Mercurial > repos > workflow4metabolomics > camera_groupcorr
view groupCorr.xml @ 0:cb57be5de070 draft default tip
planemo upload commit 24d44ee26b7c23380c2b42fae2f7f6e58472100d
| author | workflow4metabolomics |
|---|---|
| date | Sun, 24 Nov 2024 21:29:48 +0000 |
| parents | |
| children |
line wrap: on
line source
<tool id="CAMERA_groupCorr" name="CAMERA.groupCorr" version="0.1.0+camera@TOOL_VERSION@-galaxy@VERSION_SUFFIX@" profile="23.0"> <description>EIC correlation grouping of LC/ESI-MS data</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <required_files> <include type="literal" path="CAMERA_groupCorr.R"/> <include type="literal" path="lib.r"/> </required_files> <command detect_errors="exit_code"><![CDATA[ @COMMAND_RSCRIPT@CAMERA_groupCorr.R image '$image' cor_eic_th $cor_eic_th pval $pval graphMethod $graphMethod calcIso $calcIso calcCiS $calcCiS calcCaS $calcCaS #if $psg_list_block.psg_list_select == "FALSE": psg_list NULL #else psg_list $psg_list #end if cor_exp_th $cor_exp_th intval $intval numDigitsMZ $numDigitsMZ numDigitsRT $numDigitsRT convertRTMinute $convertRTMinute @COMMAND_FILE_LOAD@ ]]> </command> <inputs> <param name="image" type="data" label="RData file" format="rdata" help="output file from another function xcms (fillPeaks)" /> <param name="cor_eic_th" type="float" value="0.75" max="1" min="0" label="Correlation threshold (0..1)" /> <param name="pval" type="float" value="0.05" max="1" min="0" label="Significant correlation threshold" /> <param name="graphMethod" type="select" label="Method selection for grouping peaks after correlation analysis into pseudospectra"> <option value="hcs" selected="true">hcs</option> <option value="lpc">lpc</option> </param> <param name="calcIso" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Use isotopic relationship for peak grouping" /> <param name="calcCiS" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Use correlation inside samples for peak grouping" /> <param name="calcCaS" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Use correlation across samples for peak grouping" /> <param name="cor_exp_th" type="float" value="0.75" max="1" min="0" label="Threshold for intensity correlations across samples (0..1)" /> <param name="intval" type="select" label="Method selection for grouping peaks after correlation analysis into pseudospectra"> <option value="into" selected="true">into</option> <option value="maxo">maxo</option> <option value="intb">intb</option> <!-- <option value="intf">intf</option> <option value="maxf">maxf</option> <option value="area">area</option> --> </param> <conditional name="psg_list_block"> <param name="psg_list_select" type="select" label="Use a personal psg_list"> <option value="TRUE">TRUE</option> <option value="FALSE" selected="true">FALSE</option> </param> <when value="FALSE"> <!--<param name="psg_list" type="text" value="NULL" label="No psg_list" optional="true" />--> </when> <when value="TRUE"> <param name="psg_list" type="text" optional="true" label="Pseudospectra indices (optional)" help="Provide a comma-separated list of pseudospectra indices (e.g. 1,2,3)." /> </when> </conditional> <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert seconds to minutes when exporting tsv" /> <param name="numDigitsMZ" type="integer" value="4" max="4" min="0" label="Number of digits for MZ values (namecustom)" /> <param name="numDigitsRT" type="integer" value="4" max="4" min="0" label="Number of digits for RT values (namecustom)" /> <expand macro="input_file_load"/> </inputs> <outputs> <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.groupCorr.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" /> <data name="camera_groupCorr_rdata" format="rdata" label="${image.name[:-6]}.groupCorr.RData" from_work_dir="camera_groupCorr.RData" /> </outputs> <tests> <test expect_num_outputs="2"> <param name="image" value="xset.merged.group.retcor.group.fillPeaks.fwhm.RData" /> <!--<param name="cor_eic_th" value="0.75" /> <param name="pval" value="0.05" /> <param name="graphMethod" value="hcs" /> <param name="calcIso" value="FALSE" /> <param name="calcCiS" value="TRUE" /> <param name="calcCaS" value="FALSE" /> <param name="cor_exp_th" value="0.75" /> <param name="intval" value="into" />--> <expand macro="test_file_load_faahKO_15"/> <output name="variableMetadata" file="xset.merged.group.retcor.group.fillPeaks.fwhm.groupCorr.variableMetadata.tsv" /> <output name="camera_groupCorr_rdata" value="xset.merged.group.retcor.group.fillPeaks.fwhm.groupCorr.RData" compare="sim_size" delta="5000" /> </test> </tests> <help><![CDATA[ ================ CAMERA.groupCorr ================ ----------- Description ----------- .. _link: https://bioconductor.org/packages/release/bioc/manuals/CAMERA/man/CAMERA.pdf Peak grouping after correlation information into pseudospectrum groups for an xsAnnotate object. Return an xsAnnotate object with grouping information. Click on the link to see the "Reference Manual" : link_ . --------------------------------------------------- --------- Arguments --------- +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+ | Variables | Descriptions | +================+=============================================================================================================================================+ | object | the xsAnnotate object | +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+ | cor_eic_th | Correlation threshold for EIC correlation | +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+ | pval | p-value threshold for testing correlation of significance | +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+ | graphMethod | Clustering method for resulting correlation graph. See calcPC for more details. | +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+ | calcIso | Include isotope detection information for graph clustering | +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+ | calcCiS | Calculate correlation inside samples | +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+ | calcCaS | Calculate correlation across samples | +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+ | psg_list | Vector of pseudospectra indices. The correlation analysis will be only done for those groups | +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+ | xraw | Optional xcmsRaw object, which should be used for raw data extraction | +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+ | cor_exp_th | Threshold for intensity correlations across samples | +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+ | intval | Selection of the intensity values (such as "into") that should be used in the correlation analysis. See getPeaklist for all allowed values. | +----------------+---------------------------------------------------------------------------------------------------------------------------------------------+ --------------------------------------------------- ------------------------------------------ General schema of the metabolomic workflow ------------------------------------------ .. image:: groupCorr.png --------------------------------------------------- ------- Details ------- The algorithm calculates different informations for group peaks into so called pseudospectra. This pseudospectra contains peaks, with have a high correlation between each other. So far three different kind of information are available. Correlation of intensities across samples (need more than 3 samples), EIC correlation between peaks inside a sample and additional the informationen about recognized isotope cluster can be included. After calculation of all these informations, they are combined as edge value into a graph object. A following graph clustering algorithm separate the peaks (nodes in the graph) into the pseudospectra. --------------------------------------------------- -------------- Changelog/News -------------- .. _News: https://bioconductor.org/packages/release/bioc/news/CAMERA/NEWS @HELP_CAMERA_SUITE@ ]]> </help> <expand macro="citation"/> <expand macro="creator"/> </tool>