# HG changeset patch
# User saskia-hiltemann
# Date 1447686412 18000
# Node ID e3cb63c2b7c146071aa64d5b328eaefb4f285761
# Parent a89dd3328d2c1ed6aed5b823d8e52fcfc6b3f677
Uploaded
diff -r a89dd3328d2c -r e3cb63c2b7c1 README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Mon Nov 16 10:06:52 2015 -0500
@@ -0,0 +1,30 @@
+iReport
+=======
+
+iReport Galaxy tool - HTML reporting in Galaxy
+
+install to your Galaxy via the main tool shed: http://toolshed.g2.bx.psu.edu/
+
+direct repository link: http://saskia-hiltemann@toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/ireport
+
+email: s.hiltemann@erasmusmc.nl
+
+
+Installation Instructions
+--------------------------
+This package uses (but does not install) Bash, Perl and Python.
+
+If Pandoc ((johnmacfarlane.net/pandoc/index.html)) is installed on your system PATH (command 'pandoc'), any MarkDown text items will be rendered using Pandoc (allows many markdown syntax extensions).
+If Pandoc is not present, a simple markdown conversion script is used (only handles vanilla syntax).
+
+
+TODOs
+---------------
+- ~~option to download iReport webpage~~
+- ~~markdown instead of plain text/html in text fields.~~
+- Support for large tables
+- Multiple columns in table converted to weblinks.
+- Table colums link to archive files in history
+- ..
+- ..suggestions?
+
diff -r a89dd3328d2c -r e3cb63c2b7c1 createHTML.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/createHTML.sh Mon Nov 16 10:06:52 2015 -0500
@@ -0,0 +1,968 @@
+gbcount=0
+
+##
+## Create Cover Page
+##
+# Click here to download a copy of this iReport
+function makeIntroPage ( ){
+ echo "Creating Intro Page"
+ title="$1"
+ coverimage=$2
+ link=$3
+ htmlout=$4
+ zipireport=$5
+
+ echo -e "
+
+
Deprecated
When using fnRender, you have two options for what
+ * to do with the data, and this property serves as the switch. Firstly, you
+ * can have the sorting and filtering use the rendered value (true - default),
+ * or you can have the sorting and filtering us the original value (false).
+ *
+ * Please note that this option has now been deprecated and will be removed
+ * in the next version of DataTables. Please use mRender / mData rather than
+ * fnRender.
+ * @type boolean
+ * @deprecated
+ */
+ "bUseRendered": null,
+
+ /**
+ * Flag to indicate if the column is currently visible in the table or not
+ * @type boolean
+ */
+ "bVisible": null,
+
+ /**
+ * Flag to indicate to the type detection method if the automatic type
+ * detection should be used, or if a column type (sType) has been specified
+ * @type boolean
+ * @default true
+ * @private
+ */
+ "_bAutoType": true,
+
+ /**
+ * Developer definable function that is called whenever a cell is created (Ajax source,
+ * etc) or processed for input (DOM source). This can be used as a compliment to mRender
+ * allowing you to modify the DOM element (add background colour for example) when the
+ * element is available.
+ * @type function
+ * @param {element} nTd The TD node that has been created
+ * @param {*} sData The Data for the cell
+ * @param {array|object} oData The data for the whole row
+ * @param {int} iRow The row index for the aoData data store
+ * @default null
+ */
+ "fnCreatedCell": null,
+
+ /**
+ * Function to get data from a cell in a column. You should never
+ * access data directly through _aData internally in DataTables - always use
+ * the method attached to this property. It allows mData to function as
+ * required. This function is automatically assigned by the column
+ * initialisation method
+ * @type function
+ * @param {array|object} oData The data array/object for the array
+ * (i.e. aoData[]._aData)
+ * @param {string} sSpecific The specific data type you want to get -
+ * 'display', 'type' 'filter' 'sort'
+ * @returns {*} The data for the cell from the given row's data
+ * @default null
+ */
+ "fnGetData": null,
+
+ /**
+ * Deprecated
Custom display function that will be called for the
+ * display of each cell in this column.
+ *
+ * Please note that this option has now been deprecated and will be removed
+ * in the next version of DataTables. Please use mRender / mData rather than
+ * fnRender.
+ * @type function
+ * @param {object} o Object with the following parameters:
+ * @param {int} o.iDataRow The row in aoData
+ * @param {int} o.iDataColumn The column in question
+ * @param {array} o.aData The data for the row in question
+ * @param {object} o.oSettings The settings object for this DataTables instance
+ * @returns {string} The string you which to use in the display
+ * @default null
+ * @deprecated
+ */
+ "fnRender": null,
+
+ /**
+ * Function to set data for a cell in the column. You should never
+ * set the data directly to _aData internally in DataTables - always use
+ * this method. It allows mData to function as required. This function
+ * is automatically assigned by the column initialisation method
+ * @type function
+ * @param {array|object} oData The data array/object for the array
+ * (i.e. aoData[]._aData)
+ * @param {*} sValue Value to set
+ * @default null
+ */
+ "fnSetData": null,
+
+ /**
+ * Property to read the value for the cells in the column from the data
+ * source array / object. If null, then the default content is used, if a
+ * function is given then the return from the function is used.
+ * @type function|int|string|null
+ * @default null
+ */
+ "mData": null,
+
+ /**
+ * Partner property to mData which is used (only when defined) to get
+ * the data - i.e. it is basically the same as mData, but without the
+ * 'set' option, and also the data fed to it is the result from mData.
+ * This is the rendering method to match the data method of mData.
+ * @type function|int|string|null
+ * @default null
+ */
+ "mRender": null,
+
+ /**
+ * Unique header TH/TD element for this column - this is what the sorting
+ * listener is attached to (if sorting is enabled.)
+ * @type node
+ * @default null
+ */
+ "nTh": null,
+
+ /**
+ * Unique footer TH/TD element for this column (if there is one). Not used
+ * in DataTables as such, but can be used for plug-ins to reference the
+ * footer for each column.
+ * @type node
+ * @default null
+ */
+ "nTf": null,
+
+ /**
+ * The class to apply to all TD elements in the table's TBODY for the column
+ * @type string
+ * @default null
+ */
+ "sClass": null,
+
+ /**
+ * When DataTables calculates the column widths to assign to each column,
+ * it finds the longest string in each column and then constructs a
+ * temporary table and reads the widths from that. The problem with this
+ * is that "mmm" is much wider then "iiii", but the latter is a longer
+ * string - thus the calculation can go wrong (doing it properly and putting
+ * it into an DOM object and measuring that is horribly(!) slow). Thus as
+ * a "work around" we provide this option. It will append its value to the
+ * text that is found to be the longest string for the column - i.e. padding.
+ * @type string
+ */
+ "sContentPadding": null,
+
+ /**
+ * Allows a default value to be given for a column's data, and will be used
+ * whenever a null data source is encountered (this can be because mData
+ * is set to null, or because the data source itself is null).
+ * @type string
+ * @default null
+ */
+ "sDefaultContent": null,
+
+ /**
+ * Name for the column, allowing reference to the column by name as well as
+ * by index (needs a lookup to work by name).
+ * @type string
+ */
+ "sName": null,
+
+ /**
+ * Custom sorting data type - defines which of the available plug-ins in
+ * afnSortData the custom sorting will use - if any is defined.
+ * @type string
+ * @default std
+ */
+ "sSortDataType": 'std',
+
+ /**
+ * Class to be applied to the header element when sorting on this column
+ * @type string
+ * @default null
+ */
+ "sSortingClass": null,
+
+ /**
+ * Class to be applied to the header element when sorting on this column -
+ * when jQuery UI theming is used.
+ * @type string
+ * @default null
+ */
+ "sSortingClassJUI": null,
+
+ /**
+ * Title of the column - what is seen in the TH element (nTh).
+ * @type string
+ */
+ "sTitle": null,
+
+ /**
+ * Column sorting and filtering type
+ * @type string
+ * @default null
+ */
+ "sType": null,
+
+ /**
+ * Width of the column
+ * @type string
+ * @default null
+ */
+ "sWidth": null,
+
+ /**
+ * Width of the column when it was first "encountered"
+ * @type string
+ * @default null
+ */
+ "sWidthOrig": null
+ };
+
+
+
+ /**
+ * Initialisation options that can be given to DataTables at initialisation
+ * time.
+ * @namespace
+ */
+ DataTable.defaults = {
+ /**
+ * An array of data to use for the table, passed in at initialisation which
+ * will be used in preference to any data which is already in the DOM. This is
+ * particularly useful for constructing tables purely in Javascript, for
+ * example with a custom Ajax call.
+ * @type array
+ * @default null
+ * @dtopt Option
+ *
+ * @example
+ * // Using a 2D array data source
+ * $(document).ready( function () {
+ * $('#example').dataTable( {
+ * "aaData": [
+ * ['Trident', 'Internet Explorer 4.0', 'Win 95+', 4, 'X'],
+ * ['Trident', 'Internet Explorer 5.0', 'Win 95+', 5, 'C'],
+ * ],
+ * "aoColumns": [
+ * { "sTitle": "Engine" },
+ * { "sTitle": "Browser" },
+ * { "sTitle": "Platform" },
+ * { "sTitle": "Version" },
+ * { "sTitle": "Grade" }
+ * ]
+ * } );
+ * } );
+ *
+ * @example
+ * // Using an array of objects as a data source (mData)
+ * $(document).ready( function () {
+ * $('#example').dataTable( {
+ * "aaData": [
+ * {
+ * "engine": "Trident",
+ * "browser": "Internet Explorer 4.0",
+ * "platform": "Win 95+",
+ * "version": 4,
+ * "grade": "X"
+ * },
+ * {
+ * "engine": "Trident",
+ * "browser": "Internet Explorer 5.0",
+ * "platform": "Win 95+",
+ * "version": 5,
+ * "grade": "C"
+ * }
+ * ],
+ * "aoColumns": [
+ * { "sTitle": "Engine", "mData": "engine" },
+ * { "sTitle": "Browser", "mData": "browser" },
+ * { "sTitle": "Platform", "mData": "platform" },
+ * { "sTitle": "Version", "mData": "version" },
+ * { "sTitle": "Grade", "mData": "grade" }
+ * ]
+ * } );
+ * } );
+ */
+ "aaData": null,
+
+
+ /**
+ * If sorting is enabled, then DataTables will perform a first pass sort on
+ * initialisation. You can define which column(s) the sort is performed upon,
+ * and the sorting direction, with this variable. The aaSorting array should
+ * contain an array for each column to be sorted initially containing the
+ * column's index and a direction string ('asc' or 'desc').
+ * @type array
+ * @default [[0,'asc']]
+ * @dtopt Option
+ *
+ * @example
+ * // Sort by 3rd column first, and then 4th column
+ * $(document).ready( function() {
+ * $('#example').dataTable( {
+ * "aaSorting": [[2,'asc'], [3,'desc']]
+ * } );
+ * } );
+ *
+ * // No initial sorting
+ * $(document).ready( function() {
+ * $('#example').dataTable( {
+ * "aaSorting": []
+ * } );
+ * } );
+ */
+ "aaSorting": [[0,'asc']],
+
+
+ /**
+ * This parameter is basically identical to the aaSorting parameter, but
+ * cannot be overridden by user interaction with the table. What this means
+ * is that you could have a column (visible or hidden) which the sorting will
+ * always be forced on first - any sorting after that (from the user) will
+ * then be performed as required. This can be useful for grouping rows
+ * together.
+ * @type array
+ * @default null
+ * @dtopt Option
+ *
+ * @example
+ * $(document).ready( function() {
+ * $('#example').dataTable( {
+ * "aaSortingFixed": [[0,'asc']]
+ * } );
+ * } )
+ */
+ "aaSortingFixed": null,
+
+
+ /**
+ * This parameter allows you to readily specify the entries in the length drop
+ * down menu that DataTables shows when pagination is enabled. It can be
+ * either a 1D array of options which will be used for both the displayed
+ * option and the value, or a 2D array which will use the array in the first
+ * position as the value, and the array in the second position as the
+ * displayed options (useful for language strings such as 'All').
+ * @type array
+ * @default [ 10, 25, 50, 100 ]
+ * @dtopt Option
+ *
+ * @example
+ * $(document).ready( function() {
+ * $('#example').dataTable( {
+ * "aLengthMenu": [[10, 25, 50, -1], [10, 25, 50, "All"]]
+ * } );
+ * } );
+ *
+ * @example
+ * // Setting the default display length as well as length menu
+ * // This is likely to be wanted if you remove the '10' option which
+ * // is the iDisplayLength default.
+ * $(document).ready( function() {
+ * $('#example').dataTable( {
+ * "iDisplayLength": 25,
+ * "aLengthMenu": [[25, 50, 100, -1], [25, 50, 100, "All"]]
+ * } );
+ * } );
+ */
+ "aLengthMenu": [[10, 25, 50, 100, 250, 500, 1000, -1], [10, 25, 50, 100, 250, 500, 1000, "All"]],
+
+
+ /**
+ * The aoColumns option in the initialisation parameter allows you to define
+ * details about the way individual columns behave. For a full list of
+ * column options that can be set, please see
+ * {@link DataTable.defaults.columns}. Note that if you use aoColumns to
+ * define your columns, you must have an entry in the array for every single
+ * column that you have in your table (these can be null if you don't which
+ * to specify any options).
+ * @member
+ */
+ "aoColumns": null,
+
+ /**
+ * Very similar to aoColumns, aoColumnDefs allows you to target a specific
+ * column, multiple columns, or all columns, using the aTargets property of
+ * each object in the array. This allows great flexibility when creating
+ * tables, as the aoColumnDefs arrays can be of any length, targeting the
+ * columns you specifically want. aoColumnDefs may use any of the column
+ * options available: {@link DataTable.defaults.columns}, but it _must_
+ * have aTargets defined in each object in the array. Values in the aTargets
+ * array may be:
+ * Deprecated
When using fnRender() for a column, you may wish
+ * to use the original data (before rendering) for sorting and filtering
+ * (the default is to used the rendered data that the user can see). This
+ * may be useful for dates etc.
+ *
+ * Please note that this option has now been deprecated and will be removed
+ * in the next version of DataTables. Please use mRender / mData rather than
+ * fnRender.
+ * @type boolean
+ * @default true
+ * @dtopt Columns
+ * @deprecated
+ */
+ "bUseRendered": true,
+
+
+ /**
+ * Enable or disable the display of this column.
+ * @type boolean
+ * @default true
+ * @dtopt Columns
+ *
+ * @example
+ * // Using aoColumnDefs
+ * $(document).ready( function() {
+ * $('#example').dataTable( {
+ * "aoColumnDefs": [
+ * { "bVisible": false, "aTargets": [ 0 ] }
+ * ] } );
+ * } );
+ *
+ * @example
+ * // Using aoColumns
+ * $(document).ready( function() {
+ * $('#example').dataTable( {
+ * "aoColumns": [
+ * { "bVisible": false },
+ * null,
+ * null,
+ * null,
+ * null
+ * ] } );
+ * } );
+ */
+ "bVisible": true,
+
+
+ /**
+ * Developer definable function that is called whenever a cell is created (Ajax source,
+ * etc) or processed for input (DOM source). This can be used as a compliment to mRender
+ * allowing you to modify the DOM element (add background colour for example) when the
+ * element is available.
+ * @type function
+ * @param {element} nTd The TD node that has been created
+ * @param {*} sData The Data for the cell
+ * @param {array|object} oData The data for the whole row
+ * @param {int} iRow The row index for the aoData data store
+ * @param {int} iCol The column index for aoColumns
+ * @dtopt Columns
+ *
+ * @example
+ * $(document).ready( function() {
+ * $('#example').dataTable( {
+ * "aoColumnDefs": [ {
+ * "aTargets": [3],
+ * "fnCreatedCell": function (nTd, sData, oData, iRow, iCol) {
+ * if ( sData == "1.7" ) {
+ * $(nTd).css('color', 'blue')
+ * }
+ * }
+ * } ]
+ * });
+ * } );
+ */
+ "fnCreatedCell": null,
+
+
+ /**
+ * Deprecated
Custom display function that will be called for the
+ * display of each cell in this column.
+ *
+ * Please note that this option has now been deprecated and will be removed
+ * in the next version of DataTables. Please use mRender / mData rather than
+ * fnRender.
+ * @type function
+ * @param {object} o Object with the following parameters:
+ * @param {int} o.iDataRow The row in aoData
+ * @param {int} o.iDataColumn The column in question
+ * @param {array} o.aData The data for the row in question
+ * @param {object} o.oSettings The settings object for this DataTables instance
+ * @param {object} o.mDataProp The data property used for this column
+ * @param {*} val The current cell value
+ * @returns {string} The string you which to use in the display
+ * @dtopt Columns
+ * @deprecated
+ */
+ "fnRender": null,
+
+
+ /**
+ * The column index (starting from 0!) that you wish a sort to be performed
+ * upon when this column is selected for sorting. This can be used for sorting
+ * on hidden columns for example.
+ * @type int
+ * @default -1 Use automatically calculated column index
+ * @dtopt Columns
+ *
+ * @example
+ * // Using aoColumnDefs
+ * $(document).ready( function() {
+ * $('#example').dataTable( {
+ * "aoColumnDefs": [
+ * { "iDataSort": 1, "aTargets": [ 0 ] }
+ * ]
+ * } );
+ * } );
+ *
+ * @example
+ * // Using aoColumns
+ * $(document).ready( function() {
+ * $('#example').dataTable( {
+ * "aoColumns": [
+ * { "iDataSort": 1 },
+ * null,
+ * null,
+ * null,
+ * null
+ * ]
+ * } );
+ * } );
+ */
+ "iDataSort": -1,
+
+
+ /**
+ * This parameter has been replaced by mData in DataTables to ensure naming
+ * consistency. mDataProp can still be used, as there is backwards compatibility
+ * in DataTables for this option, but it is strongly recommended that you use
+ * mData in preference to mDataProp.
+ * @name DataTable.defaults.columns.mDataProp
+ */
+
+
+ /**
+ * This property can be used to read data from any JSON data source property,
+ * including deeply nested objects / properties. mData can be given in a
+ * number of different ways which effect its behaviour:
+ *
+END
+chomp ($_ = | ?g; +print "$_ | |
---|---|---|
$cell | "; + $first=0; + } + elsif($cell =~ /^(\d|\s)+$/) { + print "$cell | "; } + else { + print "$cell | "; } } + print "