diff --git a/client/galaxy/scripts/components/Citations.vue b/client/galaxy/scripts/components/Citations.vue
index 75906671f88..e138738d76e 100644
--- a/client/galaxy/scripts/components/Citations.vue
+++ b/client/galaxy/scripts/components/Citations.vue
@@ -1,33 +1,52 @@
-
- Citations
-
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-
-
-
+
+ Citations
+
+
+
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+
+
+
-
{{ content }}
+ {{ info.description }}
Auto-detect<\/strong><\/p>\n The system will attempt to detect Axt, Fasta, Fastqsolexa, Gff, Gff3, Html, Lav, Maf, Tabular, Wiggle, Bed and Interval (Bed with headers) formats. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed.<\/p>\n Ab1<\/strong><\/p>\n A binary sequence file in 'ab1' format with a '.ab1' file extension. You must manually select this 'File Format' when uploading the file.<\/p>\n Axt<\/strong><\/p>\n blastz pairwise alignment format. Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines. Blocks are separated from one another by blank lines. The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields.<\/p>\n Bam<\/strong><\/p>\n A binary file compressed in the BGZF format with a '.bam' file extension.<\/p>\n Bed<\/strong><\/p>\n Tab delimited format (tabular)<\/p>\n<\/li>\n Does not require header line<\/p>\n<\/li>\n Contains 3 required fields:<\/p>\n May contain 9 additional optional BED fields:<\/p>\n Example:<\/p>\n Fasta<\/strong><\/p>\n A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. The first character of the description line is a greater-than (">") symbol in the first column. All lines should be shorter than 80 characters:<\/p>\n FastqSolexa<\/strong><\/p>\n FastqSolexa is the Illumina (Solexa) variant of the Fastq format, which stores sequences and quality scores in a single file:<\/p>\n Or:<\/p>\n Gff<\/strong><\/p>\n GFF lines have nine required fields that must be tab-separated.<\/p>\n Gff3<\/strong><\/p>\n The GFF3 format addresses the most common extensions to GFF, while preserving backward compatibility with previous formats.<\/p>\n Interval (Genomic Intervals)<\/strong><\/p>\n Tab delimited format (tabular)<\/p>\n<\/li>\n File must start with definition line in the following format (columns may be in any order).:<\/p>\n CHROM - The name of the chromosome (e.g. chr3, chrY, chr2_random) or contig (e.g. ctgY1).<\/p>\n<\/li>\n START - The starting position of the feature in the chromosome or contig. The first base in a chromosome is numbered 0.<\/p>\n<\/li>\n END - The ending position of the feature in the chromosome or contig. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.<\/p>\n<\/li>\n STRAND - Defines the strand - either '+' or '-'.<\/p>\n<\/li>\n Example:<\/p>\n Lav<\/strong><\/p>\n Lav is the primary output format for BLASTZ. The first line of a .lav file begins with #:lav..<\/p>\n MAF<\/strong><\/p>\n TBA and multiz multiple alignment format. The first line of a .maf file begins with ##maf. This word is followed by white-space-separated "variable=value" pairs. There should be no white space surrounding the "=".<\/p>\n Scf<\/strong><\/p>\n A binary sequence file in 'scf' format with a '.scf' file extension. You must manually select this 'File Format' when uploading the file.<\/p>\n Sff<\/strong><\/p>\n A binary file in 'Standard Flowgram Format' with a '.sff' file extension.<\/p>\n Tabular (tab delimited)<\/strong><\/p>\n Any data in tab delimited format (tabular)<\/p>\n Table (delimiter-separated)<\/strong><\/p>\n Any delimiter-separated tabular data (CSV or TSV).<\/p>\n Wig<\/strong><\/p>\n The wiggle format is line-oriented. Wiggle data is preceded by a track definition line, which adds a number of options for controlling the default display of this track.<\/p>\n Other text type<\/strong><\/p>\n Any text file<\/p>\n",
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+ "id": "upload1",
+ "name": "Upload File"
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+ "name": "WormBase"
+ },
+ {
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+ "panel_section_id": "getext",
+ "version": "1.0.0",
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+ "min_width": "800",
+ "model_class": "DataSourceTool",
+ "hidden": "",
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+ "name": "ZebrafishMine"
+ },
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+ "panel_section_name": "Get Data",
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+ "panel_section_id": "getext",
+ "version": "1.0.0",
+ "link": "/tool_runner/data_source_redirect?tool_id=eupathdb",
+ "target": "_top",
+ "min_width": "800",
+ "model_class": "DataSourceTool",
+ "hidden": "",
+ "id": "eupathdb",
+ "name": "EuPathDB"
+ },
+ {
+ "panel_section_name": "Get Data",
+ "xrefs": [],
+ "description": "Human Hemoglobin Variants and Thalassemias",
+ "is_workflow_compatible": false,
+ "labels": [],
+ "help": "",
+ "edam_operations": [],
+ "form_style": "special",
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+ "panel_section_id": "getext",
+ "version": "2.0.0",
+ "link": "/tool_runner/data_source_redirect?tool_id=hbvar",
+ "target": "_top",
+ "min_width": "800",
+ "model_class": "DataSourceTool",
+ "hidden": "",
+ "id": "hbvar",
+ "name": "HbVar"
+ }
+ ],
+ "model_class": "ToolSection",
+ "version": "",
+ "id": "getext",
+ "name": "Get Data"
+ },
+ {
+ "elems": [
+ {
+ "panel_section_name": "Send Data",
+ "xrefs": [],
+ "description": "",
+ "is_workflow_compatible": false,
+ "labels": [],
+ "help": " Send dataset(s) from Galaxy to cloud-based storage (e.g., AWS S3).<\/p>\n Supply a name of the target bucket where the data will be sent along\nwith an id for the desired cloud authorization. To get the list of Cloud\nAuthorization IDs available for your account, visit /api/cloud/authz<\/cite>.<\/p>\n<\/dd>\n This tool leverages OpenID Connect protocol and CloudAuthz (https://github.com/galaxyproject/cloudauthz<\/a>)\nto access cloud-based resources without requiring user credentials.<\/p>\n If selecting multiple datasets, make sure each dataset is named\ndifferently; otherwise, only one copy of the selected datasets will be\ncopied.<\/p>\n<\/dd>\n<\/dl>\n",
+ "edam_operations": [],
+ "form_style": "regular",
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+ "panel_section_id": "send",
+ "version": "0.1.0",
+ "link": "/tool_runner?tool_id=send_to_cloud",
+ "target": "galaxy_main",
+ "min_width": -1,
+ "model_class": "Tool",
+ "hidden": "",
+ "id": "send_to_cloud",
+ "name": "Send to cloud"
+ }
+ ],
+ "model_class": "ToolSection",
+ "version": "",
+ "id": "send",
+ "name": "Send Data"
+ },
+ {
+ "elems": [
+ {
+ "panel_section_name": "Collection Operations",
+ "xrefs": [],
+ "description": "",
+ "is_workflow_compatible": true,
+ "labels": [],
+ "help": " This tool takes a paired dataset collection and builds two datasets from it. If mapped over a list of paired datasets, this tool will produce two lists of datasets.<\/p>\n Example<\/strong><\/p>\n If a collection consists of two forward and two reverse datasets (e.g., forward and reverse reads from a sequencing experiment) this tool will output two collections: one consisting of forward reads and one of reverse reads.<\/p>\n This tool will create new history datasets from your collection but your quota usage will not increase.<\/p>\n",
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+ "panel_section_id": "collection_operations",
+ "version": "1.0.0",
+ "link": "/tool_runner?tool_id=__UNZIP_COLLECTION__",
+ "target": "galaxy_main",
+ "min_width": -1,
+ "model_class": "UnzipCollectionTool",
+ "hidden": "",
+ "id": "__UNZIP_COLLECTION__",
+ "name": "Unzip Collection"
+ },
+ {
+ "panel_section_name": "Collection Operations",
+ "xrefs": [],
+ "description": "",
+ "is_workflow_compatible": true,
+ "labels": [],
+ "help": " This tool takes two datasets and creates a dataset pair from them. Mapping over two lists, this tool can be used to build a list of dataset pairs from two individual lists of datasets.<\/p>\n Example<\/strong><\/p>\n If you have one collection containing only forward reads and one containing only reverse, this tools will "zip" them together into a simple paired collection.<\/p>\n This tool will create new history datasets for your collection but your quota usage will not increase.<\/p>\n",
+ "edam_operations": [],
+ "form_style": "regular",
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+ "panel_section_id": "collection_operations",
+ "version": "1.0.0",
+ "link": "/tool_runner?tool_id=__ZIP_COLLECTION__",
+ "target": "galaxy_main",
+ "min_width": -1,
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+ "hidden": "",
+ "id": "__ZIP_COLLECTION__",
+ "name": "Zip Collection"
+ },
+ {
+ "panel_section_name": "Collection Operations",
+ "xrefs": [],
+ "description": "datasets from a collection",
+ "is_workflow_compatible": true,
+ "labels": [],
+ "help": " This tool takes a dataset collection and filters out datasets in the failed state. This is useful for continuing a multi-sample analysis when one of more of the samples fails at some point.<\/p>\n This tool will create new history datasets from your collection but your quota usage will not increase.<\/p>\n",
+ "edam_operations": [],
+ "form_style": "regular",
+ "edam_topics": [],
+ "panel_section_id": "collection_operations",
+ "version": "1.0.0",
+ "link": "/tool_runner?tool_id=__FILTER_FAILED_DATASETS__",
+ "target": "galaxy_main",
+ "min_width": -1,
+ "model_class": "FilterFailedDatasetsTool",
+ "hidden": "",
+ "id": "__FILTER_FAILED_DATASETS__",
+ "name": "Filter failed"
+ },
+ {
+ "panel_section_name": "Collection Operations",
+ "xrefs": [],
+ "description": "datasets from a collection",
+ "is_workflow_compatible": true,
+ "labels": [],
+ "help": " This tool takes a dataset collection and filters out empty datasets. This is useful for continuing a multi-sample analysis when downstream tools require datasets to have content.<\/p>\n This tool will create new history datasets from your collection but your quota usage will not increase.<\/p>\n",
+ "edam_operations": [],
+ "form_style": "regular",
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+ "panel_section_id": "collection_operations",
+ "version": "1.0.0",
+ "link": "/tool_runner?tool_id=__FILTER_EMPTY_DATASETS__",
+ "target": "galaxy_main",
+ "min_width": -1,
+ "model_class": "FilterEmptyDatasetsTool",
+ "hidden": "",
+ "id": "__FILTER_EMPTY_DATASETS__",
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+ },
+ {
+ "panel_section_name": "Collection Operations",
+ "xrefs": [],
+ "description": "into a flat list of datasets",
+ "is_workflow_compatible": true,
+ "labels": [],
+ "help": " This tool takes nested collections such as a list of lists or a list of dataset pairs - and produces a flat list from the inputs. The collection identifiers are merged together to create new collection identifiers in the flattened result.<\/p>\n This tool will create new history datasets from your collection but your quota usage will not increase.<\/p>\n",
+ "edam_operations": [],
+ "form_style": "regular",
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+ "panel_section_id": "collection_operations",
+ "version": "1.0.0",
+ "link": "/tool_runner?tool_id=__FLATTEN__",
+ "target": "galaxy_main",
+ "min_width": -1,
+ "model_class": "FlattenTool",
+ "hidden": "",
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+ {
+ "panel_section_name": "Collection Operations",
+ "xrefs": [],
+ "description": "into single list of datasets",
+ "is_workflow_compatible": true,
+ "labels": [],
+ "help": " This tool takes two lists and creates a single unified list.<\/p>\n This tool will create new history datasets for your collection but your quota usage will not increase.<\/p>\n",
+ "edam_operations": [],
+ "form_style": "regular",
+ "edam_topics": [],
+ "panel_section_id": "collection_operations",
+ "version": "1.0.0",
+ "link": "/tool_runner?tool_id=__MERGE_COLLECTION__",
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+ "id": "__MERGE_COLLECTION__",
+ "name": "Merge Collections"
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+ {
+ "panel_section_name": "Collection Operations",
+ "xrefs": [],
+ "description": "from contents of a file",
+ "is_workflow_compatible": true,
+ "labels": [],
+ "help": " This tool will take an input list and a text file with new identifiers\nand build a new list with the same datasets but these new identifiers.\nThe order and number of entries in the text file must match the order\nof the items you want to rename in your dataset collection.<\/p>\n Alternatively a tabular file may be supplied, where the first column\nif the current identifier that should be renamed, and the second column\ncontains the new label. This file may contain less entries than items\nin the collection. In that case only matching list identifiers will be\nrelabeled.<\/p>\n Valid identifiers must contain only characters (a-z, A-Z), numbers (0-9),\ndash and underscore (-, _). Punctuation or whitespace are not allowed.<\/p>\n This tool will create new history datasets from your collection\nbut your quota usage will not increase.<\/p>\n",
+ "edam_operations": [],
+ "form_style": "regular",
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+ "panel_section_id": "collection_operations",
+ "version": "1.0.0",
+ "link": "/tool_runner?tool_id=__RELABEL_FROM_FILE__",
+ "target": "galaxy_main",
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+ "hidden": "",
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+ {
+ "panel_section_name": "Collection Operations",
+ "xrefs": [],
+ "description": "from contents of a file",
+ "is_workflow_compatible": true,
+ "labels": [],
+ "help": " This tool will take an input list and a text file with\nnames (i.e. identifiers). It will split the input list into\ntwo new lists - one filtered to contain only the list members\nwhose names are listed in the text file, and one containing\nall the other elements.<\/p>\n This tool will create new history datasets from your collection\nbut your quota usage will not increase.<\/p>\n",
+ "edam_operations": [],
+ "form_style": "regular",
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+ "panel_section_id": "collection_operations",
+ "version": "1.0.0",
+ "link": "/tool_runner?tool_id=__FILTER_FROM_FILE__",
+ "target": "galaxy_main",
+ "min_width": -1,
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+ "hidden": "",
+ "id": "__FILTER_FROM_FILE__",
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+ },
+ {
+ "panel_section_name": "Collection Operations",
+ "xrefs": [],
+ "description": "of list of datasets",
+ "is_workflow_compatible": true,
+ "labels": [],
+ "help": " This tool takes list-type collections - and produces a sorted ist from the inputs. The collection identifiers are sorted either alphabetically or numerically (where the characters other than 0-9 are stripped before sorting).<\/p>\n This tool will create new history datasets from your collection but your quota usage will not increase.<\/p>\n",
+ "edam_operations": [],
+ "form_style": "regular",
+ "edam_topics": [],
+ "panel_section_id": "collection_operations",
+ "version": "1.0.0",
+ "link": "/tool_runner?tool_id=__SORTLIST__",
+ "target": "galaxy_main",
+ "min_width": -1,
+ "model_class": "SortTool",
+ "hidden": "",
+ "id": "__SORTLIST__",
+ "name": "Sort Collection"
+ },
+ {
+ "panel_section_name": "Collection Operations",
+ "xrefs": [],
+ "description": "from contents of a file",
+ "is_workflow_compatible": true,
+ "labels": [],
+ "help": " This tool will take an input collection and a tabular file,\nwhere the first column indicates an element identifier and the\nremaining columns contains the new tags. This file may contain\nless entries than elements in the collection.\nIn that case only matching list identifiers will be tagged.<\/p>\n This tool will create new history datasets from your collection\nbut your quota usage will not increase.<\/p>\n",
+ "edam_operations": [],
+ "form_style": "regular",
+ "edam_topics": [],
+ "panel_section_id": "collection_operations",
+ "version": "1.0.0",
+ "link": "/tool_runner?tool_id=__TAG_FROM_FILE__",
+ "target": "galaxy_main",
+ "min_width": -1,
+ "model_class": "TagFromFileTool",
+ "hidden": "",
+ "id": "__TAG_FROM_FILE__",
+ "name": "Tag elements from file"
+ },
+ {
+ "panel_section_name": "Collection Operations",
+ "xrefs": [],
+ "description": "",
+ "is_workflow_compatible": true,
+ "labels": [],
+ "help": " This tool allows one to process an existing Galaxy dataset collection's metadata as tabular data,\napply a series of rules to it, and generate a new collection. When used interactively in the tool\nform, a dynamic preview of the processing will be available in a tabular data viewer but this tool\nmay be used in workflows as well where no such preview can be generated.<\/p>\n This tool is an advanced feature but has a lot of flexibility - it can be used to process collections\nwith arbitrary nesting and can do many kinds of filtering, re-sorting, nesting,\nflattening, and arbitrary combinations thereof not possible with Galaxy's other, more simple\ncollection operation tools.<\/p>\n
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\nchr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512\nchr22 2000 6000 cloneB 900 - 2000 6000 0 2 433,399, 0,3601\n<\/pre>\n<\/li>\n<\/ul>\n
\n\n>sequence1\natgcgtttgcgtgc\ngtcggtttcgttgc\n>sequence2\ntttcgtgcgtatag\ntggcgcggtga\n<\/pre>\n
\n\n@seq1\nGACAGCTTGGTTTTTAGTGAGTTGTTCCTTTCTTT\n+seq1\nhhhhhhhhhhhhhhhhhhhhhhhhhhPW@hhhhhh\n@seq2\nGCAATGACGGCAGCAATAAACTCAACAGGTGCTGG\n+seq2\nhhhhhhhhhhhhhhYhhahhhhWhAhFhSIJGChO\n<\/pre>\n
\n@seq1\nGAATTGATCAGGACATAGGACAACTGTAGGCACCAT\n+seq1\n40 40 40 40 35 40 40 40 25 40 40 26 40 9 33 11 40 35 17 40 40 33 40 7 9 15 3 22 15 30 11 17 9 4 9 4\n@seq2\nGAGTTCTCGTCGCCTGTAGGCACCATCAATCGTATG\n+seq2\n40 15 40 17 6 36 40 40 40 25 40 9 35 33 40 14 14 18 15 17 19 28 31 4 24 18 27 14 15 18 2 8 12 8 11 9\n<\/pre>\n
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\n#CHROM START END STRAND\n<\/pre>\n<\/li>\n
\n#CHROM START END STRAND NAME COMMENT\nchr1 10 100 + exon myExon\nchrX 1000 10050 - gene myGene\n<\/pre>\n<\/li>\n<\/ul>\n
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