 <data name="createMSP_output" format="msp" from_work_dir="lcmsms_spectra.msp" label="${tool.name} on ${on_string}: msp"/>
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121 </outputs>
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122 <tests>
12
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123
0
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124 <test>
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125 <!-- 3) Test all average with metadata -->
0
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126 <param name="method" value="av_all"/>
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127 <param name="rdata_input" value="averageFragSpectra_output_all.RData"/>
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128 <param name="metadata_cond|metadata_select" value="true"/>
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129 <param name="metadata_cond|metadata" value="createMSP_input_metadata.tsv"/>
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130 <param name="xcms_group_cond|xcms_group_select" value="true"/>
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131 <param name="xcms_group_cond|xcms_groupids" value="8,12"/>
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132 <param name="metadata_cond|adduct_split" value="true"/>
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133 <output name="createMSP_output" file="createMSP_output_av_all_metadata.msp"/>
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134 </test>
12
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135
0
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136 </tests>
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137 <help><![CDATA[
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138 ------------------------------
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139 Create MSP Files from msPurity
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140 ------------------------------
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141
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142 Description
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143 -----------
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144
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145 | This tool will extract the MSMS spectra data from an msPurity-frag4feature object into a file with MSP data format.
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146
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147
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148
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149
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150 Developers and contributors
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151 ---------------------------
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152
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153 - **Jordi Capellades (j.capellades.to@gmail.com) - Universitat Rovira i Virgili (SP)**
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154 - **Andris Jankevics (a.jankevics@bham.ac.uk) - University of Birmingham (UK)**
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155 - **Thomas N. Lawson (t.n.lawson@bham.ac.uk) - University of Birmingham (UK)**
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156 - **Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)**
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157
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158 ]]></help>
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159
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160 <expand macro="citations" />
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161
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162 </tool>