Mercurial > repos > mmonsoor > probmetab
diff ProbMetab.xml @ 3:abcfa1648b66 draft
planemo upload commit c897279aa8cae0a4ad889bb05b143f32d2b6d712
| author | lecorguille |
|---|---|
| date | Fri, 07 Apr 2017 07:14:12 -0400 |
| parents | c4bd0c40eb3b |
| children |
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--- a/ProbMetab.xml Mon Jul 04 11:58:10 2016 -0400 +++ b/ProbMetab.xml Fri Apr 07 07:14:12 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="Probmetab" name="ProbMetab Tool" version="1.0.1"> +<tool id="Probmetab" name="ProbMetab Tool" version="1.1.0"> <description>Wrapper function for ProbMetab R package.</description> @@ -12,201 +12,243 @@ <command> @COMMAND_CAMERA_SCRIPT@ #if $acquisition_options.mode == "one": - mode_acquisition $acquisition_options.mode xa $acquisition_options.xa + mode_acquisition $acquisition_options.mode + image '$acquisition_options.image' ##if $acquisition_options.xsetnofill_options.option == "show": - ##xsetnofill $acquisition_options.xsetnofill_options.xsetnofill - ##end if + ##xsetnofill $acquisition_options.xsetnofill_options.xsetnofill + ##end if + + @COMMAND_FILE_LOAD_ONE@ + #else - mode_acquisition $acquisition_options.mode inputs_mode $acquisition_options.input_mode.option + mode_acquisition $acquisition_options.mode + inputs_mode $acquisition_options.input_mode.option #if $acquisition_options.input_mode.option== "two": - image_pos $acquisition_options.input_mode.image_pos image_neg $acquisition_options.input_mode.image_neg - ##if $acquisition_options.input_mode.xsetnofill_options.option == "show": - ##xsetPnofill $acquisition_options.input_mode.xsetnofill_options.xsetPnofill xsetNnofill $acquisition_options.input_mode.xsetnofill_options.xsetNnofill - ##end if + image_pos '$acquisition_options.input_mode.image_pos' + image_neg '$acquisition_options.input_mode.image_neg' + ##if $acquisition_options.input_mode.xsetnofill_options.option == "show": + ##xsetPnofill $acquisition_options.input_mode.xsetnofill_options.xsetPnofill + ##xsetNnofill $acquisition_options.input_mode.xsetnofill_options.xsetNnofill + ##end if + + @COMMAND_FILE_LOAD_POSITIVE@ + @COMMAND_FILE_LOAD_NEGATIVE@ ##else - ##image_combinexsannos $acquisition_options.input_mode.image_combinexsannos image_pos $acquisition_options.input_mode.image_pos + ##image_combinexsannos $acquisition_options.input_mode.image_combinexsannos + ##image_pos $acquisition_options.input_mode.image_pos #end if #end if - #if $option_toexclude.option == "show": - toexclude $option_toexclude.toexclude + ## Extraction of CAMERA annotation [get.annot] + allowMiss $getannot.allowMiss + #if $getannot.option_toexclude.option == "show": + toexclude $getannot.option_toexclude.toexclude #end if - allowMiss $allowMiss html $html kegg_db $kegg_db ppm_tol $ppm_tol - opt $opt corths $corths corprob $corprob pcorprob $pcorprob prob $prob - - @COMMAND_ZIPFILE_LOAD@ + + ## Database matching [create.reactionM] + kegg_db $db.kegg_db + ppm_tol $db.ppm_tol + + ## Probability calculations matrix export [export.class.table] + prob $export.prob + html $export.html + + ## Calculate the correlations and partial correlations and cross reference then with reactions [reac2cor] + opt $reac2cor.opt + corprob $reac2cor.corprob + pcorprob $reac2cor.pcorprob + corths $reac2cor.corths + + @COMMAND_LOG_EXIT@ </command> <inputs> <conditional name="acquisition_options"> - <param name="mode" type="select" label="Choose your acquisition mode" > - <option value="one" selected="true" >One acquisition charge mode</option> - <option value="two" >Two acquisition charge mode (positif and negatif)</option> - </param> - - <!-- One acquisition mode--> - <when value="one"> - <param name="xa" type="data" label="Annotate RData" format="rdata.camera.positive,rdata.camera.negative,rdata" help="Output file from annotate step " /> - <!-- - <conditional name="xsetnofill_options"> - <param name="option" type="select" label="RData group step" help="xcmsSet xcms object after missing data replacement, to retrieve SNR to isotopic peaks." > - <option value="show">show</option> - <option value="hide" selected="true">hide</option> - </param> - <when value="show"> - <param name="xsetnofill" type="data" label="Positive or Negative RData from group step before fillpeaks " format="rdata" help=" output from group step" /> - </when> - - </conditional> - --> - </when> - <!-- Two acquisition modes--> - <when value="two"> + <param name="mode" type="select" label="Choose your acquisition mode" > + <option value="one" selected="true" >One acquisition charge mode</option> + <option value="two" >Two acquisition charge mode (positif and negatif)</option> + </param> - - <conditional name="input_mode"> - <param name="option" type="select" label="Choose your input type method:" > - <!-- Bug combinexsannos TODO <option value="one">Input from combinexsAnnos step</option> --> - <option value="two" selected="true">Rdata inputs from annotate</option> - </param> - <!-- - <when value="one"> - <param name="image_combinexsannos" type="data" label="RData output from combinexsAnnos step" format="rdata" help="output file from combinexAnnos step " /> - <param name="image_pos" type="data" label="Positive RData ion mode from annotatediffreport step" format="rdata" help="output file from annotatediffreport step " /> - </when> - --> - <when value="two"> - <param name="image_pos" type="data" label="Positive annotate RData" format="rdata.camera.positive,rdata" help="output file from annotate step " /> - <param name="image_neg" type="data" label="Negative annotate RData" format="rdata.camera.negative,rdata" help="output file from annotate step" /> - <!-- - <conditional name="xsetnofill_options"> - <param name="option" type="select" label="Two RData group step (positive and negative)" help="xcmsSet xcms objects after missing data replacement from your two acquisition modes, to retrieve SNR to isotopic peaks." > - <option value="show">show</option> - <option value="hide" selected="true">hide</option> - </param> - <when value="show"> - <param name="xsetPnofill" type="data" label="Positive RData from group step before fillpeaks " format="rdata.xcms.group,rdata" help="" /> - <param name="xsetNnofill" type="data" label="Negative RData from group step before fillpeaks" format="rdata.xcms.group,rdata" help="" /> - </when> - </conditional> - --> - </when> - </conditional> - </when> - + <!-- One acquisition mode--> + <when value="one"> + <param name="image" type="data" label="Annotate RData" format="rdata.camera.positive,rdata.camera.negative,rdata" help="Output file from annotate step " /> + <!-- + <conditional name="xsetnofill_options"> + <param name="option" type="select" label="RData group step" help="xcmsSet xcms object after missing data replacement, to retrieve SNR to isotopic peaks." > + <option value="show">show</option> + <option value="hide" selected="true">hide</option> + </param> + <when value="show"> + <param name="xsetnofill" type="data" label="Positive or Negative RData from group step before fillpeaks " format="rdata" help=" output from group step" /> + </when> + </conditional> + --> + <expand macro="input_file_load"/> + </when> + <!-- Two acquisition modes--> + <when value="two"> + <conditional name="input_mode"> + <param name="option" type="select" label="Choose your input type method:" > + <!-- Bug combinexsannos TODO <option value="one">Input from combinexsAnnos step</option> --> + <option value="two" selected="true">Rdata inputs from annotate</option> + </param> + <!-- + <when value="one"> + <param name="image_combinexsannos" type="data" label="RData output from combinexsAnnos step" format="rdata" help="output file from combinexAnnos step " /> + <param name="image_pos" type="data" label="Positive RData ion mode from annotatediffreport step" format="rdata" help="output file from annotatediffreport step " /> + </when> + --> + <when value="two"> + <param name="image_pos" type="data" label="Positive annotate RData" format="rdata.camera.positive,rdata" help="output file from annotate step " /> + <param name="image_neg" type="data" label="Negative annotate RData" format="rdata.camera.negative,rdata" help="output file from annotate step" /> + <!-- + <conditional name="xsetnofill_options"> + <param name="option" type="select" label="Two RData group step (positive and negative)" help="xcmsSet xcms objects after missing data replacement from your two acquisition modes, to retrieve SNR to isotopic peaks." > + <option value="show">show</option> + <option value="hide" selected="true">hide</option> + </param> + <when value="show"> + <param name="xsetPnofill" type="data" label="Positive RData from group step before fillpeaks " format="rdata.xcms.group,rdata" help="" /> + <param name="xsetNnofill" type="data" label="Negative RData from group step before fillpeaks" format="rdata.xcms.group,rdata" help="" /> + </when> + </conditional> + --> + </when> + </conditional> + <expand macro="input_file_load" polarity="Positive"/> + <expand macro="input_file_load" polarity="Negative"/> + </when> </conditional> - - <param name="allowMiss" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Retrieves peaks with no eviendence of adduct or isotope" help=" [allowMiss] (ionAnnot function) Logical, annotate also the peaks as single charged molecules [M+/-H]." /> - <conditional name="option_toexclude"> - <param name="option" type="select" label="Exclude samples" > - <option value="show">show</option> - <option value="hide" selected="true">hide</option> - </param> - <when value="show"> - <param name="toexclude" type="text" value="blank,medium,QC" label="samples to be excluded of peak counting to non-annotated peak selection." help="" /> - </when> - <when value="hide" /> - </conditional> - <!-- - <conditional name="useIso_options"> - <param name="option" type="select" label="Calculates the relative isotopic abundance ratio (Carbon 13)" > - <option value="show">Yes</option> - <option value="hide" selected="true">No</option> - </param> - <when value="show"> - <param name="var" type="select" label="var (incorporate.isotopes)" help="1 to use standard mean/sd estimators to carbon number prediction, 2 for median/mad estimators." > - <option value="1">1</option> - <option value="2" selected="true">2</option> - </param> - </when> - </conditional> - --> - <param name="html" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Logical, check if you want to generate a HTML ProbMetab report" help=" [html] (export.class.table function).This parameter uses the raw data to plot EICs and may be time consuming." /> + <section name="getannot" title="Extraction of CAMERA annotation [get.annot]" expanded="True"> + <param name="allowMiss" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Retrieves peaks with no eviendence of adduct or isotope" help=" [allowMiss] (ionAnnot function) Logical, annotate also the peaks as single charged molecules [M+/-H]." /> + <conditional name="option_toexclude"> + <param name="option" type="select" label="Exclude samples" > + <option value="show">show</option> + <option value="hide" selected="true">hide</option> + </param> + <when value="show"> + <param name="toexclude" type="text" value="blank,medium,QC" label="Samples to be excluded of peak counting to non-annotated peak selection." help="[toexclude]" /> + </when> + <when value="hide" /> + </conditional> + </section> - <param name="kegg_db" type="text" size="40" label="Search on KEGG database or multiple organisms " help="Search on all KEGG organisms or multiple organisms (id1,id2,id3,...).By default,the value is KEGG which means searching on all KEGG organism. The list of KEGG IDs are available at http://rest.kegg.jp/list/organism" value="KEGG" > - <validator type="empty_field"/> - </param> - <param name="ppm_tol" type="integer" value="8" label="Parts per million mass tolerance allowed in the mass search" help="[ppm.tol] (create.reactionMfunction) " /> - - - <param name="opt" type="select" label="Correlation option" help="[opt] (reac2cor function) cor for correlation, and pcor for partial correlation." > - <option value="cor" selected="true">cor</option> - <option value="pcor">pcor</option> - </param> - - - <param name="corprob" type="float" value="0.8" label="Probability that the correlation is considered significant" help="[corprob] (reac2cor function) " /> - + <section name="db" title="Database matching [create.reactionM]" expanded="True"> + <param name="kegg_db" type="text" size="40" label="Search on KEGG database or multiple organisms " help="Search on all KEGG organisms or multiple organisms (id1,id2,id3,...).By default,the value is KEGG which means searching on all KEGG organism. The list of KEGG IDs are available at http://rest.kegg.jp/list/organism" value="KEGG" > + <validator type="empty_field"/> + </param> + <param name="ppm_tol" type="integer" value="8" label="Parts per million mass tolerance allowed in the mass search" help="[ppm.tol]" /> + <!-- + <conditional name="useIso_options"> + <param name="option" type="select" label="Calculates the relative isotopic abundance ratio (Carbon 13)" > + <option value="show">Yes</option> + <option value="hide" selected="true">No</option> + </param> + <when value="show"> + <param name="var" type="select" label="var (incorporate.isotopes)" help="1 to use standard mean/sd estimators to carbon number prediction, 2 for median/mad estimators." > + <option value="1">1</option> + <option value="2" selected="true">2</option> + </param> + </when> + </conditional> + --> + </section> - <param name="pcorprob" type="float" value="0.8" label="Probability that the partial correlation is considered significant." help="[pcorprob](reac2cor function)" /> - <param name="corths" type="float" value="0.75" label="Correlation intensity threshold" help="[corths] (reac2cor function)" /> + <section name="export" title="Probability calculations matrix export [export.class.table]" expanded="True"> + <param name="prob" type="select" label=" Calculation of the probability to attribute a mass to a compound" help="[prob] Default is 'count'. See the tool help for more details." > + <option value="count" selected="true">Count</option> + <option value="mean">Mean</option> + </param> + + <param name="html" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Logical, check if you want to generate a HTML ProbMetab report" help="[html] This parameter uses the raw data to plot EICs and may be time consuming." /> + </section> - <param name="prob" type="select" label=" Calculation of the probability to attribute a mass to a compound" help="[prob] (export.class.table function). Default is 'count'. See the tool help for more details." > - <option value="count" selected="true">Count</option> - <option value="mean">Mean</option> - </param> + <section name="reac2cor" title="Calculate the correlations and partial correlations and cross reference then with reactions [reac2cor]" expanded="True"> + <param name="opt" type="select" label="Correlation option" help="[opt] cor for correlation, and pcor for partial correlation." > + <option value="cor" selected="true">cor</option> + <option value="pcor">pcor</option> + </param> + + <param name="corprob" type="float" value="0.8" label="Probability that the correlation is considered significant" help="[corprob]" /> + + <param name="pcorprob" type="float" value="0.8" label="Probability that the partial correlation is considered significant." help="[pcorprob]" /> + <param name="corths" type="float" value="0.75" label="Correlation intensity threshold" help="[corths]" /> + </section> + <!-- + <section name="cytoscape" title="CytoScape options"> <param name="organismId" type="text" size="40" value="NULL" label="organismIdorganismId" help="(create.pathway.node.attributes function) KEGG organism id (http://www.kegg.jp/kegg/catalog/org_list.html) to filter possible pathways for known pathways for that organism. Only works for KEGG database for now. Default is NULL (all KEGG organisms). -" /> + " /> + </section> + --> - --> - - <expand macro="zipfile_load"/> </inputs> <outputs> <!-- <data name="output_image" format="rdata" from_work_dir="probmetab.RData" label="Probmetab.RData" /> --> <data name="html_output" format="html" from_work_dir="AnalysisExample.html" label="Probmetab.Analysis_Report_html" > - <filter>(html)</filter> + <filter>(export['html'])</filter> </data> <data name="tsv_output" format="tabular" from_work_dir="Analysis_Report.tsv" label="Probmetab.CytoScape_output_Attribute_List.tsv" /> <data name="eics" format="zip" from_work_dir="Analysis_Report.zip" label="Probmetab.Analysis_Report_EICs_plots.zip" > - <filter>(html)</filter> + <filter>(export['html'])</filter> </data> <data name="sif_output" format="tabular" from_work_dir="sif.tsv" label="Probmetab.CytoScape_output.sif" /> - <data name="log" format="txt" from_work_dir="probmetab.log" label="Probmetab.log" /> <data name="variableMetadata" format="tabular" from_work_dir="variableMetadata.tsv" label="variableMetadata.tsv" > - <filter>(acquisition_options['mode'] == 'one')</filter> + <filter>(acquisition_options['mode'] == 'one')</filter> </data> <data name="CombineMolIon" format="tabular" from_work_dir="CombineMolIon.tsv" label="CombineMolIon.tsv" > - <filter>(acquisition_options['mode'] == 'two')</filter> + <filter>(acquisition_options['mode'] == 'two')</filter> </data> <data name="variableMetadata_Positive" format="tabular" from_work_dir="variableMetadata_Positive.tsv" label="variableMetadata_Positive.tsv" > - <filter>(acquisition_options['mode'] == 'two')</filter> + <filter>(acquisition_options['mode'] == 'two')</filter> </data> <data name="variableMetadata_Negative" format="tabular" from_work_dir="variableMetadata_Negative.tsv" label="variableMetadata_Negative.tsv" > - <filter>(acquisition_options['mode'] == 'two')</filter> + <filter>(acquisition_options['mode'] == 'two')</filter> </data> </outputs> <tests> <test> - <param name="acquisition_options|mode" value="one" /> - <param name="acquisition_options|xa" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata" /> - <param name="zipfile_load_conditional|zipfile_load_select" value="yes" /> - <param name="zipfile_load_conditional|zip_file" value="faahKO_reduce.zip" ftype="zip" /> - <output name="log"> - <assert_contents> - <has_text text="ko15 ko16 wt15 wt16" /> - <has_text text="Step 1... determine cutoff point" /> - <has_text text="Step 2... estimate parameters of null distribution and eta0" /> - <has_text text="Step 3... compute p-values and estimate empirical PDF/CDF" /> - <has_text text="Step 4... compute q-values and local fdr" /> - </assert_contents> - </output> + <conditional name="acquisition_options"> + <param name="mode" value="one" /> + <param name="image" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata" /> + </conditional> + <expand macro="test_commun"/> + <expand macro="test_file_load_zip"/> + <assert_stdout> + <has_text text="Step 1... determine cutoff point" /> + <has_text text="Step 2... estimate parameters of null distribution and eta0" /> + <has_text text="Step 3... compute p-values and estimate empirical PDF/CDF" /> + <has_text text="Step 4... compute q-values and local fdr" /> + </assert_stdout> + </test> + <test> + <conditional name="acquisition_options"> + <param name="mode" value="one" /> + <param name="image" value="faahOK-single.xset.merged.group.retcor.group.fillPeaks.annotate.negative.Rdata" /> + </conditional> + <expand macro="test_commun"/> + <expand macro="test_file_load_single"/> + <assert_stdout> + <has_text text="Step 1... determine cutoff point" /> + <has_text text="Step 2... estimate parameters of null distribution and eta0" /> + <has_text text="Step 3... compute p-values and estimate empirical PDF/CDF" /> + <has_text text="Step 4... compute q-values and local fdr" /> + </assert_stdout> </test> </tests> <help> - + @HELP_AUTHORS@ ========= @@ -225,7 +267,7 @@ **Details** ProbMetab assumes peak detection, retention time correction and peak grouping [4, 5] in order to -perform mass peak to compound assignment. +perform mass peak to compound assignment. Once the initial annotation for different forms of the same ion (adducts and isotopes), is defined, one can seek for a non-redundant set of putative molecules (after charge and possible adduct @@ -235,7 +277,7 @@ experimental condition. In order to address this issue, a flexible workflow, which allows users to integrate different methods, would improve true molecular ions recovery. -The ion annotation table has the following core information: exact mass of putative molecule with experimental error; isotopic pattern associated; adduct form associated, and the original reference to raw data. +The ion annotation table has the following core information: exact mass of putative molecule with experimental error; isotopic pattern associated; adduct form associated, and the original reference to raw data. @@ -250,9 +292,9 @@ ========================= ========================================== ======= ========== Name Output file Format Parameter ========================= ========================================== ======= ========== -xcms.annotate xset.annotate_POS (or NEG).RData RData RData file +xcms.annotate xset.annotate_POS (or NEG).RData RData RData file ========================= ========================================== ======= ========== - + **General schema of the metabolomic workflow** @@ -295,7 +337,7 @@ **Calculate** -**intervals** +**intervals** A vector of SNR numerical intervals, to which different carbon offset should be added to predicted C-number. **offset** @@ -309,7 +351,7 @@ Which noise model to use, "erfc" to complementary error function, or "gaussian" to standard gaussian with two sd corresponding to the given p.p.m precision. -**precision** +**precision** Equipment mass accuracy, usually the same used in exact mass search. @@ -384,6 +426,12 @@ Changelog/News -------------- +**Version 1.1.0 - 06/04/2017** + +- IMPROVEMENT: add some sections within to separate the different parts of the process + +- IMPROVEMENT: Probmetab is now compatible with merged individual data from xcms.xcmsSet + **Version 1.0.1 - 16/05/2016** - TEST: refactoring to pass planemo test using conda dependencies @@ -393,10 +441,8 @@ - NEW: ProbMetab first version - + </help> <expand macro="citation" /> </tool> - -