Mercurial > repos > mmonsoor > probmetab
changeset 5:1dd90aa7815d draft
planemo upload commit f9da57d32476742b887a77435eb77c70494ccf96
| author | lecorguille |
|---|---|
| date | Fri, 07 Apr 2017 03:31:35 -0400 |
| parents | a1b528cba999 |
| children | 9876c52c51c6 |
| files | ProbMetab.xml macros.xml probmetab.r |
| diffstat | 3 files changed, 120 insertions(+), 92 deletions(-) [+] |
line wrap: on
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--- a/ProbMetab.xml Thu Apr 06 05:26:35 2017 -0400 +++ b/ProbMetab.xml Fri Apr 07 03:31:35 2017 -0400 @@ -41,18 +41,25 @@ #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 + + ## 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@ @@ -80,6 +87,7 @@ </when> </conditional> --> + <expand macro="input_file_load"/> </when> <!-- Two acquisition modes--> <when value="two"> @@ -111,77 +119,88 @@ --> </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> + <section name="getannot" title="Extraction of CAMERA annotation [get.annot]"> + <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> + + <section name="db" title="Database matching [create.reactionM]"> + <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> - <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 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> - </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." /> + <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="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) " /> + <section name="export" title="Probability calculations matrix export [export.class.table]"> + <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="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="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="corprob" type="float" value="0.8" label="Probability that the correlation is considered significant" help="[corprob] (reac2cor function) " /> + <section name="reac2cor" title="Calculate the correlations and partial correlations and cross reference then with reactions [reac2cor]"> + <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="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)" /> + <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> - <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> <!-- - <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 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="input_file_load"/> - <expand macro="input_file_load" polarity="Positive"/> - <expand macro="input_file_load" polarity="Negative"/> </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="variableMetadata" format="tabular" from_work_dir="variableMetadata.tsv" label="variableMetadata.tsv" > - <filter>(drop_new-file_path['mode'] == 'one')</filter> + <filter>(acquisition_options['mode'] == 'one')</filter> </data> <data name="CombineMolIon" format="tabular" from_work_dir="CombineMolIon.tsv" label="CombineMolIon.tsv" > @@ -202,7 +221,7 @@ <param name="mode" value="one" /> <param name="image" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata" /> </conditional> - <param name="html" value="FALSE" /> + <expand macro="test_commun"/> <expand macro="test_file_load_zip"/> <assert_stdout> <has_text text="Step 1... determine cutoff point" /> @@ -216,7 +235,7 @@ <param name="mode" value="one" /> <param name="image" value="faahOK-single.xset.merged.group.retcor.group.fillPeaks.annotate.negative.Rdata" /> </conditional> - <param name="html" value="FALSE" /> + <expand macro="test_commun"/> <expand macro="test_file_load_single"/> <assert_stdout> <has_text text="Step 1... determine cutoff point" /> @@ -407,7 +426,9 @@ Changelog/News -------------- -**Version 1.1.0 - 15/02/2017** +**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
--- a/macros.xml Thu Apr 06 05:26:35 2017 -0400 +++ b/macros.xml Fri Apr 07 03:31:35 2017 -0400 @@ -27,32 +27,30 @@ <!-- raw file load for planemo test --> <token name="@COMMAND_FILE_LOAD_NEUTRAL@"> #if $file_load_section_selected.file_load_conditional.file_load_select == "yes": - #if $file_load_section_selected.file_load_conditional.inputs.input == "zip_file": - zipfile$polarity '$file_load_section_selected.file_load_conditional.inputs.zip_file' + #if $file_load_section_selected.file_load_conditional.input[0].is_of_type("mzxml") or $file_load_section_selected.file_load_conditional.input[0].is_of_type("mzml") or $file_load_section_selected.file_load_conditional.input[0].is_of_type("mzdata") or $file_load_section_selected.file_load_conditional.input[0].is_of_type("netcdf"): + #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section_selected.file_load_conditional.input ] ) + #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section_selected.file_load_conditional.input ] ) + singlefile_galaxyPath$polarity '$singlefile_galaxyPath' singlefile_sampleName$polarity '$singlefile_sampleName' #else - #set singlefile_galaxyPath = ','.join( [ str( $single_file ) for $single_file in $file_load_section_selected.file_load_conditional.inputs.single_file ] ) - #set singlefile_sampleName = ','.join( [ str( $single_file.name ) for $single_file in $file_load_section_selected.file_load_conditional.inputs.single_file ] ) - - singlefile_galaxyPath$polarity '$singlefile_galaxyPath' - singlefile_sampleName$polarity '$singlefile_sampleName' + zipfile$polarity '$file_load_section_selected.file_load_conditional.input' #end if #end if </token> <token name="@COMMAND_FILE_LOAD_ONE@"> - #set file_load_section_selected = $file_load_section + #set file_load_section_selected = $acquisition_options.file_load_section #set polarity="" @COMMAND_FILE_LOAD_NEUTRAL@ </token> <token name="@COMMAND_FILE_LOAD_POSITIVE@"> - #set file_load_section_selected = $file_load_sectionPositive + #set file_load_section_selected = $acquisition_options.file_load_sectionPositive #set polarity="Positive" @COMMAND_FILE_LOAD_NEUTRAL@ </token> <token name="@COMMAND_FILE_LOAD_NEGATIVE@"> - #set file_load_section_selected = $file_load_sectionNegative + #set file_load_section_selected = $acquisition_options.file_load_sectionNegative #set polarity="Negative" @COMMAND_FILE_LOAD_NEUTRAL@ </token> @@ -67,31 +65,40 @@ <when value="no"> </when> <when value="yes"> - <conditional name="inputs"> - <param name="input" type="select" label="Choose your inputs method" > - <option value="zip_file" selected="true">Zip file from your history containing your chromatograms</option> - <option value="single_file">A mzXML or netCDF file from your history</option> - </param> - <when value="zip_file"> - <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" /> - </when> - <when value="single_file"> - <param name="single_file" type="data" format="mzxml,netcdf" label="Single file" multiple="true"/> - </when> - </conditional> + <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" multiple="true" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." /> </when> </conditional> </section> </xml> + <xml name="test_commun"> + <section name="getannot"> + <param name="allowMiss" value="TRUE" /> + <conditional name="option_toexclude"> + <param name="option" value="hide" /> + </conditional> + </section> + <section name="db"> + <param name="kegg_db" value="KEGG" /> + <param name="ppm_tol" value="8" /> + </section> + <section name="export"> + <param name="prob" value="count" /> + <param name="html" value="FALSE" /> + </section> + <section name="reac2cor"> + <param name="opt" value="cor" /> + <param name="corprob" value="0.8" /> + <param name="pcorprob" value="0.8" /> + <param name="corths" value="0.75" /> + </section> + </xml> + <xml name="test_file_load_zip"> <section name="file_load_section"> <conditional name="file_load_conditional"> <param name="file_load_select" value="yes" /> - <conditional name="inputs"> - <param name="input" value="zip_file" /> - <param name="zip_file" value="faahKO_reduce.zip" ftype="zip" /> - </conditional> + <param name="input" value="faahKO_reduce.zip" ftype="zip" /> </conditional> </section> </xml> @@ -100,10 +107,7 @@ <section name="file_load_section@POLARITY@"> <conditional name="file_load_conditional"> <param name="file_load_select" value="yes" /> - <conditional name="inputs"> - <param name="input" value="single_file" /> - <param name="single_file" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" /> - </conditional> + <param name="input" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF" ftype="netcdf" /> </conditional> </section> </xml> @@ -118,7 +122,7 @@ .. class:: infomark -**Galaxy integration** Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABIMS TEAM, Station biologique de Roscoff. +**Galaxy integration** Misharl Monsoor misharl.monsoor@sb-roscoff.fr (and Gildas Le Corguillé) from ABIMS TEAM, Station biologique de Roscoff. | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.