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ToolsView/ schema.org page to support new api structure
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228 changes: 103 additions & 125 deletions
228
client/src/components/ToolsView/testData/toolsList.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,126 +1,104 @@ | ||
| [ | ||
| { | ||
| "elems": [ | ||
| { | ||
| "panel_section_name": "Collection Operations", | ||
| "xrefs": [], | ||
| "description": "", | ||
| "is_workflow_compatible": true, | ||
| "labels": [], | ||
| "help": "<p>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<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>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<p class=\"infomark\">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=__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": "<p>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<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>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<p class=\"infomark\">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=__ZIP_COLLECTION__", | ||
| "target": "galaxy_main", | ||
| "min_width": -1, | ||
| "model_class": "ZipCollectionTool", | ||
| "hidden": "", | ||
| "id": "__ZIP_COLLECTION__", | ||
| "name": "Zip Collection" | ||
| }, | ||
| { | ||
| "panel_section_name": "Collection Operations", | ||
| "xrefs": [], | ||
| "description": "datasets from a collection", | ||
| "is_workflow_compatible": true, | ||
| "labels": [], | ||
| "help": "<p>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<p class=\"infomark\">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": "<p>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<p class=\"infomark\">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_EMPTY_DATASETS__", | ||
| "target": "galaxy_main", | ||
| "min_width": -1, | ||
| "model_class": "FilterEmptyDatasetsTool", | ||
| "hidden": "", | ||
| "id": "__FILTER_EMPTY_DATASETS__", | ||
| "name": "Filter empty" | ||
| } | ||
| ], | ||
| "model_class": "ToolSection", | ||
| "version": "", | ||
| "id": "collection_operations", | ||
| "name": "Collection Operations" | ||
| }, | ||
| { | ||
| "elems": [ | ||
| { | ||
| "panel_section_name": "Lift-Over", | ||
| "xrefs": [], | ||
| "description": "between assemblies and genomes", | ||
| "is_workflow_compatible": true, | ||
| "labels": [], | ||
| "help": "<p class=\"warningmark\">Make sure that the genome build of the input dataset is specified (click the pencil icon in the history item to set it if necessary).<\/p>\n<p class=\"warningmark\">This tool can work with interval, GFF, and GTF datasets. It requires the interval datasets to have chromosome in column 1,\nstart co-ordinate in column 2 and end co-ordinate in column 3. BED comments\nand track and browser lines will be ignored, but if other non-interval lines\nare present the tool will return empty output datasets.<\/p>\n<hr class=\"docutils\" />\n<p class=\"infomark\"><strong>What it does<\/strong><\/p>\n<p>This tool is based on the LiftOver utility and Chain track from <a class=\"reference external\" href=\"http://genome.ucsc.edu/\">the UC Santa Cruz Genome Browser<\/a>.<\/p>\n<p>It converts coordinates and annotations between assemblies and genomes. It produces 2 files, one containing all the mapped coordinates and the other containing the unmapped coordinates, if any.<\/p>\n<blockquote>\n<\/blockquote>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>Converting the following hg16 intervals to hg18 intervals:<\/p>\n<pre class=\"literal-block\">\nchrX 85170 112199 AK002185 0 +\nchrX 110458 112199 AK097346 0 +\nchrX 112203 121212 AK074528 0 -\n<\/pre>\n<p>will produce the following hg18 intervals:<\/p>\n<pre class=\"literal-block\">\nchrX 132991 160020 AK002185 0 +\nchrX 158279 160020 AK097346 0 +\nchrX 160024 169033 AK074528 0 -\n<\/pre>\n", | ||
| "edam_operations": [], | ||
| "form_style": "regular", | ||
| "edam_topics": [], | ||
| "panel_section_id": "liftOver", | ||
| "version": "1.0.6", | ||
| "link": "/tool_runner?tool_id=liftOver1", | ||
| "target": "galaxy_main", | ||
| "min_width": -1, | ||
| "model_class": "Tool", | ||
| "hidden": "", | ||
| "id": "liftOver1", | ||
| "name": "Convert genome coordinates" | ||
| } | ||
| ], | ||
| "model_class": "ToolSection", | ||
| "version": "", | ||
| "id": "liftOver", | ||
| "name": "Lift-Over" | ||
| }, | ||
| { | ||
| "model_class": "ToolSectionLabel", | ||
| "id": "testlabel3", | ||
| "text": null, | ||
| "version": "", | ||
| "description": null, | ||
| "links": null | ||
| { | ||
| "tools": { | ||
| "__UNZIP_COLLECTION__": { | ||
| "panel_section_name": "Collection Operations", | ||
| "xrefs": [], | ||
| "description": "", | ||
| "is_workflow_compatible": true, | ||
| "labels": [], | ||
| "help": "<p>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<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>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<p class=\"infomark\">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=__UNZIP_COLLECTION__", | ||
| "target": "galaxy_main", | ||
| "min_width": -1, | ||
| "model_class": "UnzipCollectionTool", | ||
| "hidden": "", | ||
| "id": "__UNZIP_COLLECTION__", | ||
| "name": "Unzip Collection" | ||
| }, | ||
| "__ZIP_COLLECTION__": { | ||
| "panel_section_name": "Collection Operations", | ||
| "xrefs": [], | ||
| "description": "", | ||
| "is_workflow_compatible": true, | ||
| "labels": [], | ||
| "help": "<p>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<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>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<p class=\"infomark\">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=__ZIP_COLLECTION__", | ||
| "target": "galaxy_main", | ||
| "min_width": -1, | ||
| "model_class": "ZipCollectionTool", | ||
| "hidden": "", | ||
| "id": "__ZIP_COLLECTION__", | ||
| "name": "Zip Collection" | ||
| }, | ||
| "__FILTER_FAILED_DATASETS__": { | ||
| "panel_section_name": "Collection Operations", | ||
| "xrefs": [], | ||
| "description": "datasets from a collection", | ||
| "is_workflow_compatible": true, | ||
| "labels": [], | ||
| "help": "<p>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<p class=\"infomark\">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" | ||
| }, | ||
| "__FILTER_EMPTY_DATASETS__": { | ||
| "panel_section_name": "Collection Operations", | ||
| "xrefs": [], | ||
| "description": "datasets from a collection", | ||
| "is_workflow_compatible": true, | ||
| "labels": [], | ||
| "help": "<p>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<p class=\"infomark\">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_EMPTY_DATASETS__", | ||
| "target": "galaxy_main", | ||
| "min_width": -1, | ||
| "model_class": "FilterEmptyDatasetsTool", | ||
| "hidden": "", | ||
| "id": "__FILTER_EMPTY_DATASETS__", | ||
| "name": "Filter empty" | ||
| }, | ||
| "liftOver1": { | ||
| "panel_section_name": "Lift-Over", | ||
| "xrefs": [], | ||
| "description": "between assemblies and genomes", | ||
| "is_workflow_compatible": true, | ||
| "labels": [], | ||
| "help": "<p class=\"warningmark\">Make sure that the genome build of the input dataset is specified (click the pencil icon in the history item to set it if necessary).<\/p>\n<p class=\"warningmark\">This tool can work with interval, GFF, and GTF datasets. It requires the interval datasets to have chromosome in column 1,\nstart co-ordinate in column 2 and end co-ordinate in column 3. BED comments\nand track and browser lines will be ignored, but if other non-interval lines\nare present the tool will return empty output datasets.<\/p>\n<hr class=\"docutils\" />\n<p class=\"infomark\"><strong>What it does<\/strong><\/p>\n<p>This tool is based on the LiftOver utility and Chain track from <a class=\"reference external\" href=\"http://genome.ucsc.edu/\">the UC Santa Cruz Genome Browser<\/a>.<\/p>\n<p>It converts coordinates and annotations between assemblies and genomes. It produces 2 files, one containing all the mapped coordinates and the other containing the unmapped coordinates, if any.<\/p>\n<blockquote>\n<\/blockquote>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>Converting the following hg16 intervals to hg18 intervals:<\/p>\n<pre class=\"literal-block\">\nchrX 85170 112199 AK002185 0 +\nchrX 110458 112199 AK097346 0 +\nchrX 112203 121212 AK074528 0 -\n<\/pre>\n<p>will produce the following hg18 intervals:<\/p>\n<pre class=\"literal-block\">\nchrX 132991 160020 AK002185 0 +\nchrX 158279 160020 AK097346 0 +\nchrX 160024 169033 AK074528 0 -\n<\/pre>\n", | ||
| "edam_operations": [], | ||
| "form_style": "regular", | ||
| "edam_topics": [], | ||
| "panel_section_id": "liftOver", | ||
| "version": "1.0.6", | ||
| "link": "/tool_runner?tool_id=liftOver1", | ||
| "target": "galaxy_main", | ||
| "min_width": -1, | ||
| "model_class": "Tool", | ||
| "hidden": "", | ||
| "id": "liftOver1", | ||
| "name": "Convert genome coordinates" | ||
| } | ||
| } | ||
| ] | ||
| } |
28 changes: 28 additions & 0 deletions
28
client/src/components/ToolsView/testData/toolsListInPanel.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,28 @@ | ||
| { | ||
| "default": { | ||
| "collection_operations": { | ||
| "tools": [ | ||
| "__UNZIP_COLLECTION__", "__ZIP_COLLECTION__", "__FILTER_FAILED_DATASETS__", "__FILTER_EMPTY_DATASETS__" | ||
| ], | ||
| "model_class": "ToolSection", | ||
| "version": "", | ||
| "id": "collection_operations", | ||
| "name": "Collection Operations" | ||
| }, | ||
| "liftOver": { | ||
| "tools": ["liftOver1"], | ||
| "model_class": "ToolSection", | ||
| "version": "", | ||
| "id": "liftOver", | ||
| "name": "Lift-Over" | ||
| }, | ||
| "testlabel1": { | ||
| "model_class": "ToolSectionLabel", | ||
| "id": "testlabel1", | ||
| "text": null, | ||
| "version": "", | ||
| "description": null, | ||
| "links": null | ||
| } | ||
| } | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters