Mercurial > repos > tomnl > mspurity_createmsp
diff createMSP.xml @ 0:df2efceff4cd draft
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 |
| parents | |
| children | 6d1312ad450c |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/createMSP.xml Fri May 24 09:06:56 2019 -0400 @@ -0,0 +1,167 @@ +<tool id="mspurity_createmsp" name="msPurity.createMSP" version="0.2.0"> + <description>Create MSP files from msPurity processed data</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"> + </expand> + <stdio> + <exit_code range="1:" /> + </stdio> + <command interpreter="Rscript" ><![CDATA[ + createMSP.R + --rdata_input "$rdata_input" + --method "$method" + + #if $metadata_cond.metadata_select == "true" + --metadata "$metadata_cond.metadata" + --metadata_cols "$metadata_cond.metadata_cols" + --adduct_split "$metadata_cond.adduct_split" + #end if + + #if $xcms_group_cond.xcms_group_select == "true" + --xcms_groupids "$xcms_group_cond.xcms_groupids" + #end if + + $filter + + --msp_schema "$msp_schema" + --intensity_ra "$intensity_ra" + + --out_dir '.' + ]]></command> + <inputs> + <param name="rdata_input" type="data" format="rdata" label="msPurity purityA dataset" argument="--purity_dataset" + help="RData file containing the purityA object following frag4feature and/or averageFragmentation"/> + <param name="method" type="select" label="How to choose fragmentation spectra (if precursor was fragmented in >1 scans per XCMS group feature)" + help="'Average all' will use the averaged MS/MS spectra of the XCMS grouped feature, ignoring inter and intra file relationships, + 'Average' (intra)' will use the intra file (within file) averaged MS/MS spectra of the XCMS grouped feature, + 'Average (inter)' will use the inter file (across file) MS/MS averaged spectra, + 'All scans' will export all matching MS/MS spectra to XCMS grouped features, + 'Max intensity' will choose the most MS/MS spectra with the most intense precursor ion for each XCMS grouped feature" + argument="--method"> + <option value="av_all" selected="true">Average (all)</option> + <option value="av_intra">Average (intra)</option> + <option value="av_inter">Average (inter)</option> + <option value="all">All scans</option> + <option value="max" >Max intensity</option> + </param> + + <conditional name="metadata_cond"> + <param name="metadata_select" type="boolean" label="Use additional metadata?" /> + <when value="true"> + <param type="data" name="metadata" label="Metadata for each feature" format="tsv,tabular" + help="Metadata for each grouped XCMS feature, the data will be added to the MSP metadata. + Using the MassBank format e.g. https://github.com/MassBank/MassBank-data/blob/master/MetaboLights/ML003001.txt "/> + + <param name="metadata_cols" type="text" label="Metadata columns for name" value="CH$NAME, MS$FOCUSED_ION: PRECURSOR_TYPE" help="Comma separated string of column names where the corresponding values in the metadata will be used for the MSP spectra name"/> + <param name="adduct_split" type="boolean" checked="true" label="Create MSP spectra for each adduct?" help="If either 'adduct' or 'MS$FOCUSED_ION: PRECURSOR_TYPE' + column is in metadata then each adduct will have it's own MSP spectra. + (Useful, if the MSP file will be used for further annotation)" /> + </when> + <when value="false"> + </when> + </conditional> + + <conditional name="xcms_group_cond"> + <param name="xcms_group_select" type="boolean" label="Select XCMS groups?" help="if set to no, all XCMS group features will be used" /> + <when value="true"> + <param name="xcms_groupids" type="text" label="XCMS peak group ids" value="" + help="Comma separated string of XCMS group ids to export MSP spectra for. If blank all XCMS peak groups will be used"/> + </when> + <when value="false"> + </when> + </conditional> + + <param name="intensity_ra" type="select" label="Include intensity, relative abundanace or both in the MSP file" + argument="--intensity_ra"> + <option value="intensity_ra" selected="true">Both intensity and relative abundance</option> + <option value="intensity">Intensity only</option> + <option value="ra">Relative abundance only</option> + </param> + + <param name="msp_schema" type="select" label="MSP schema to use for files" + argument="--msp_schema"> + <option value="massbank" selected="true">MassBank (Europe)</option> + <option value="mona">MoNA</option> + + </param> + + <param name="filter" type="boolean" checked="true" truevalue="--filter" falsevalue="" label="Filter peaks that have been flagged in prior processing steps" help="" /> + + </inputs> + <outputs> + <data name="createMSP_output" format="msp" from_work_dir="lcmsms_spectra.msp" label="${tool.name} on ${on_string}: msp"/> + </outputs> + <tests> + <test> + <param name="method" value="all"/> + <param name="rdata_input" value="frag4feature_output.RData"/> + <output name="createMSP_output" file="createMSP_output_scans_all.msp"/> + </test> + <test> + <param name="method" value="av_all"/> + <param name="rdata_input" value="averageFragSpectra_output_all.RData"/> + <output name="createMSP_output" file="createMSP_output_av_all.msp"/> + </test> + <test> + <param name="method" value="av_all"/> + <param name="rdata_input" value="averageFragSpectra_output_all.RData"/> + <param name="metadata_cond|metadata_select" value="true"/> + <param name="metadata_cond|metadata" value="createMSP_input_metadata.tsv"/> + <param name="metadata_cond|metadata_cols" value="AC$CHROMATOGRAPHY: COLUMN_NAME, AC$MASS_SPECTROMETRY: ION_MODE, AC$MASS_SPECTROMETRY: MS_TYPE, CH$LINK: INCHIKEY, CH$LINK: PUBCHEM CH$NAME +"/> + <param name="xcms_group_cond|xcms_group_select" value="true"/> + <param name="xcms_group_cond|xcms_groupids" value="8,12"/> + <param name="metadata_cond|adduct_split" value="true"/> + <output name="createMSP_output" file="createMSP_output_av_all_metadata.msp"/> + </test> + <test> + <param name="method" value="av_all"/> + <param name="rdata_input" value="averageFragSpectra_output_all.RData"/> + <param name="xcms_group_cond|xcms_group_select" value="true"/> + <param name="xcms_group_cond|xcms_groupids" value="8,12"/> + <output name="createMSP_output" file="createMSP_output_av_all_and_all_xcms.msp"/> + </test> + <test> + <param name="method" value="av_intra"/> + <param name="rdata_input" value="averageFragSpectra_output_intra.RData"/> + <output name="createMSP_output" file="createMSP_output_av_intra.msp"/> + </test> + <test> + <param name="method" value="av_inter"/> + <param name="rdata_input" value="averageFragSpectra_output_inter.RData"/> + <output name="createMSP_output" file="createMSP_output_av_inter.msp"/> + </test> + <test> + <param name="method" value="max"/> + <param name="rdata_input" value="frag4feature_output.RData"/> + <output name="createMSP_output" file="createMSP_output_max.msp"/> + </test> + </tests> + <help><![CDATA[ +------------------------------ +Create MSP Files from msPurity +------------------------------ + +Description +----------- + +| This tool will extract the MSMS spectra data from an msPurity-frag4feature object into a file with MSP data format. + + + + +Developers and contributors +--------------------------- + +- **Jordi Capellades (j.capellades.to@gmail.com) - Universitat Rovira i Virgili (SP)** +- **Andris Jankevics (a.jankevics@bham.ac.uk) - University of Birmingham (UK)** +- **Thomas N. Lawson (t.n.lawson@bham.ac.uk) - University of Birmingham (UK)** +- **Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)** + + ]]></help> + +<expand macro="citations" /> + +</tool>