Mercurial > repos > computational-metabolomics > mspurity_createmsp

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
author computational-metabolomics
date Thu, 04 Mar 2021 12:19:07 +0000
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eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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1 <tool id="mspurity_createmsp" name="msPurity.createMSP" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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2 <description>Create MSP files from msPurity processed data</description>
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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3 <macros>
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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4 <import>macros.xml</import>
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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5 </macros>
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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6 <expand macro="requirements">
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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7 </expand>
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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8 <command detect_errors="exit_code"><![CDATA[
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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9 Rscript '$__tool_directory__/createMSP.R'
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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10 --rdata_input '$rdata_input'
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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11 --method '$method'
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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13 #if $metadata_cond.metadata_select == "true"
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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14 --metadata '$metadata_cond.metadata'
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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15 --metadata_cols '$metadata_cond.metadata_cols'
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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16 --metadata_cols_filter '$metadata_cond.metadata_cols_filter'
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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17
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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18 #end if
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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20 #if $xcms_group_cond.xcms_group_select == "true"
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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21 --xcms_groupids '$xcms_group_cond.xcms_groupids'
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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22 #end if
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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24 $filter
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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25 $adduct_split
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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26
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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27 --msp_schema $msp_schema
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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28 --intensity_ra $intensity_ra
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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29 --include_adducts $include_adducts
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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30 #if $include_adducts_custom
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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31 --include_adducts_custom "$include_adducts_custom"
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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32 #end if
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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33
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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34 --out_dir '.'
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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35 ]]></command>
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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36 <inputs>
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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37 <param argument="--rdata_input" type="data" format="rdata" label="msPurity purityA dataset"
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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38 help="RData file containing the purityA object following frag4feature and/or averageFragmentation"/>
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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39 <param argument="--method" type="select" label="How to choose fragmentation spectra (if precursor was fragmented in >1 scans per XCMS group feature)"
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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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,
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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41 'Average' (intra)' will use the intra file (within file) averaged MS/MS spectra of the XCMS grouped feature,
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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42 'Average (inter)' will use the inter file (across file) MS/MS averaged spectra,
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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43 'All scans' will export all matching MS/MS spectra to XCMS grouped features,
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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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"
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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45 >
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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46 <option value="av_all" selected="true">Average (all)</option>
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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47 <option value="av_intra">Average (intra)</option>
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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48 <option value="av_inter">Average (inter)</option>
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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49 <option value="all">All scans</option>
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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50 <option value="max" >Max intensity</option>
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51 </param>
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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52
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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53 <conditional name="metadata_cond">
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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54 <param name="metadata_select" type="boolean" label="Use additional metadata?" />
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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55 <when value="true">
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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56 <param argument="--metadata" type="data" label="Metadata for each feature" format="tsv,tabular"
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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57 help="Metadata for each grouped XCMS feature, e.g. could be the adduct calculated from CAMERA "/>
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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58
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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59 <param argument="--metadata_cols_filter" type="text" label="Metadata columns to use" value=""
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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60 help="Comma separated string of column names where the corresponding values in the metadata will be used"/>
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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61
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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62 <param argument="--metadata_cols" type="text" label="Metadata columns for MSP spectra name" value=""
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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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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65
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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66 </when>
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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67 <when value="false">
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68 </when>
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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69 </conditional>
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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70
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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71 <conditional name="xcms_group_cond">
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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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" />
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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73 <when value="true">
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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74 <param argument="--xcms_groupids" type="text" label="XCMS peak group ids" value=""
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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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"/>
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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76 </when>
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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77 <when value="false">
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78 </when>
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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79 </conditional>
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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80
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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81 <param argument="--intensity_ra" type="select" label="Include intensity, relative abundanace or both in the MSP file">
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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82 <option value="intensity_ra" selected="true">Both intensity and relative abundance</option>
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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83 <option value="intensity">Intensity only</option>
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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84 <option value="ra">Relative abundance only</option>
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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85 </param>
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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86
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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87 <param argument="--msp_schema" type="select" label="MSP schema to use for files">
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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88 <option value="massbank" selected="true">MassBank (Europe)</option>
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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89 <option value="mona">MoNA</option>
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90
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91 </param>
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92
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93 <param argument="--filter" type="boolean" checked="true" truevalue="--filter" falsevalue=""
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94 label="Filter peaks that have been flagged in prior processing steps" help="" />
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95
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96
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97 <param argument="--include_adducts" type="select" label="Always include the following adduct descriptions in the MSP file"
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98 help="Additional adducts to include, can be useful for downstream processing" multiple="true">
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99 <option value="[M+H]+">[M+H]+</option>
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100 <option value="[M+Na]+">[M+Na]+</option>
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101 <option value="[M+NH4]+">[M+NH4]+</option>
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102 <option value="[M+K]+" >[M+K]+</option>
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103 <option value="[M+CH3OH+H]+">[M+CH3OH+H]+</option>
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104 <option value="[M+ACN+H]+">[M+ACN+H]+</option>
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105 <option value="[M+ACN+Na]+">[M+ACN+Na]+</option>
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106 <option value="[M+2ACN+H]+">[M+2ACN+H]+</option>
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107 <option value="[M-H]-">[M-H]-</option>
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108 <option value="[M+HCOO]-" >[M+HCOO]-</option>
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109 <option value="[M+CH3COO]-" >[M+CH3COO]-</option>
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110 <option value="[M-H+CH3COOH]-" >[M-H+CH3COOH]-</option>
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111 </param>
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112 <param argument="--include_adducts_custom" type="text" label="Always include the following custom adducts"
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113 help="Additional custom adducts to include, should be comma separated" optional="true">
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114 <expand macro="text-adduct-regex-validator"/>
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115 </param>
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116
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117 <param argument="--adduct_split" type="boolean" checked="true" label="Create MSP spectra for each adduct?"
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118 help="Useful if the MSP file will be used for further annotation" truevalue="--adduct_split" falsevalue=""/>
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119
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120 </inputs>
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121 <outputs>
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122 <data name="createMSP_output" format="msp" from_work_dir="lcmsms_spectra.msp" label="${tool.name} on ${on_string}: msp"/>
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123 </outputs>
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124 <tests>
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125
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126 <test>
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127 <!-- Test all average with metadata -->
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128 <param name="method" value="av_all"/>
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129 <param name="rdata_input" value="averageFragSpectra_output_all.RData"/>
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130 <param name="metadata_cond|metadata_select" value="true"/>
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131 <param name="metadata_cond|metadata" value="createMSP_input_metadata.tsv"/>
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132 <param name="xcms_group_cond|xcms_group_select" value="true"/>
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133 <param name="xcms_group_cond|xcms_groupids" value="8,12"/>
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134 <param name="metadata_cond|adduct_split" value="true"/>
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135 <output name="createMSP_output" file="createMSP_output_av_all_metadata.msp"/>
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136 </test>
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137
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138 <test>
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139 <!-- Test custom adducts average with metadata -->
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140 <param name="method" value="av_all"/>
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141 <param name="rdata_input" value="averageFragSpectra_output_all.RData"/>
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142 <param name="metadata_cond|metadata_select" value="true"/>
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143 <param name="metadata_cond|metadata" value="createMSP_input_metadata.tsv"/>
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144 <param name="xcms_group_cond|xcms_group_select" value="true"/>
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145 <param name="xcms_group_cond|xcms_groupids" value="8,12"/>
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146 <param name="metadata_cond|adduct_split" value="true"/>
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147 <param name="include_adducts_custom" value="[M+]+,[M-H]-,[M+TEST SPACE+]+"/>
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148 <output name="createMSP_output" file="createMSP_output_av_all_metadata_custom_adducts.msp"/>
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149 </test>
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150
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151
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152
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153 </tests>
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154 <help><![CDATA[
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155 ------------------------------
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156 Create MSP Files from msPurity
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157 ------------------------------
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158
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159 Description
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160 -----------
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161
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162 | This tool will extract the MSMS spectra data from an msPurity-frag4feature object into a file with MSP data format.
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163
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164
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165
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166
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167 Developers and contributors
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168 ---------------------------
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169
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170 - **Jordi Capellades (j.capellades.to@gmail.com) - Universitat Rovira i Virgili (SP)**
eeb5d343374c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
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171 - **Andris Jankevics (a.jankevics@bham.ac.uk) - University of Birmingham (UK)**
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172 - **Thomas N. Lawson (t.n.lawson@bham.ac.uk) - University of Birmingham (UK)**
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173 - **Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)**
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174
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175 ]]></help>
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176
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177 <expand macro="citations" />
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178
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179 </tool>