Mercurial > repos > workflow4metabolomics > camera_findadducts
diff findAdducts.xml @ 0:3b2f7cb74c33 draft default tip
planemo upload commit 24d44ee26b7c23380c2b42fae2f7f6e58472100d
| author | workflow4metabolomics |
|---|---|
| date | Sun, 24 Nov 2024 21:31:14 +0000 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/findAdducts.xml Sun Nov 24 21:31:14 2024 +0000 @@ -0,0 +1,206 @@ +<tool id="CAMERA_findAdducts" name="CAMERA.findAdducts" version="0.1.0+camera@TOOL_VERSION@-galaxy@VERSION_SUFFIX@" profile="23.0"> + + <description>Annotate adducts</description> + + <macros> + <import>macros.xml</import> + </macros> + + <expand macro="requirements"/> + + <required_files> + <include type="literal" path="CAMERA_findAdducts.R"/> + <include type="literal" path="lib.r"/> + </required_files> + + <command detect_errors="exit_code"><![CDATA[ + @COMMAND_RSCRIPT@CAMERA_findAdducts.R + image '$image' + ppm $ppm + mzabs $mzabs + polarity $polarity + + #if $rules_block.rules_select == "FALSE": + rules NULL + #else + rules $rules_block.rules + #end if + + #if $advanced.advanced_select == "FALSE": + multiplier 3 + max_peaks 100 + psg_list NULL + #else + multiplier $advanced.multiplier + max_peaks $advanced.max_peaks + #if $advanced.psg_list_block.psg_list_select == "FALSE": + psg_list NULL + #else + psg_list $advanced.psg_list_block.psg_list + #end if + #end if + + intval $intval + convertRTMinute $convertRTMinute + numDigitsMZ $numDigitsMZ + numDigitsRT $numDigitsRT + + @COMMAND_FILE_LOAD@ + ]]> + </command> + <inputs> + <param name="image" type="data" label="RData file" format="rdata" help="Output file from another function CAMERA (findIsotopes)" /> + <param name="ppm" type="integer" value="5" label="General ppm error" /> + <param name="mzabs" type="float" value="0.015" label="General absolute error in m/z" /> + <param name="polarity" type="select" label="Which polarity mode was used for measuring of the MS sample"> + <option value="positive">positive</option> + <option value="negative" selected="true">negative</option> + </param> + + <conditional name="rules_block"> + <param name="rules_select" type="select" label="Use a personal ruleset file"> + <option value="TRUE">TRUE</option> + <option value="FALSE" selected="true">FALSE</option> + </param> + <when value="FALSE"> + <!--<param name="rules" type="text" value="NULL" label="No personal ruleset file (using default ruleset)" optional="true" />--> + </when> + <when value="TRUE"> + <param name="rules" type="data" format="csv" label="User defined ruleset" /> + </when> + </conditional> + + <param name="intval" type="select" label="Choose intensity values"> + <option value="into" selected="true">into</option> + <option value="maxo">maxo</option> + <option value="intb">intb</option> + </param> + + <conditional name="advanced"> + <param name="advanced_select" type="select" label="Advanced parameters"> + <option value="TRUE">TRUE</option> + <option value="FALSE" selected="true">FALSE</option> + </param> + <when value="FALSE"> + <!--<param name="multiplier" type="integer" value="3" label="Highest number(n) of allowed clusterion [nM+ion]" optional="true" /> + <param name="max_peaks" type="integer" value="100" label="How many peaks will be calculated in every thread (parallel mode)" optional="true" /> + <param name="psg_list" type="text" value="NULL" label="No psg_list" optional="true" />--> + </when> + <when value="TRUE"> + <param name="multiplier" type="integer" value="3" label="Highest number(n) of allowed clusterion [nM+ion]" /> + <param name="max_peaks" type="integer" value="100" label="How many peaks will be calculated in every thread (parallel mode)" /> + + <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> + </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]}.findAdducts.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" /> + <data name="camera_findAdducts_rdata" format="rdata" label="${image.name[:-6]}.findAdducts.RData" from_work_dir="camera_findAdducts.RData" /> + </outputs> + <tests> + <test expect_num_outputs="2"> + <param name="image" value="xset.merged.group.retcor.group.fillPeaks.fwhm.groupCorr.findIsotopes.RData" /> + <!--<param name="ppm" value="5" /> + <param name="mzabs" value="0.015" /> + <param name="polarity" value="positive" /> + <param name="rules" value="NULL" /> + <param name="intval" value="into" /> + <param name="multiplier" value="3" /> + <param name="max_peaks" value="100" /> + <param name="psg_list" value="NULL" />--> + <expand macro="test_file_load_faahKO_15"/> + <output name="variableMetadata" file="xset.merged.group.retcor.group.fillPeaks.fwhm.groupCorr.findIsotopes.findAdducts.variableMetadata.tsv" /> + <output name="camera_findAdducts_rdata" value="xset.merged.group.retcor.group.fillPeaks.fwhm.groupCorr.findIsotopes.findAdducts.RData" compare="sim_size" delta="5000" /> + </test> + </tests> + <help><![CDATA[ + +=================== +CAMERA.findAdducts +=================== + +----------- +Description +----------- + +.. _link: https://bioconductor.org/packages/release/bioc/manuals/CAMERA/man/CAMERA.pdf + +Annotate adducts (and fragments) for a `xsAnnotate` object. Returns a `xsAnnotate` object with annotated pseudospectra. Click on the link to see the "Reference Manual" : link_ . + +--------------------------------------------------- + +--------- +Arguments +--------- + ++--------------+-------------------------------------------------------------------+ +| Variables | Descriptions | ++==============+===================================================================+ +| object | the xsAnnotate object | ++--------------+-------------------------------------------------------------------+ +| ppm | ppm error for the search | ++--------------+-------------------------------------------------------------------+ +| mzabs | allowed variance for the search | ++--------------+-------------------------------------------------------------------+ +| multiplier | highest number(n) of allowed clusterion [nM+ion] | ++--------------+-------------------------------------------------------------------+ +| polarity | Which polarity mode was used for measuring of the ms sample | ++--------------+-------------------------------------------------------------------+ +| rules | personal ruleset or with NULL standard ruleset will be calculated | ++--------------+-------------------------------------------------------------------+ +| max_peaks | If run in parallel mode, this number defines how many peaks will | +| | be calculated in every thread | ++--------------+-------------------------------------------------------------------+ +| psg_list | Vector of pseudospectra indices. The correlation analysis will be | +| | only done for those groups | ++--------------+-------------------------------------------------------------------+ +| intval | choose intensity values. Allowed values are into, maxo, intb | ++--------------+-------------------------------------------------------------------+ + +--------------------------------------------------- + +------------------------------------------ +General schema of the metabolomic workflow +------------------------------------------ + +.. image:: findAdducts.png + +--------------------------------------------------- + +------- +Details +------- + +Adducts (and fragments) are annotated for a `xsAnnotate` object. For every pseudospectra group, generated by `groupFWHM` and `groupCorr`, all possible Adducts are calculated and mapped to the peaks. If at least two adducts match, a possible molecule-mass for the group can be calculated. After the annotation, every mass hypothesis is checked against the charge of the calculated isotopes. It is recommended to call `findIsotopes()` before the annotation step. + +--------------------------------------------------- + +-------------- +Changelog/News +-------------- + +.. _News: https://bioconductor.org/packages/release/bioc/news/CAMERA/NEWS + +@HELP_CAMERA_SUITE@ + +]]> </help> + + <expand macro="citation"/> + <expand macro="creator"/> +</tool>