Mercurial > repos > lecorguille > camera_annotate
diff abims_CAMERA_annotateDiffreport.xml @ 25:230f0bc9e792 draft
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
| author | lecorguille |
|---|---|
| date | Fri, 10 Feb 2017 11:11:27 -0500 |
| parents | 2a4a811c663d |
| children | 591d26b9027e |
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--- a/abims_CAMERA_annotateDiffreport.xml Wed Feb 01 12:23:07 2017 -0500 +++ b/abims_CAMERA_annotateDiffreport.xml Fri Feb 10 11:11:27 2017 -0500 @@ -1,7 +1,7 @@ -<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.5"> +<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.0"> <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description> - + <macros> <import>macros.xml</import> </macros> @@ -11,55 +11,57 @@ <command><![CDATA[ @COMMAND_CAMERA_SCRIPT@ - xfunction annotatediff - image $image + xfunction annotatediff + image '$image' - variableMetadataOutput $variableMetadata - dataMatrixOutput $datamatrix - xsetRdataOutput $rdata + variableMetadataOutput '$variableMetadata' + dataMatrixOutput '$datamatrix' + xsetRdataOutput '$rdata' - convert_param $convert_param num_digits $num_digits nSlaves \${GALAXY_SLOTS:-1} - sigma $sigma perfwhm $perfwhm + sigma $sigma perfwhm $perfwhm maxcharge $maxcharge maxiso $maxiso minfrac $minfrac - ppm $ppm mzabs $mzabs intval $intval + ppm $ppm mzabs $mzabs max_peaks $max_peaks quick $quick_block.quick #if $quick_block.quick == "FALSE" polarity $quick_block.polarity cor_eic_th $quick_block.cor_eic_th - graphMethod $quick_block.graphMethod - pval $quick_block.pval + graphMethod $quick_block.graphMethod + pval $quick_block.pval calcCiS $quick_block.calcCiS calcIso $quick_block.calcIso calcCaS $quick_block.calcCaS - multiplier $quick_block.multiplier + #if $quick_block.rules_block.rules_select == "FALSE" + multiplier $quick_block.rules_block.multiplier + #else + rules $quick_block.rules_block.rules + #end if #end if + @COMMAND_PEAKLIST@ + #if $options.option == "show": runDiffreport TRUE eicmax $options.eicmax eicwidth $options.eicwidth value $options.value - sortpval $options.sortpval + sortpval $options.sortpval h $options.h w $options.w mzdec $options.mzdec new_file_path ${__new_file_path__}/primary_${output_diffreport.id}_ #end if - - @COMMAND_ZIPFILE_LOAD@ + + @COMMAND_FILE_LOAD@ ]]></command> <inputs> - - + + <param name="image" type="data" label="RData file" format="rdata.xcms.fillpeaks,rdata" help="output file from another function xcms (fillPeaks)" /> - <param name="convert_param" 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="num_digits" type="integer" value="4" label="" help="Number of decimal places for mass values reported in ions identifiers. A minimum of 4 decimal places should be set" /> - <param name="sigma" type="integer" value="6" label="groupFWHM: multiplier of the standard deviation" help="[sigma]" /> <param name="perfwhm" type="float" value="0.6" max="1" min="0" label="groupFWHM: percentage of FWHM width" help="[perfwhm]" /> <param name="maxcharge" type="integer" value="3" label="findIsotopes: max. ion charge" help="[maxcharge]" /> @@ -67,14 +69,8 @@ <param name="minfrac" type="float" value="0.5" max="1" min="0" label="findIsotopes: The percentage number of samples, which must satisfy the C12/C13 rule for isotope annotation" help="[minfrac]" /> <param name="ppm" type="integer" value="5" label="General ppm error" help="[ppm]" /> <param name="mzabs" type="float" value="0.015" label="mzabs" help="General absolut error in m/z" /> - <param name="intval" type="select" label="General used intensity value" help="[intval] See the help section below"> - <option value="into" selected="true">into</option> - <option value="maxo" >maxo</option> - <option value="intb">intb</option> - </param> - + <param name="max_peaks" type="integer" value="100" label="How much peaks will be calculated in every thread using the parallel mode" help="[max_peaks]" /> - <param name="max_peaks" type="integer" value="100" label="How much peaks will be calculated in every thread using the parallel mode" help="[max_peaks]" /> <conditional name="quick_block"> <param name="quick" type="select" label="Quick mode" help="[quick] If TRUE, use only groupFWHM and findIsotopes functions. Else if FALSE, use also groupCorr and findAdducts"> <option value="TRUE">TRUE</option> @@ -84,7 +80,7 @@ <param name="polarity" type="select" label="findAdducts: Which polarity mode was used for measuring of the ms sample" help="polarity"> <option value="positive" >positive</option> <option value="negative" selected="true">negative</option> - </param> + </param> <param name="cor_eic_th" type="float" value="0.75" max="1" min="0" label="groupCorr: correlation threshold (0..1)" help="[cor_eic_th]" /> <param name="graphMethod" type="select" label="groupCorr: Method selection for grouping peaks after correlation analysis into pseudospectra" help="[graphMethod]"> <option value="hcs" selected="true">hcs</option> @@ -94,19 +90,31 @@ <param name="calcCiS" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use correlation inside samples for peak grouping" help="[calcCiS]"/> <param name="calcIso" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use isotopic relationship for peak grouping" help="[calcIso]"/> <param name="calcCaS" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use correlation across samples for peak grouping" help="[calcCaS]"/> - <param name="multiplier" type="integer" value="3" label="findAdducts: If no ruleset is provided, calculate ruleset with max. number n of [nM+x] clusterions" help="[multiplier]" /> - </when> - <when value="TRUE"> + <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="multiplier" type="integer" value="3" label="findAdducts: If no ruleset is provided, calculate ruleset with max. number n of [nM+x] clusterions" help="[multiplier]" /> + </when> + <when value="TRUE"> + <param name="rules" type="data" format="csv" label="findAdducts: User defined ruleset" help="[rules]" /> + </when> + </conditional> + </when> + <when value="TRUE"> <param name="polarity" type="hidden" value="quick" label="for the output label" help="for the output label" /> - </when> + </when> </conditional> - - + + <expand macro="input_peaklist"/> + <!-- Annotatediffreport specific parameters --> <conditional name="options"> <param name="option" type="select" label="Number of condition"> <option value="hide" selected="true">One condition</option> - <option value="show">Two or more conditions</option> + <option value="show">Two or more conditions</option> </param> <when value="show"> <param name="eicmax" type="integer" value="0" label="diffreport: number of the most significantly different analytes to create EICs for" help="[eicmax]" /> @@ -115,8 +123,8 @@ <option value="into" selected="true">into</option> <option value="maxo" >maxo</option> <option value="intb">intb</option> - </param> - <param name="h" type="integer" value="480" label="diffreport: Numeric variable for the height of the eic and boxplots that are printed out" help="[height]" /> + </param> + <param name="h" type="integer" value="480" label="diffreport: Numeric variable for the height of the eic and boxplots that are printed out" help="[height]" /> <param name="w" type="integer" value="640" label="diffreport: Numeric variable for the width of the eic and boxplots print out made" help="[width]" /> <param name="mzdec" type="integer" value="2" label="diffreport: Number of decimal places of title m/z values in the eic plot" help="[mzdec]" /> <param name="sortpval" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="diffreport: logical indicating whether the reports should be sorted by p-value" help="[sortpval]"/> @@ -124,8 +132,8 @@ <when value="hide"> </when> </conditional> - - <expand macro="zipfile_load"/> + + <expand macro="file_load"/> </inputs> <outputs> @@ -137,11 +145,11 @@ <when input="quick_block.polarity" value="negative" format="rdata.camera.negative" /> </change_format> </data> - <data name="output_diffreport" format="text" label="${image.name[:-6]}.annotateDiffreport" hidden="True"> - <filter>(options['option'] == 'show')</filter> - </data> + <data name="output_diffreport" format="text" label="${image.name[:-6]}.annotateDiffreport" hidden="true"> + <filter>(options['option'] == 'show')</filter> + </data> </outputs> - + <tests> <!--<test> <param name="image" value="xset.group.retcor.group.fillPeaks.RData"/> @@ -179,8 +187,50 @@ </test>--> <test> <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData"/> - <param name="convert_param" value="False"/> - <param name="num_digits" value="0"/> + <param name="sigma" value="6"/> + <param name="perfwhm" value="0.6"/> + <param name="maxcharge" value="3"/> + <param name="maxiso" value="4"/> + <param name="minfrac" value="0.5"/> + <param name="ppm" value="5"/> + <param name="mzabs" value="0.015"/> + <param name="max_peaks" value="100"/> + <conditional name="quick_block"> + <param name="quick" value="FALSE"/> + <param name="polarity" value="negative"/> + <param name="cor_eic_th" value="0.75"/> + <param name="graphMethod" value="hcs"/> + <param name="pval" value="0.05"/> + <param name="calcCiS" value="True"/> + <param name="calcIso" value="False"/> + <param name="calcCaS" value="False"/> + <conditional name="rules_block"> + <param name="rules_select" value="FALSE"/> + <param name="multiplier" value="3"/> + </conditional> + </conditional> + <param name="convertRTMinute" value="False"/> + <param name="numDigitsMZ" value="4" /> + <param name="numDigitsRT" value="1" /> + <param name="intval" value="into"/> + <conditional name="options"> + <param name="option" value="show"/> + <param name="eicmax" value="200"/> + <param name="eicwidth" value="200"/> + <param name="value" value="into"/> + <param name="h" value="480"/> + <param name="w" value="640"/> + <param name="mzdec" value="2"/> + <param name="sortpval" value="False"/> + </conditional> + <param name="file_load_conditional|file_load_select" value="yes" /> + <param name="file_load_conditional|inputs|input" value="zip_file" /> + <param name="file_load_conditional|inputs|zip_file" value="faahKO_reduce.zip" ftype="zip" /> + <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" /> + <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" /> + </test> + <test> + <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData"/> <param name="sigma" value="6"/> <param name="perfwhm" value="0.6"/> <param name="maxcharge" value="3"/> @@ -188,36 +238,91 @@ <param name="minfrac" value="0.5"/> <param name="ppm" value="5"/> <param name="mzabs" value="0.015"/> + <param name="max_peaks" value="100"/> + <conditional name="quick_block"> + <param name="quick" value="FALSE"/> + <param name="polarity" value="negative"/> + <param name="cor_eic_th" value="0.75"/> + <param name="graphMethod" value="hcs"/> + <param name="pval" value="0.05"/> + <param name="calcCiS" value="True"/> + <param name="calcIso" value="False"/> + <param name="calcCaS" value="False"/> + <conditional name="rules_block"> + <param name="rules_select" value="FALSE"/> + <param name="multiplier" value="3"/> + </conditional> + </conditional> + <param name="convertRTMinute" value="False"/> + <param name="numDigitsMZ" value="4" /> + <param name="numDigitsRT" value="1" /> <param name="intval" value="into"/> - <param name="max_peaks" value="100"/> - <param name="quick_block|quick" value="FALSE"/> - <param name="quick_block|polarity" value="negative"/> - <param name="quick_block|cor_eic_th" value="0.75"/> - <param name="quick_block|graphMethod" value="hcs"/> - <param name="quick_block|pval" value="0.05"/> - <param name="quick_block|calcCiS" value="True"/> - <param name="quick_block|calcIso" value="False"/> - <param name="quick_block|calcCaS" value="False"/> - <param name="quick_block|multiplier" value="3"/> - <param name="options|option" value="show"/> - <param name="options|eicmax" value="200"/> - <param name="options|eicwidth" value="200"/> - <param name="options|value" value="into"/> - <param name="options|h" value="480"/> - <param name="options|w" value="640"/> - <param name="options|mzdec" value="2"/> - <param name="options|sortpval" value="False"/> - <param name="zipfile_load_conditional|zipfile_load_select" value="yes" /> - <param name="zipfile_load_conditional|zip_file" value="faahKO_reduce.zip" ftype="zip" /> + <conditional name="options"> + <param name="option" value="show"/> + <param name="eicmax" value="200"/> + <param name="eicwidth" value="200"/> + <param name="value" value="into"/> + <param name="h" value="480"/> + <param name="w" value="640"/> + <param name="mzdec" value="2"/> + <param name="sortpval" value="False"/> + </conditional> + <param name="file_load_conditional|file_load_select" value="yes" /> + <param name="file_load_conditional|inputs|input" value="single_file" /> + <param name="file_load_conditional|inputs|single_file" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" /> <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" /> <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" /> </test> + <test> + <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData"/> + <param name="sigma" value="6"/> + <param name="perfwhm" value="0.6"/> + <param name="maxcharge" value="3"/> + <param name="maxiso" value="4"/> + <param name="minfrac" value="0.5"/> + <param name="ppm" value="5"/> + <param name="mzabs" value="0.015"/> + <param name="max_peaks" value="100"/> + <conditional name="quick_block"> + <param name="quick" value="FALSE"/> + <param name="polarity" value="negative"/> + <param name="cor_eic_th" value="0.75"/> + <param name="graphMethod" value="hcs"/> + <param name="pval" value="0.05"/> + <param name="calcCiS" value="True"/> + <param name="calcIso" value="False"/> + <param name="calcCaS" value="False"/> + <conditional name="rules_block"> + <param name="rules_select" value="TRUE"/> + <param name="rules" value="CASMI_extended_NEG_rules.csv" ftype="csv"/> + </conditional> + </conditional> + <param name="convertRTMinute" value="False"/> + <param name="numDigitsMZ" value="4" /> + <param name="numDigitsRT" value="1" /> + <param name="intval" value="into"/> + <conditional name="options"> + <param name="option" value="show"/> + <param name="eicmax" value="200"/> + <param name="eicwidth" value="200"/> + <param name="value" value="into"/> + <param name="h" value="480"/> + <param name="w" value="640"/> + <param name="mzdec" value="2"/> + <param name="sortpval" value="False"/> + </conditional> + <param name="file_load_conditional|file_load_select" value="yes" /> + <param name="file_load_conditional|inputs|input" value="single_file" /> + <param name="file_load_conditional|inputs|single_file" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" /> + <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.variableMetadata.tsv" /> + <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.dataMatrix.tsv" /> + </test> </tests> - - - + + + <help><![CDATA[ - + @HELP_AUTHORS@ ================ @@ -239,7 +344,7 @@ **What it does?** -The CAMERA annotation procedure can be split into two parts: We want to answer the questions which peaks occur from the same molecule and secondly compute its exact mass and annotate the ion species. Therefore CAMERA annotation workflow contains following primary functions: 1. peak grouping after retention time (**groupFWHM**) 2. peak group verification with peakshape correlation (**groupCorr**) Both methods separate peaks into different groups, which we define as ”pseu- dospectra”. Those pseudospectra can consists from one up to 100 ions, de- pending on the molecules amount and ionizability. Afterwards the exposure of the ion species can be performed with: 2 1. annotation of possible isotopes (**findIsotopes**) 2. annotation of adducts and calculating hypothetical masses for the group (**findAdducts**) This workflow results in a data-frame similar to a xcms peak table, that can be easily stored in a comma separated table .csv (Excel-readable). +The CAMERA annotation procedure can be split into two parts: We want to answer the questions which peaks occur from the same molecule and secondly compute its exact mass and annotate the ion species. Therefore CAMERA annotation workflow contains following primary functions: 1. peak grouping after retention time (**groupFWHM**) 2. peak group verification with peakshape correlation (**groupCorr**) Both methods separate peaks into different groups, which we define as ”pseu- dospectra”. Those pseudospectra can consists from one up to 100 ions, de- pending on the molecules amount and ionizability. Afterwards the exposure of the ion species can be performed with: 2 1. annotation of possible isotopes (**findIsotopes**) 2. annotation of adducts and calculating hypothetical masses for the group (**findAdducts**) This workflow results in a data-frame similar to a xcms peak table, that can be easily stored in a comma separated table .csv (Excel-readable). If you have two or more conditions, it will return a diffreport result within the annotation results. The diffreport result shows the most significant differences between two sets of samples. Optionally @@ -328,7 +433,7 @@ xset.annotate.dataMatrix.tsv | A tabular file which represents for each metabolite (row), the value of the intensity in each sample (column). - + xset.annotate.zip | It contains filebase_eic, filebase_box and filebase.tsv for one conditon vs another (Anova analysis). @@ -336,10 +441,10 @@ xset.annotate.Rdata rdata.camera.quick or rdata.camera.positive or rdata.camera.negative | Rdata file, that be used outside Galaxy in R. - + ------ -.. class:: infomark +.. class:: infomark The output **"xset.annotate.dataMatrix.tsv"** is a tabular file. You can continue your analysis using it in the following tools of the workflow: @@ -349,7 +454,7 @@ | PCA (Statistical analysis) | Hierarchical Clustering (Statistical analysis) - + --------------------------------------------------- --------------- @@ -377,7 +482,7 @@ | eicmax -> **200** | eicwidth -> **200 (default)** - + Output files ------------ @@ -386,7 +491,7 @@ .. image:: annotatediffreport_dataMatrix.png -**Example of a part of xset.annotate.variableMetadata.tsv output** +**Example of a part of xset.annotate.variableMetadata.tsv output** .. image:: annotatediffreport_variableMetadata.png @@ -396,9 +501,22 @@ Changelog/News -------------- +**Version 2.2.0 - 03/02/2017** + +- BUGFIX: the diffreport ids didn't convert the rt in minute as the other export + +- UPDATE: the settings (digits, convertion in minutes) of the identifiants will no longer modify the native one. Because we want to be conservative and because it can be dangerous for the data integrity during a futur merge of the table, we decide to put those customization in a new column namecustom within the variableMetadata. + +- IMPROVEMENT: add the possibility to set the MZ digit within the identifiants + +- IMPROVEMENT: add the possibility to use defined ruleset + +- IMPROVEMENT: CAMERA.annotate is now compatible with merged individual data from xcms.xcmsSet + + **Version 2.1.5 - 21/04/2016** -- UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0 +- UPGRADE: upgrade the CAMERA version from 1.22.0 to 1.26.0 **Version 2.1.4 - 18/04/2016** @@ -437,5 +555,3 @@ </tool> - -