Mercurial > repos > eschen42 > w4mjoinpn
diff w4mjoinpn.xml @ 0:948bac693947 draft
planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit cedf2e01903099ef5f1bbe624afe4c2845d6bf23
| author | eschen42 |
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| date | Sun, 29 Oct 2017 10:05:05 -0400 |
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| children | dcfaffec48c8 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/w4mjoinpn.xml Sun Oct 29 10:05:05 2017 -0400 @@ -0,0 +1,143 @@ +<tool id="w4mjoinpn" name="Join +/- Ions" version="0.98.1"> + <description>Join positive and negative ionization-mode W4M datasets for the same samples</description> + <requirements> + <requirement type="package" version="8.25">coreutils</requirement> + <requirement type="package" version="4.2.3.dev0">sed</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" /> + </stdio> + <command><![CDATA[ + echo "These are the the paths to the tools used by this script:" 1>&2 ; + which cut sed head paste cat cp bash test 1>&2 ; + $__tool_directory__/w4mjoinpn.sh + dmneg $dmneg + dmpos $dmpos + dmout $dmout + smneg $smneg + smpos $smpos + smout $smout + vmneg $vmneg + vmpos $vmpos + vmout $vmout + ]]></command> + <inputs> + <param name="dmpos" label="Data matrix positive" type="data" format="tabular" help="Positive ionization-mode: Features x samples (tabular data - decimal: '.'; missing: NA; mode: numerical; separator: tab character)" /> + <param name="smpos" label="Sample metadata positive" type="data" format="tabular" help="Positive ionization-mode: Samples x metadata (tabular data - decimal: '.'; missing: NA; mode: character or numerical; separator: tab character)" /> + <param name="vmpos" label="Variable metadata positive" type="data" format="tabular" help="Positive ionization-mode: Features x metadata (tabular data - decimal: '.'; missing: NA; mode: character or numerical; separator: tab character)" /> + <param name="dmneg" label="Data matrix negative" type="data" format="tabular" help="Negative ionization-mode: Features x samples (tabular data - decimal: '.'; missing: NA; mode: numerical; separator: tab character)" /> + <param name="smneg" label="Sample metadata negative" type="data" format="tabular" help="Negative ionization-mode: Samples x metadata (tabular data - decimal: '.'; missing: NA; mode: character or numerical; separator: tab character)" /> + <param name="vmneg" label="Variable metadata negative" type="data" format="tabular" help="Negative ionization-mode: Features x metadata (tabular data - decimal: '.'; missing: NA; mode: character or numerical; separator: tab character)" /> + </inputs> + <outputs> + <data name="dmout" label="${dmneg.name}.posneg" format="tabular" ></data> + <data name="smout" label="${smneg.name}.posneg" format="tabular" ></data> + <data name="vmout" label="${vmneg.name}.posneg" format="tabular" ></data> + </outputs> + <help><![CDATA[ +**Join positive and negative ionization-mode W4M datasets for the same samples** +-------------------------------------------------------------------------------- + +**Author** - Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu) + + +Motivation +---------- + +Workflow4Metabolomics (W4M, Giacomoni *et al.*, 2014; http://workflow4metabolomics.org; https://github.com/workflow4metabolomics) +provides a suite of Galaxy tools for processing and analyzing metabolomics data. + +W4M uses the XCMS package (Smith *et al.*, 2006) to extract features and align +their retention times among multiple samples. + +After peak extraction and alignment, W4M uses the CAMERA package (Kuhl *et al.*, 2012) +"to postprocess XCMS feature lists and to collect all features related to a compound into a compound spectrum." + +Both of these steps are done using data collected in a single ionization mode (i.e., only negative or only positive) +because it would not make sense to attempt to use CAMERA otherwise. + +However, performing and interpreting statistical analysis would be more convenient and statistically powerful +with all variables (features), negative and positive, combined for one analysis. + + +Description +----------- + +This tool joins two sets of MS1 datasets for **exactly** the same set of samples, where one was gathered in positive ionization +mode and the other in negative ionization-mode, for reasons set forth above. These datasets must be post-XCMS and post-CAMERA. + +This tool will fail: + +* when the samples are not listed in exactly the same order in the negative-mode dataMatrix and the positive-mode dataMatrix +* when the samples are not listed in exactly the same order in the negative-mode sampleMetadata and the positive-mode sampleMetadata + +Otherwise: + +* the two dataMatrix files are concatenated, and the names of features identified from positive ionization-mode data are prefixed with "P"; negative, with "N". +* the two variableMetadata files are concatenated, and the names of features are prefixed in the same way. +* if sampleMetadata has a polarity column, its value is set to "posneg" in the output. (In fact, the sampleMetadata file in the output is copied from the negative ionization-mode sampleMetadata, with the polarity replaced.) + +Workflow Position +----------------- + +* Upstream tool category: Preprocessing +* Downstream tool categories: Normalisation, Statistical Analysis, Quality Control, Filter and Sort + +Working example +--------------- + +**Input files** + + +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+ + | Input File | Download from URL | + +=============================================+=======================================================================================================================+ + | Data matrix, negative ionization-mode | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/input_dataMatrix_neg.tsv | + +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+ + | Sample metadata, negative ionization-mode | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/input_sampleMetadata_neg.tsv | + +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+ + | Variable metadata, negative ionization-mode | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/input_variableMetadata_neg.tsv | + +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+ + | Data matrix, positive ionization-mode | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/input_dataMatrix_pos.tsv | + +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+ + | Sample metadata, positive ionization-mode | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/input_sampleMetadata_pos.tsv | + +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+ + | Variable metadata, positive ionization-mode | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/input_variableMetadata_pos.tsv | + +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+ + +**Output files** + + +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+ + | Output File | Download from URL | + +=============================================+=======================================================================================================================+ + | Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/output_dataMatrix.tsv | + +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+ + | Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/output_sampleMetadata.tsv | + +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+ + | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mjoinpn_galaxy_wrapper/master/test-data/output_variableMetadata.tsv | + +---------------------------------------------+-----------------------------------------------------------------------------------------------------------------------+ + + ]]></help> + <citations> + <citation type="doi">10.5281/zenodo.1038289</citation> + <!-- + <citation type="bibtex"> + @misc{ + w4mjoinpn_galaxy_wrapper, + author = {Eschenlauer, Arthur}, + year = {2017}, + title = {w4mjoinpn_galaxy_wrapper}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper}, + doi = 10.5281/zenodo.1038290 + } + </citation> + --> + <!-- Giacomoni, 2014 Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics --> + <citation type="doi">10.1093/bioinformatics/btu813</citation> + <!-- Kuhl et al., 2012 --> + <citation type="doi">10.1021/ac202450g</citation> + <!-- Smith, 2006 XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification. --> + <citation type="doi">10.1021/ac051437y</citation> + </citations> +</tool>