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author | galaxyp |
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date | Tue, 02 Oct 2018 16:30:33 -0400 |
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<tool id="lfq_protein_quant" name="Label free protein" version="1.0"> <description> summarisation and quantitation </description> <requirements> <requirement type="package" version="2.2.0">bioconductor-msnbase</requirement> <requirement type="package" version="2.12.0">bioconductor-mzr</requirement> <requirement type="package" version="1.2.1">r-tidyverse</requirement> <requirement type="package" version="1.1_18_1">r-lme4</requirement> <requirement type="package" version="0.1.0">r-furrr</requirement> <requirement type="package" version="0.7.5">r-msqrob</requirement> </requirements> <command detect_errors="exit_code"> <![CDATA[ ln -s '${moff_file}' moff.tsv && ln -s '${meta_file}' meta.tsv && Rscript '$__tool_directory__/quantitation.r' moff.tsv meta.tsv $only_summarisation \${GALAXY_SLOTS:-4} ]]> </command> <inputs> <param name="moff_file" type="data" format="tabular" label="Peptide summary output from moFF or other peptide quantitation tools" /> <param name="meta_file" type="data" format="tabular" label="Metadata with sample names and condition" /> <param name="only_summarisation" type="boolean" truevalue="1" falsevalue="0" label="Only summarisiation" help="This option will deactivate the quantifiation of data." /> </inputs> <outputs> <data format="tabular" name="quant" from_work_dir="quantitation.tsv" label="${tool.name} on ${on_string}: quantification"> <filter>not only_summarisation</filter> </data> <data format="tabular" name="summary" from_work_dir="summarised_proteins.tsv" label="${tool.name} on ${on_string}: summary"/> </outputs> <tests> <test> <param name="moff_file" value="moff.tab"/> <param name="meta_file" value="meta.tab"/> <param name="only_summerisation" value="true"/> <output name="quant" file="quantitation.tsv" /> <output name="summary" file="summarised_proteins.tsv" /> </test> </tests> <help> <![CDATA[ **What it does** Protein summarisation and label free quantitation. ---- **Inputs** - Quantification input: Tabular file with the summary output from moFF or in case other tools were used for peptide quantitation with the following columns: 'peptides' containing the amino acid sequence; 'prot' with the Uniprot Accession and then one column per sample with the quantitation values. :: peptides prot sample1 sample2 AAABDEK B9DM54 1809446 563862 TELATASDR Q9CFE8 294282 457023 AMGLATK P85660 194023 428277 ... ... - Metadata input: Separate columns with sample names, condition and optionally also lab and machine. Sample names must match exactly the sample names from the peptide quantitation columns in the previous tabular file. :: sample condition sample1 healthy sample2 disease ... ... **Options** - Summarisation only: Summarisation is done through robust regression to take also the peptide effect into account. In case only sample column is provided median protein intensity is calculated. - Summarisation and quantification: Relative quantification is performed according to the information provided in the metadata file. **Outputs** - Summarised protein output: Uniprot accession and quantitation values per sample and protein - Quantification output: Uniprot accession, comparison between conditions, fold change, p-value, q-value ]]> </help> <citations> <citation type="doi">10.1074/mcp.M115.055897</citation> <citation type="doi">10.1093/bioinformatics/btr645</citation> </citations> </tool>