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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
author | recetox |
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date | Thu, 12 Oct 2023 13:31:24 +0000 |
parents | cfd2e19f00a9 |
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<tool id="recetox_xmsannotator_advanced" name="recetox-xMSannotator" version="@TOOL_VERSION@+galaxy1"> <description>annotate peak intensity table including scores and confidence levels</description> <macros> <import>macros.xml</import> </macros> <expand macro="creator"/> <xrefs> <xref type="bio.tools">recetox-xmsannotator</xref> </xrefs> <expand macro="requirements" /> <command detect_errors="aggressive"><![CDATA[ Rscript -e 'source("${__tool_directory__}/utils.R")' -e "n_workers <- \${GALAXY_SLOTS:-1}" -e "source('${wrapper}')" ]]></command> <configfiles> <configfile name="wrapper"><![CDATA[ metadata_table <- load_table("$metadata_table", "$metadata_table.ext") intensity_table <- load_table("$intensity_table", "$intensity_table.ext") peak_table <- create_peak_table(metadata_table, intensity_table) filter_by <- create_filter_by_adducts("$filter_by") annotation <- advanced_annotation( peak_table = peak_table, adduct_table = load_table("$adduct_table", "$adduct_table.ext"), adduct_weights = load_table("$adduct_weights", "$adduct_weights.ext"), compound_table = load_table("$compound_table", "$compound_table.ext"), mass_tolerance = 1e-6 * ${mass_tolerance_ppm}, time_tolerance = $time_tolerance, correlation_threshold = as.double($clustering.correlation_threshold), min_cluster_size = as.integer($clustering.min_cluster_size), deep_split = as.integer($clustering.deep_split), network_type = "$clustering.network_type", redundancy_filtering = $scoring.redundancy_filtering, n_workers = n_workers, intensity_deviation_tolerance = as.double($intensity_deviation_tolerance), mass_defect_tolerance = as.double($mass_defect_tolerance), mass_defect_precision = as.double($mass_defect_precision), peak_rt_width = as.integer($peak_rt_width), maximum_isotopes = as.integer($maximum_isotopes), min_ions_per_chemical = as.integer($min_ions_per_chemical), filter_by = filter_by ) save_table(annotation, "$output_file", "$output_file.ext") ]]></configfile> </configfiles> <inputs> <expand macro="inputs"/> <expand macro="tolerance"> <param name="time_tolerance" type="float" value="10" min="0"> <label>Retention time tolerance [s]</label> <help> Retention time tolerance in seconds for finding peaks derived from the same parent compound. </help> </param> </expand> <section name="clustering" title="Clustering"> <param name="correlation_threshold" type="float" value="0.7"> <label>Correlation threshold</label> <help>Correlation threshold between peaks to qualify as adducts/isotopes of the same metabolite.</help> </param> <param name="min_cluster_size" type="integer" value="10" min="1"> <label>Minimum cluster size</label> <help>The minimum number of nodes to be considered as a cluster.</help> </param> <param name="deep_split" type="integer" value="2" min="0" max="4"> <label>Deep split</label> <help> Deep split provides a rough control over sensitivity to cluster splitting. The higher the value, the more and smaller clusters will be produced (see WGCNA package documentation). </help> </param> <param name="network_type" type="select" display="radio"> <label>Network type</label> <help> Network type parameter affects how the network's adjacency matrix is created from the correlation matrix (see WGCNA package documentation). </help> <option value="signed">Signed</option> <option value="unsigned" selected="true">Unsigned</option> </param> </section> <section name="scoring" title="Scoring" expanded="true"> <param name="strict_boosting" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"> <label>Strict boosting</label> <help> Boost the scores of metabolites that not only belongs to the same pathway but also to the same cluster. Otherwise, do not account for cluster membership. </help> </param> <param name="min_isp" type="integer" min="0" value="1"> <label>Minimum number of expected isotopes</label> <help> Minimum number of adducts/isotopes to be present for a match to be considered as a high confidence match. </help> </param> <param name="max_isp" type="integer" min="0" value="5"> <label>Maximum number of expected isotopes</label> <help> Maximum number of adducts/isotopes to be present for a match to be considered as a high confidence match. </help> </param> <param name="redundancy_filtering" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"> <label>Redundancy filtering</label> <help>Whether to filter out low-scored multiple matcher or not.</help> </param> </section> <param name="intensity_deviation_tolerance" type="float" value="0.1"> <label>Tolerance of intensity deviation</label> <help>A numeric threshold by which an intensity ratio of two isotopic peaks may differ from their actual abundance ratio.</help> </param> <param name="mass_defect_tolerance" type="float" value="0.1"> <label>Tolerance of mass defect</label> <help>Maximum difference in mass defect between two peaks of the same compound.</help> </param> <param name="mass_defect_precision" type="float" value="0.01"> <label>Precision for computing mass defect</label> </param> <param name="peak_rt_width" type="integer" value="1"> <label>Estimated chromatographic peak width</label> </param> <param name="maximum_isotopes" type="integer" value="10"> <label>Maximum isotopes</label> </param> <param name="min_ions_per_chemical" type="integer" value="2"> <label>Minimum ions per chemical</label> </param> <param name="filter_by" type="select" label="Adducts to filter by" multiple="true" optional="true"> <option value="M-H" selected="true">M-H</option> <option value="M+H" selected="true">M+H</option> <option value="2M-H">2M-H</option> <option value="M-2H">M-2H</option> </param> </inputs> <outputs> <expand macro="outputs"/> </outputs> <tests> <test> <param name="metadata_table" value="metadata_table.parquet" ftype="parquet" /> <param name="intensity_table" value="intensity_table.parquet" ftype="parquet" /> <param name="compound_table" value="database.parquet" ftype="parquet" /> <param name="adduct_table" value="adduct_table.parquet" ftype="parquet" /> <output name="output_file" file="expected_output.parquet" ftype="parquet"/> </test> <test> <param name="metadata_table" value="metadata_table.csv" ftype="csv" /> <param name="intensity_table" value="intensity_table.csv" ftype="csv" /> <param name="compound_table" value="database.csv" ftype="csv" /> <param name="adduct_table" value="adduct_table.csv" ftype="csv" /> <output name="output_file" file="expected_output.csv" ftype="csv"/> </test> </tests> <help> <![CDATA[ @HELP@ ]]> </help> <citations> <expand macro="citations"/> </citations> </tool>