Mercurial > repos > workflow4metabolomics > camera_combinexsannos
diff abims_CAMERA_combinexsAnnos.xml @ 0:139ff66b0b5d draft
planemo upload commit f69695e76674862ed9c77c1c127f459b4df42464
author | workflow4metabolomics |
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date | Fri, 26 Jul 2019 16:49:18 -0400 |
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children | ea15115a5b3f |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abims_CAMERA_combinexsAnnos.xml Fri Jul 26 16:49:18 2019 -0400 @@ -0,0 +1,267 @@ +<tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.2.5"> + + <description>Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations.</description> + + <macros> + <import>macros.xml</import> + </macros> + + <expand macro="requirements"/> + <expand macro="stdio"/> + + <command><![CDATA[ + @COMMAND_RSCRIPT@/CAMERA_combinexsAnnos.r + image_pos '$image_pos' + image_neg '$image_neg' + + pos $pos tol + $tol ruleset + $ruleset keep_meta + $keep_meta + + convertRTMinute $export.convertRTMinute + numDigitsMZ $export.numDigitsMZ + numDigitsRT $export.numDigitsRT + + ]]></command> + + <inputs> + <param name="image_pos" type="data" label="Positive RData ion mode" format="rdata.camera.positive,rdata" help="output file from CAMERA.annotate using a positive polarity mode" /> + <param name="image_neg" type="data" label="Negative RData ion mode" format="rdata.camera.negative,rdata" help="output file from CAMERA.annotate using a positive negative mode" /> + + <param name="pos" type="select" label="Returned peaklist polarity mode"> + <option value="TRUE" selected="true">positive</option> + <option value="FALSE" >negative</option> + </param> + + <param name="tol" type="integer" value="2" label="Retention time window in seconds" help="[pos] As first step it searches for pseudospectra from the positive and the negative sample within a retention time window" /> + <param name="ruleset" type="text" value="1,1" label="Matrix of matching rules" help="[ruleset] Matrix of matching rules. By default, the matrix (1,1) would create the M+H/M-H rule, since the first rule of xsa.pos@ruleset and xsa.neg@ruleset is M+H respectively M-H. Only rules with identical charge can be combined!" /> + <param name="keep_meta" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Keep only the metabolites which match a difference "/> + + <section name="export" title="Export options"> + <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/> + <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" /> + <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" /> + </section> + </inputs> + + <outputs> + <data name="variableMetadata" format="tabular" label="${image_pos.name[:-6]}.combinexsAnnos.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" /> + <!-- + <data name="rdata" format="rdata" label="${image_pos.name[:-6]}.combinexsAnnos.Rdata" from_work_dir="combinexsAnnos.RData" /> + --> + </outputs> + + <tests> + <test> + <!-- TODO: generer des vrais dataset pos et neg--> + <param name="image_pos" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.Rdata"/> + <param name="image_neg" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata"/> + <param name="pos" value="TRUE"/> + <param name="tol" value="2"/> + <param name="ruleset" value="1,1"/> + <section name="export"> + <param name="convertRTMinute" value="True"/> + <param name="numDigitsMZ" value="4" /> + <param name="numDigitsRT" value="1" /> + </section> + <output name="variableMetadata" file="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv" /> + </test> + </tests> + + + <help><![CDATA[ + +@HELP_AUTHORS@ + +======================= +Xcms.combinexsAnnos +======================= + +----------- +Description +----------- + +**What it does?** + +This function check annotations of ion species with the help of a sample from opposite ion mode. +As first step it searches for pseudospectra from the positive and the negative sample within a reten- +tion time window. For every result the m/z differences between both samples are matched against +specific rules, which are combinations from pos. and neg. ion species. As example M+H and M-H +with a m/z difference of 2.014552. If two ions matches such a difference, the ion annotations are +changed (previous annotation is wrong), confirmed or added. Returns the peaklist from one ion +mode with recalculated annotations. + +**Details** + +Both xsAnnotate object should be full processed (grouping and annotation). Without previous anno- +tation the resulting peaklist only includes annotation with matches peaks from both mode according +to the rule(s). With ruleset=NULL the function only looks for M+H/M-H pairs. The ruleset is +a two column matrix with includes rule indices from the rule table of both xsAnnotate objects. +A ruleset (1,1) would create the M+H/M-H rule, since the first rule of xsa.pos@ruleset and +xsa.neg@ruleset is M+H respectively M-H. Only rules with identical charge can be combined! + + + +----------------- +Workflow position +----------------- + + +**Upstream tools** + +========================= ======================= ===================== ========== +Name Output file Format Parameter +========================= ======================= ===================== ========== +xcms.annotatediffreport xset.annotate_POS.RData rdata.camera.positive RData file +------------------------- ----------------------- --------------------- ---------- +xcms.annotatediffreport xset.annotate_NEG.RData rdata.camera.positive RData file +========================= ======================= ===================== ========== + +**Downstream tools** + ++---------------------------+-----------------------------------------+--------+ +| Name | Output file | Format | ++===========================+=========================================+========+ +|Batch_correction |xset.combinexsAnnos.variableMetadata.tsv | Tabular| ++---------------------------+-----------------------------------------+--------+ +|Filters |xset.combinexsAnnos.variableMetadata.tsv | Tabular| ++---------------------------+-----------------------------------------+--------+ +|Univariate |xset.combinexsAnnos.variableMetadata.tsv | Tabular| ++---------------------------+-----------------------------------------+--------+ +|Multivariate |xset.combinexsAnnos.variableMetadata.tsv | Tabular| ++---------------------------+-----------------------------------------+--------+ + + + +The output file **xset.annotateDiffreport.variableMetadata.tsv** is a tabular file. You can continue your analysis using it in the following tools: + | Batch_correction + | Filters + | Univariate + | Multivariate PCA, PLS and OPLS + + +**Place of CAMERA.combinexsannot after XCMS part of the metabolomic workflow** + +.. image:: combinexsannos_workflow_zoom.png + +**General schema of the metabolomic workflow** + +.. image:: combinexsannos_workflow.png + + +----------- +Input files +----------- + ++---------------------------+----------------------------+ +| Parameter : label | Format | ++===========================+============================+ +| Positive RData ion mode | rdata.camera.positive | ++---------------------------+----------------------------+ +| Negative RData ion mode | rdata.camera.negative | ++---------------------------+----------------------------+ + +------------ +Output files +------------ + +xset.combinexsAnnos.variableMetadata.tsv + + | A tabular file which is similar to the diffreport result , within additional columns containing the annotation results. + | For each metabolite (row) : + | the value of the intensity in each sample, fold, tstat, pvalue, anova, mzmed, mzmin, mzmax, rtmed, rtmin, rtmax, npeaks, isotopes, adduct, pcgroup and neg (or pos). Mode + +xset.combinexsAnnos.Rdata + + | Rdata file, that be used outside Galaxy in R. + + +--------------------------------------------------- + +--------------- +Working example +--------------- + +Input files +----------- + + | Positive RData ion mode -> **POS.xset.annotateDiffreport.RData** + | Negative RData ion mode -> **NEG.xset.annotateDiffreport.RData** + +Parameters +---------- + + | pos -> **positive** + | tol -> **2 (default)** + | ruleset -> **1,1 (default)** + +Output files +------------ + +**Example of an xset.combinexsAnnos.variableMetadata.tsv output:** + +.. image:: combinexsannos_variableMetadata.png + + +--------------------------------------------------- + +Changelog/News +-------------- + +.. _News: https://bioconductor.org/packages/release/bioc/news/CAMERA/NEWS + +**Version 2.2.5 - 09/04/2019** + +- UPGRADE: upgrade the CAMERA version from 1.34.0 to 1.38.1 (see CAMERA News_) + +- UPGRADE: refactoring of internal code + +**Version 2.2.2 - 01/03/2018** + +- UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0 + +**Version 2.0.7 - 29/11/2017** + +- BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C + + +**Version 2.0.6 - 10/02/2017** + +- IMPROVEMENT: Synchronize the variableMetadata export option with the other tools (xcms.group, xcms.fillpeaks, camera.annotate) + + +**Version 2.0.5 - 22/12/2016** + +- IMPROVEMENT: add the possibility to add a personal Matrix of matching rules (ruleset) + +**Version 2.0.4 - 21/04/2016** + +- UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0 + + +**Version 2.0.3 - 10/02/2016** + +- BUGFIX: better management of errors. Datasets remained green although the process failed + +- UPDATE: refactoring of internal management of inputs/outputs + + +**Version 2.0.1 - 07/06/2015** + +- IMPROVEMENT: new datatype/dataset formats (rdata.camera.positive, rdata.camera.negative, rdata.camera.quick ...) will facilitate the sequence of tools and so avoid incompatibility errors. + +- IMPROVEMENT: parameter labels have changed to facilitate their reading. + + +**Version 2.0.0 - 09/06/2015** + +- NEW: combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode + + + ]]></help> + + <expand macro="citation" /> + + +</tool>