| Nozzle: a Report Generation Toolkit for Data Analysis Pipelines | Nozzle.R1-package nozzle |
| Add the URL, title, and signficance status of a related report, e.g. one summarizing the same type of analysis but on a different input set. | addRelatedReport |
| Add child elements to a parent element. | addTo |
| Add elements to the "Input" subsection in the "Methods & Data" section of a standard report. | addToInput |
| Add elements to the "Introduction" subsection in the "Overview" section of a standard report. | addToIntroduction |
| Add elements to the "Meta" section of a standard report. | addToMeta |
| Add elements to the "Methds & Data" section of a standard report. | addToMethods |
| Add elements to the "Overview" section of a standard report. | addToOverview |
| Add elements to the "References" subsection in the "Methods & Data" section of a standard report. | addToReferences |
| Add elements to the "Results" section of a standard report. | addToResults |
| Add elements to the "Summary" subsection in the "Overview" section of a standard report. | addToSummary |
| Format text as code. | asCode |
| Format text with emphasis (usually resulting in text set in italics). | asEmph |
| Format text as filename. | asFilename |
| Format text as a hyperlink. | asLink |
| Format text as parameter. | asParameter |
| Reference a citation, figure or table element. | asReference |
| Format text with strong emphasis (usually resulting in text set in bold). | asStrong |
| Include a result in text. This is a legacy method and provided only for backwards compatibility. | asSummary |
| Format text as value. | asValue |
| Default DOI resolver URL. | DEFAULT.DOI.RESOLVER |
| Default filename for reports. | DEFAULT.REPORT.FILENAME |
| Name of entities that are labeled as signficiant. | DEFAULT.SIGNIFICANT.ENTITY |
| Get the collection date of 'report'. The collection date is the date when the collection that this report is part of was created. | getCollectionDate |
| Get the collection version of 'report'. The collection version is the version string of the collection that this report is part of. | getCollectionVersion |
| Get contact email address for 'report'. | getContactInformationEmail |
| Get label for contact button for 'report'. | getContactInformationLabel |
| Get contact email default message for 'report'. | getContactInformationMessage |
| Get contact email subject line for 'report'. | getContactInformationSubject |
| Get name of the copyright owner for 'report'. | getCopyrightOwner |
| Get copyright statement for 'report'. This text is linked to the copyright URL. | getCopyrightStatement |
| Get copyright URL for 'report', which is linked to the copyright statement. | getCopyrightUrl |
| Get copyright year 'report'. | getCopyrightYear |
| Get date when 'report' was created. | getCreatorDate |
| Get name and version of the Nozzle package that was used to create 'report'. | getCreatorName |
| Get the path or URL of the CSS file to be used to overwrite the default print (not: screen) style sheet. | getCustomPrintCss |
| Get the path or URL of the CSS file to be used to overwrite the default screen (not: print) style sheet. | getCustomScreenCss |
| Get the DOI (document object identifier, http://www.doi.org) for 'report'. | getDoi |
| Get the DOI creator for 'report'. | getDoiCreator |
| Get the DOI publisher for 'report'. | getDoiPublisher |
| Get the DOI resolver URL (e.g. http://dx.doi.org) for 'report'. | getDoiResolver |
| Get the DOI title for 'report'. | getDoiTitle |
| Get the DOI version for 'report'. | getDoiVersion |
| Get the DOI year for 'report'. | getDoiYear |
| Get an exported element from a report. This can be used to generate aggregate reports. This is an experimental feature of Nozzle and may not lead to the expected results. | getExportedElement |
| Get the IDs of exported elements from 'report'. This is an experimental feature of Nozzle and may not lead to the expected results. | getExportedElementIds |
| Get path or URL of image file associated with a figure element. | getFigureFile |
| Get path or URL of high-resolution of vector-based image file associated with a figure element. | getFigureFileHighRes |
| Get Google Analytics tracking ID for 'report'. | getGoogleAnalyticsId |
| Get logo file for one of six positions (three at the top, three at the bottom) in 'report'. | getLogo |
| Get affiliation of maintainer of 'report'. | getMaintainerAffiliation |
| Get email address of maintainer of 'report'. | getMaintainerEmail |
| Get name of maintainer of 'report'. | getMaintainerName |
| Get date when 'report' was rendered. | getRendererDate |
| Get name and version of the Nozzle package that was used to render 'report'. | getRendererName |
| Get the ID (a UUID) of 'report'. | getReportId |
| Get the subtitle of 'report'. | getReportSubTitle |
| Get the title of 'report'. | getReportTitle |
| Get name of entities that are called out as significant, e.g. "gene". This is currently not being used and might become obsolete in future versions of Nozzle. | getSignificantEntity |
| Get the total number of significant results in 'report'. | getSignificantResultsCount |
| Get the name of the software that used Nozzle to generate 'report'. | getSoftwareName |
| Get the version of the software that used Nozzle to generate 'report'. | getSoftwareVersion |
| Get the first element of the "Summary" subsection in the "Overview" section in a standard report. | getSummary |
| Get path or URL of file associatd with table element. | getTableFile |
| Output type. | HTML.FRAGMENT |
| Output type. | HTML.REPORT |
| Image type. | IMAGE.TYPE.PDF |
| Image type. | IMAGE.TYPE.RASTER |
| Image type. | IMAGE.TYPE.SVG |
| Test if 'element' is a figure element. | isFigure |
| Test if 'element' is a table element. | isTable |
| Logo position. | LOGO.BOTTOM.CENTER |
| Logo position. | LOGO.BOTTOM.LEFT |
| Logo position. | LOGO.BOTTOM.RIGHT |
| Logo position. | LOGO.TOP.CENTER |
| Logo position. | LOGO.TOP.LEFT |
| Logo position. | LOGO.TOP.RIGHT |
| Create a citation element. | newCitation |
| Create a new custom report without pre-defined sections. | newCustomReport |
| Create a new list element. | newFigure |
| Create a new freeform HTML element. THIS MUST BE USED WITH EXTRAORDINARTY CARE! | newHtml |
| Create a citation element that represents a document published in a journal. This is a convenience wrapper for 'newCitation'. | newJournalCitation |
| Create a new list element. | newList |
| Create a new paragraph element. | newParagraph |
| Create a new parameter list element. A parameter list is an unnumbered list of the form param_1 = value_1, ..., param_n = value_n where param_i is formated as a parameter and value_i is formatted as a value. | newParameterList |
| Create a new report with pre-defined sections Overview/Introduction, Overview/Summary, Results, Methods & Data/Input, Methods & Data/References and Meta Data. | newReport |
| Create a new result element. | newResult |
| Create a new section element. | newSection |
| Create a new subsection element. | newSubSection |
| Create a new subsubsection element. | newSubSubSection |
| Create new table element. | newTable |
| Create a citation element that represents a document published online. This is a convenience wrapper for 'newCitation'. | newWebCitation |
| Group visibility. | PROTECTION.GROUP |
| Private visibility. | PROTECTION.PRIVATE |
| Public visibility. | PROTECTION.PUBLIC |
| Group visibility. | PROTECTION.TCGA |
| Output type. | RDATA.REPORT |
| Section class. | SECTION.CLASS.META |
| Section class. | SECTION.CLASS.RESULTS |
| Set the collection date of 'report'. The collection date is the date when the collection that this report is part of was created. | setCollectionDate |
| Set the collection version of 'report'. The collection version is the version string of the collection that this report is part of. | setCollectionVersion |
| Set contact information for 'report'. This is used to create a "contact" button in the top right corner of the report, e.g. to collect feedback about the report. | setContactInformation |
| Set copyright messsage for 'report'. | setCopyright |
| Set the path or URL of the CSS file to be used to overwrite the default print (not: screen) style sheet. Can be relative or absolute. | setCustomPrintCss |
| Set the path or URL of the CSS file to be used to overwrite the default screen (not: print) style sheet. Can be relative or absolute. | setCustomScreenCss |
| Set the DOI (document object identifier, http://www.doi.org) for 'report'. A warning will be emitted if the report has been assigned a DOI before. | setDoi |
| Set the DOI meta data creator for 'report'. | setDoiCreator |
| Set the DOI meta data publisher for 'report'. | setDoiPublisher |
| Set the DOI resolver URL (e.g. http://dx.doi.org) for 'report'. The URL must not end with a slash! | setDoiResolver |
| Set the DOI meta data title for 'report'. | setDoiTitle |
| Set the DOI meta data version for 'report'. | setDoiVersion |
| Set the DOI meta data year for 'report'. | setDoiYear |
| Set path or URL of image file associated with a figure element. Paths can relative or absolute. | setFigureFile |
| Set path or URL of high-resolution or vector-based image file associated with a figure element. Paths can be relative or absolute. | setFigureFileHighRes |
| Set the Google Analytics tracking ID to be embedded in this report ("web property id", usually starts with "UA-"). | setGoogleAnalyticsId |
| Set a logo file for one of six positions (three at the top, three at the bottom) in 'report', e.g. an institute logo. | setLogo |
| Set affiliation of maintainer of 'report'. | setMaintainerAffiliation |
| Set email address of maintainer of 'report'. | setMaintainerEmail |
| Set name of maintainer of 'report'. | setMaintainerName |
| Set the URL and title of the "next" report after 'report'. This will be accessible through the utility menu. | setNextReport |
| Set the URL and title of the "parent" report above 'report'. This will be accessible through the utility menu. | setParentReport |
| Set the URL and title of the "previous" report before 'report'. This will be accessible through the utility menu. | setPreviousReport |
| Set the subtitle of 'report'. | setReportSubTitle |
| Set the title of 'report'. | setReportTitle |
| Set name of entities that are called out as significant, e.g. "gene". This is currently not being used and might become obsolete in future versions of Nozzle. | setSignificantEntity |
| Set the name of the software that used Nozzle to generate 'report', e.g. "My Report Generator Script". | setSoftwareName |
| Set the name of the software that used Nozzle to generate 'report', e.g. "Version 1.2". | setSoftwareVersion |
| Set path or URL of file associatd with table element. | setTableFile |
| Default number of significant digits to be used to trim numeric columns in tables. | TABLE.SIGNIFICANT.DIGITS |
| Write 'report' to file. | writeReport |
