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Merge pull request #11068 from nekrut/collection_tool_fixes
Changes to Collection Operation Help sections and parameter names
This commit is contained in:
John Chilton
@@ -1,5 +1,5 @@
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<tool id="__APPLY_RULES__"
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name="Apply Rule to Collection"
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name="Apply rules"
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version="1.1.0"
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tool_type="apply_rules_to_collection">
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<type class="ApplyRulesTool" module="galaxy.tools" />
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@@ -19,18 +19,28 @@
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</outputs>
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<help><![CDATA[
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========
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Synopsis
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========
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This tool allows one to process an existing Galaxy dataset collection's metadata as tabular data,
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apply a series of rules to it, and generate a new collection. When used interactively in the tool
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form, a dynamic preview of the processing will be available in a tabular data viewer but this tool
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apply a series of rules to it, and generate a new collection.
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===========
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Description
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===========
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When used interactively in the tool form, a dynamic preview of the processing will be available in a tabular data viewer but this tool
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may be used in workflows as well where no such preview can be generated.
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This tool is an advanced feature but has a lot of flexibility - it can be used to process collections
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with arbitrary nesting and can do many kinds of filtering, re-sorting, nesting,
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flattening, and arbitrary combinations thereof not possible with Galaxy's other, more simple
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This tool is an advanced feature but has a lot of flexibility - it can be used to process collections with arbitrary nesting and can do many kinds of filtering, re-sorting, nesting, flattening, and arbitrary combinations thereof not possible with Galaxy's other, more simple
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collection operation tools.
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More information about the rule processor in general can be found `here
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<https://github.com/jmchilton/training-material/blob/rules/topics/introduction/tutorials/galaxy-intro-rules/tutorial.md>`__ (this link is to documentation that is pretty rough still).
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More information about the rule processor in general can be found at `our training site`_.
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.. _our training site: https://training.galaxyproject.org/training-material/search?query=rule+builder
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.. class:: infomark
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@@ -1,8 +1,8 @@
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<tool id="__BUILD_LIST__"
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name="Build List"
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name="Build list"
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version="1.1.0"
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tool_type="build_list">
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<description>from one or more datasets</description>
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<description></description>
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<type class="BuildListCollectionTool" module="galaxy.tools" />
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<action module="galaxy.tools.actions.model_operations"
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class="ModelOperationToolAction"/>
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@@ -10,8 +10,8 @@
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<edam_operation>operation_2409</edam_operation>
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</edam_operations>
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<inputs>
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<repeat name="datasets" title="Dataset">
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<param type="data" name="input" optional="true" label="Input Dataset" />
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<repeat name="datasets" title="Dataset" help="If collections are provided they should contain the same number of items.">
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<param type="data" name="input" optional="true" label="Input Dataset" help="If providing a collection here the tool will be run in batch and one collection per element is created."/>
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</repeat>
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</inputs>
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<outputs>
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@@ -20,8 +20,33 @@
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</outputs>
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<help><![CDATA[
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========
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Synopsis
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========
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Builds a new list collection from individual datasets or collections.
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===========
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Description
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===========
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This tool combines individual datasets or collections into a new collection. The simplest scenario is building a new colection from individual datasets (case **A** in the image below). You can merge a collection with individual dataset(s). In this case (see **B** in the image below) the individual dataset(s) will be merged with each element of the input collection to create a nested collection. Finally, two or more collection can be merged together creating a nested collection (case **C** in the image below).
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.. class:: warningmark
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**Note**: When merging collections (e.g., case **C** below) the input collection **must** have equal number of elements.
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------
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.. image:: ${static_path}/images/tools/collection_ops/build_list.svg
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:width: 800
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:alt: Unzipping operation
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-------
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.. class:: infomark
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This tool will create a new collection from your history datasets but your quota usage will not increase.
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]]></help>
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@@ -1,8 +1,8 @@
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<tool id="__EXTRACT_DATASET__"
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name="Extract Dataset"
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name="Extract dataset"
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version="1.0.1"
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tool_type="extract_element">
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<description>from a list</description>
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<description></description>
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<type class="ExtractDatasetCollectionTool" module="galaxy.tools" />
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<action module="galaxy.tools.actions.model_operations"
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class="ModelOperationToolAction"/>
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@@ -30,7 +30,7 @@
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</param>
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</when>
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<when value="by_index">
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<param name="index" label="Element index:" type="integer" value="0" help="Starting from 0.">
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<param name="index" label="Element index:" type="integer" value="0" help="Starting from 0">
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</param>
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</when>
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</conditional>
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@@ -40,6 +40,22 @@
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</outputs>
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<help><![CDATA[
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|
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========
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Synopsis
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========
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Extracts datasets from a collection based on either position or identifier.
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===========
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Description
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===========
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The tool allow extracting datasets based on position (**The first dataset** and **Select by index** options) or name (**Select by element identifier** option). This tool effectively collapses the inner-most collection into a dataset. For nested collections (e.g a list of lists of lists: outer:middle:inner, extracting the inner dataset element) a new list is created where the selected element takes the position of the inner-most collection (so outer:middle, where middle is not a collection but the inner dataset element).
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.. class:: warningmark
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**Note**: Dataset index (numbering) begins with 0 (zero).
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.. class:: infomark
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This tool will create new history datasets from your collection but your quota usage will not increase.
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@@ -1,8 +1,8 @@
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<tool id="__FILTER_EMPTY_DATASETS__"
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name="Filter empty"
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name="Filter empty datasets"
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version="1.0.0"
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tool_type="filter_empty_datasets_collection">
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<description>datasets from a collection</description>
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<description></description>
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<type class="FilterEmptyDatasetsTool" module="galaxy.tools" />
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<action module="galaxy.tools.actions.model_operations"
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class="ModelOperationToolAction"/>
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@@ -34,7 +34,19 @@
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</tests>
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<help><![CDATA[
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||||
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.
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========
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Synopsis
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========
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Removes empty elements from a collection.
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This tool takes a dataset collection and filters out (removes) empty datasets. This is useful for continuing a multi-sample analysis when downstream tools require datasets to have content.
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.. image:: ${static_path}/images/tools/collection_ops/filter_empty.svg
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:width: 500
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:alt: Filtering empty datasets
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-----
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.. class:: infomark
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@@ -1,8 +1,8 @@
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<tool id="__FILTER_FAILED_DATASETS__"
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name="Filter failed"
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name="Filter failed datasets"
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version="1.0.0"
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tool_type="filter_failed_datasets_collection">
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<description>datasets from a collection</description>
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<description></description>
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<type class="FilterFailedDatasetsTool" module="galaxy.tools" />
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<action module="galaxy.tools.actions.model_operations"
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class="ModelOperationToolAction"/>
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@@ -39,7 +39,23 @@
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</tests>
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<help><![CDATA[
|
||||
|
||||
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 or more of the samples fails at some point.
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========
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Synopsis
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||||
========
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Removes datasets in error (red) from a collection.
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||||
===========
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||||
Description
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||||
===========
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||||
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This tool takes a dataset collection and filters out (removes) datasets in the failed (red) state. This is useful for continuing a multi-sample analysis when one or more of the samples fails at some point.
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.. image:: ${static_path}/images/tools/collection_ops/filter_error.svg
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:width: 500
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:alt: Filter failed datasets
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-----
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.. class:: infomark
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@@ -1,8 +1,8 @@
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<tool id="__FILTER_FROM_FILE__"
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name="Filter List"
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name="Filter collection"
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version="1.0.0"
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tool_type="filter_from_file">
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<description>from contents of a file</description>
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<description></description>
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<type class="FilterFromFileTool" module="galaxy.tools" />
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<action module="galaxy.tools.actions.model_operations"
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class="ModelOperationToolAction"/>
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@@ -10,11 +10,11 @@
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<edam_operation>operation_3695</edam_operation>
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</edam_operations>
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<inputs>
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<param type="data_collection" name="input" label="Input Collection" help="A list whose elements will be filtered."/>
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<param type="data_collection" name="input" label="Input Collection" help="A collection whose elements will be filtered."/>
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<conditional name="how">
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<param type="select" name="how_filter" label="How should the elements to remove be determined?">
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<option value="remove_if_absent" selected="true">Remove if identifiers are absent from supplied text file.</option>
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<option value="remove_if_present">Remove if identifiers are present in supplied text file.</option>
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<option value="remove_if_absent" selected="true">Remove if identifiers are ABSENT from file</option>
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<option value="remove_if_present">Remove if identifiers are PRESENT in file</option>
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</param>
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<when value="remove_if_absent">
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<param type="data" name="filter_source" format="txt" label="Filter out identifiers absent from" />
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@@ -82,15 +82,69 @@
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</tests>
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<help><![CDATA[
|
||||
|
||||
========
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||||
Synopsis
|
||||
========
|
||||
|
||||
Filters elements from a collection using a list supplied in a file.
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||||
|
||||
===========
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||||
Description
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||||
===========
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This tools allow filtering elements from a data collection. It takes an input collection and a text file with names (i.e. identifiers). The tool behavious is controlled by **How should the elements to remove be determined?** drop-down. It has the following options:
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**Remove if identifiers are ABSENT from file**
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Given a collection::
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Collection: [Dataset A]
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[Dataset B]
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[Dataset X]
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|
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and a text file::
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A
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B
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Z
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the tool will return two collections::
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(filtered): [Dataset A]
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[Dataset B]
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(discarded): [Dataset X]
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|
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------
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**Remove if identifiers are PRESENT in file**
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Given a collection::
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|
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Collection: [Dataset A]
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[Dataset B]
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||||
[Dataset X]
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|
||||
and a text file::
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A
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B
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Z
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the tool will return two collections::
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|
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(filtered): [Dataset X]
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(discarded): [Dataset A]
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[Dataset B]
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.. class:: warningmark
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**Note** how the tool deals with the ``Z`` entry.
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.. class:: infomark
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|
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This tool will take an input list and a text file with
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names (i.e. identifiers). It will split the input list into
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two new lists - one filtered to contain only the list members
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whose names are listed in the text file, and one containing
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all the other elements.
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||||
|
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This tool will create new history datasets from your collection
|
||||
but your quota usage will not increase.
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||||
This tool will create new history datasets from your collection but your quota usage will not increase.
|
||||
]]></help>
|
||||
</tool>
|
||||
|
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@@ -1,8 +1,8 @@
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<tool id="__FLATTEN__"
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name="Flatten Collection"
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name="Flatten collection"
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version="1.0.0"
|
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tool_type="filter_collection">
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<description>into a flat list of datasets</description>
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<description></description>
|
||||
<type class="FlattenTool" module="galaxy.tools" />
|
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<action module="galaxy.tools.actions.model_operations"
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class="ModelOperationToolAction"/>
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@@ -11,7 +11,7 @@
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</edam_operations>
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<inputs>
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<param type="data_collection" name="input" label="Input Collection" />
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<param type="select" name="join_identifier" label="Join collection identifiers using" help="">
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<param type="select" name="join_identifier" label="Join collection identifiers using" help="Separator for merging dataset identifiers">
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<option value="_">underscore ( _ )</option>
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<option value=":">colon ( : )</option>
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<option value="-">dash ( - )</option>
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@@ -49,7 +49,23 @@
|
||||
</tests>
|
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<help><![CDATA[
|
||||
|
||||
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.
|
||||
========
|
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Synopsis
|
||||
========
|
||||
|
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Flattens nested collection into a simple list.
|
||||
|
||||
===========
|
||||
Description
|
||||
===========
|
||||
|
||||
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. It effectively "flattens" the hierarchy. The collection identifiers are merged together (using "_" as default) to create new collection identifiers in the flattened result:
|
||||
|
||||
.. image:: ${static_path}/images/tools/collection_ops/flatten.svg
|
||||
:width: 500
|
||||
:alt: Flattening operation
|
||||
|
||||
----
|
||||
|
||||
.. class:: infomark
|
||||
|
||||
|
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@@ -1,8 +1,8 @@
|
||||
<tool id="__MERGE_COLLECTION__"
|
||||
name="Merge Collections"
|
||||
name="Merge collections"
|
||||
version="1.0.0"
|
||||
tool_type="merge_collection">
|
||||
<description>into single list of datasets</description>
|
||||
<description></description>
|
||||
<type class="MergeCollectionTool" module="galaxy.tools" />
|
||||
<action module="galaxy.tools.actions.model_operations"
|
||||
class="ModelOperationToolAction"/>
|
||||
@@ -59,7 +59,7 @@
|
||||
<section name="advanced" title="Advanced Options">
|
||||
<conditional name="conflict">
|
||||
<param name="duplicate_options" type="select" label="How should conflicts (or potential conflicts) be handled?"
|
||||
help="Collection elements must have unique element identifiers, when appending how should unique identifiers be assured.">
|
||||
help="Collection elements must have unique element identifiers, when appending how should unique identifiers be assured. See Help section below for examples.">
|
||||
<option value="suffix_conflict">Append suffix to conflicted element identifers</option>
|
||||
<option value="suffix_conflict_rest">Append suffix to conflicted element identifers after first one encountered</option>
|
||||
<option value="suffix_every">Append suffix to every element identifer</option>
|
||||
@@ -275,7 +275,148 @@
|
||||
</tests>
|
||||
<help><![CDATA[
|
||||
|
||||
This tool takes two lists and creates a single unified list.
|
||||
========
|
||||
Synopsis
|
||||
========
|
||||
|
||||
Takes two or more collections and creates a single collection from them.
|
||||
|
||||
===========
|
||||
Description
|
||||
===========
|
||||
|
||||
By default the tool assumes that collections that are being merged have unique dataset names. If it not the case only one (the first) of the datasets with a repeated name will be included in the merged collection. For example, suppose you have two collections. Each has two datasets named "A" and "B"::
|
||||
|
||||
Collection 1: [Dataset A]
|
||||
[Dataset B]
|
||||
[Dataset X]
|
||||
Collection 2: [Dataset A]
|
||||
[Dataset B]
|
||||
[Dataset Y]
|
||||
|
||||
Merging them will produce a single collection with only two datasets::
|
||||
|
||||
Merged Collection: [Dataset A]
|
||||
[Dataset B]
|
||||
[Dataset X]
|
||||
[Dataset Y]
|
||||
|
||||
This behavior can be changed by clicking on "*Advanced Options*" link. The following options are available:
|
||||
|
||||
**Keep first instance (Default behavior)**
|
||||
|
||||
Input::
|
||||
|
||||
Collection 1: [Dataset A]
|
||||
[Dataset B]
|
||||
[Dataset X]
|
||||
Collection 2: [Dataset A]
|
||||
[Dataset B]
|
||||
[Dataset Y]
|
||||
|
||||
Output::
|
||||
|
||||
Merged Collection: [Dataset A]
|
||||
[Dataset B]
|
||||
[Dataset X]
|
||||
[Dataset Y]
|
||||
|
||||
Here if two collection have identical dataset names, a dataset is chosen from the *first* collection.
|
||||
|
||||
-----
|
||||
|
||||
**Keep first instance**
|
||||
|
||||
Input::
|
||||
|
||||
Collection 1: [Dataset A]
|
||||
[Dataset B]
|
||||
[Dataset X]
|
||||
Collection 2: [Dataset A]
|
||||
[Dataset B]
|
||||
[Dataset Y]
|
||||
Output::
|
||||
|
||||
Merged Collection: [Dataset A]
|
||||
[Dataset B]
|
||||
[Dataset X]
|
||||
[Dataset Y]
|
||||
|
||||
Here if two collection have identical dataset names, a dataset is chosen from the *last* collection.
|
||||
|
||||
-----
|
||||
|
||||
**Append suffix to conflicted element identifiers**
|
||||
|
||||
Input::
|
||||
|
||||
Collection 1: [Dataset A]
|
||||
[Dataset B]
|
||||
[Dataset X]
|
||||
Collection 2: [Dataset A]
|
||||
[Dataset B]
|
||||
[Dataset Y]
|
||||
|
||||
Output::
|
||||
|
||||
Merged Collection: [Dataset A_1]
|
||||
[Dataset B_1]
|
||||
[Dataset A_2]
|
||||
[Dataset B_2]
|
||||
[Dataset X]
|
||||
[Dataset Y]
|
||||
|
||||
----
|
||||
|
||||
**Append suffix to conflicted element identifiers after first on encountered**
|
||||
|
||||
Input::
|
||||
|
||||
Collection 1: [Dataset A]
|
||||
[Dataset B]
|
||||
[Dataset X]
|
||||
Collection 2: [Dataset A]
|
||||
[Dataset B]
|
||||
[Dataset Y]
|
||||
|
||||
Output::
|
||||
|
||||
Merged Collection: [Dataset A]
|
||||
[Dataset B]
|
||||
[Dataset A_2]
|
||||
[Dataset B_2]
|
||||
[Dataset X]
|
||||
[Dataset Y]
|
||||
|
||||
------
|
||||
|
||||
**Append suffix to every element identifier**
|
||||
|
||||
Input::
|
||||
|
||||
Collection 1: [Dataset A]
|
||||
[Dataset B]
|
||||
[Dataset X]
|
||||
Collection 2: [Dataset A]
|
||||
[Dataset B]
|
||||
[Dataset Y]
|
||||
|
||||
Output::
|
||||
|
||||
Merged Collection: [Dataset A_1]
|
||||
[Dataset B_2]
|
||||
[Dataset A_2]
|
||||
[Dataset B_2]
|
||||
[Dataset X_1]
|
||||
[Dataset Y_2]
|
||||
|
||||
-----
|
||||
|
||||
**Fail collection creation**
|
||||
|
||||
This option will simply trigger an error.
|
||||
|
||||
------
|
||||
|
||||
.. class:: infomark
|
||||
|
||||
|
||||
@@ -1,8 +1,8 @@
|
||||
<tool id="__RELABEL_FROM_FILE__"
|
||||
name="Relabel List Identifiers"
|
||||
name="Relabel identifiers"
|
||||
version="1.0.0"
|
||||
tool_type="relabel_from_file">
|
||||
<description>from contents of a file</description>
|
||||
<description></description>
|
||||
<type class="RelabelFromFileTool" module="galaxy.tools" />
|
||||
<action module="galaxy.tools.actions.model_operations"
|
||||
class="ModelOperationToolAction"/>
|
||||
@@ -10,7 +10,7 @@
|
||||
<edam_operation>operation_3096</edam_operation>
|
||||
</edam_operations>
|
||||
<inputs>
|
||||
<param type="data_collection" name="input" label="Input Collection" help="A list whose identifiers will be relabelled."/>
|
||||
<param type="data_collection" name="input" label="Input Collection" help="collection to change identifiers in"/>
|
||||
<conditional name="how">
|
||||
<param type="select" name="how_select" label="How should the new labels be specified?">
|
||||
<option value="txt">Using lines in a simple text file.</option>
|
||||
@@ -22,7 +22,7 @@
|
||||
</when>
|
||||
<when value="tabular">
|
||||
<param type="data" name="labels" format="tabular" label="New Identifiers" />
|
||||
<param name="strict" type="boolean" label="Ensure strict mapping" help="If selected, the target file must contain exactly the correct number of lines and each input identifier must match exactly one element of the input collection." truevalue="true" falsevalue="false" />
|
||||
<param name="strict" type="boolean" label="Ensure strict mapping" help="If checked, the target file must contain exactly the correct number of lines and each input identifier must match exactly one element of the input collection." truevalue="true" falsevalue="false" />
|
||||
</when>
|
||||
</conditional>
|
||||
</inputs>
|
||||
@@ -137,23 +137,71 @@
|
||||
</tests>
|
||||
<help><![CDATA[
|
||||
|
||||
========
|
||||
Synopsis
|
||||
========
|
||||
|
||||
Changes identifiers of datasets within a collection using identifiers from a supplied file.
|
||||
|
||||
===========
|
||||
Description
|
||||
===========
|
||||
|
||||
New identifiers can be supplied as either a simple list or a tab-delimited file mapping old identifier to the new ones. This is controlled using **How should the new identifiers be specified?** drop-down:
|
||||
|
||||
**Using lines in a simple text file**
|
||||
|
||||
Given a collection::
|
||||
|
||||
Collection: [Dataset A]
|
||||
[Dataset B]
|
||||
[Dataset X]
|
||||
|
||||
and a simple text file::
|
||||
|
||||
Alpha
|
||||
Beta
|
||||
Gamma
|
||||
|
||||
the tool will return::
|
||||
|
||||
Collection: [Dataset Alpha]
|
||||
[Dataset Beta]
|
||||
[Dataset Gamma]
|
||||
|
||||
.. class:: infomark
|
||||
|
||||
This tool will take an input list and a text file with new identifiers
|
||||
and build a new list with the same datasets but these new identifiers.
|
||||
The order and number of entries in the text file must match the order
|
||||
of the items you want to rename in your dataset collection.
|
||||
**Note** that the order and number of entries in the text file must match the order of the items you want to rename in your dataset collection.
|
||||
|
||||
Alternatively a tabular file may be supplied, where the first column
|
||||
if the current identifier that should be renamed, and the second column
|
||||
contains the new label. This file may contain less entries than items
|
||||
in the collection. In that case only matching list identifiers will be
|
||||
relabeled.
|
||||
-------
|
||||
|
||||
Valid identifiers must contain only characters (a-z, A-Z), numbers (0-9),
|
||||
dash and underscore (-, _). Punctuation or whitespace are not allowed.
|
||||
**Map original identifiers to new ones using a two column table**
|
||||
|
||||
This tool will create new history datasets from your collection
|
||||
but your quota usage will not increase.
|
||||
Given a collection::
|
||||
|
||||
Collection: [Dataset A]
|
||||
[Dataset B]
|
||||
[Dataset X]
|
||||
|
||||
and a simple text file (you can see that entries do not have to be in order here)::
|
||||
|
||||
B Beta
|
||||
X Gamma
|
||||
A Alpha
|
||||
|
||||
the tool will return::
|
||||
|
||||
Collection: [Dataset Alpha]
|
||||
[Dataset Beta]
|
||||
[Dataset Gamma]
|
||||
|
||||
|
||||
.. class:: warningmark
|
||||
|
||||
Valid identifiers must contain only characters (a-z, A-Z), numbers (0-9), dash and underscore (-, _). Punctuation or whitespace are not allowed.
|
||||
|
||||
.. class:: infomark
|
||||
|
||||
This tool will create new history datasets from your collection but your quota usage will not increase.
|
||||
]]></help>
|
||||
</tool>
|
||||
|
||||
@@ -1,8 +1,8 @@
|
||||
<tool id="__SORTLIST__"
|
||||
name="Sort Collection"
|
||||
name="Sort collection"
|
||||
version="1.0.0"
|
||||
tool_type="sort_collection">
|
||||
<description>of list of datasets</description>
|
||||
<description></description>
|
||||
<type class="SortTool" module="galaxy.tools" />
|
||||
<action module="galaxy.tools.actions.model_operations"
|
||||
class="ModelOperationToolAction"/>
|
||||
@@ -12,10 +12,10 @@
|
||||
<inputs>
|
||||
<param type="data_collection" collection_type="list,list:paired" name="input" label="Input Collection" />
|
||||
<conditional name="sort_type">
|
||||
<param type="select" name="sort_type" label="Sort collection identifiers" help="All element identifiers must be present once.">
|
||||
<option value="alpha">alphabetically</option>
|
||||
<option value="numeric">numerically (strips all characters except numbers)</option>
|
||||
<option value="file">Sort collection using order of identifiers in text file</option>
|
||||
<param type="select" name="sort_type" label="Sort type" help="All element identifiers must be present once.">
|
||||
<option value="alpha">alphabetical</option>
|
||||
<option value="numeric">numeric (non numeric characters are ignored)</option>
|
||||
<option value="file">from file</option>
|
||||
</param>
|
||||
<when value="alpha" />
|
||||
<when value="numeric" />
|
||||
@@ -142,7 +142,53 @@
|
||||
</tests>
|
||||
<help><![CDATA[
|
||||
|
||||
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).
|
||||
========
|
||||
Synopsis
|
||||
========
|
||||
|
||||
Sorts dataset collection alphabetically, numerically, or using predetermined order from a supplied file.
|
||||
|
||||
===========
|
||||
Description
|
||||
===========
|
||||
|
||||
**Numeric sort**
|
||||
|
||||
The tool sort in ascending order. When *numeric* sort is chosen, the tool ignores non-numeric characters. For example, if a collection contains the following elements::
|
||||
|
||||
Collection: [Horse123]
|
||||
[Donkey543]
|
||||
[Mule176]
|
||||
|
||||
The tool will output::
|
||||
|
||||
Collection: [Horse123]
|
||||
[Mule176]
|
||||
[Donkey543]
|
||||
|
||||
-------
|
||||
|
||||
**Sorting from file**
|
||||
|
||||
Alternative, one can supply a single column text file containing elements identifiers in the desired sort order. For example, suppose there a collection::
|
||||
|
||||
Collection: [Horse123]
|
||||
[Donkey543]
|
||||
[Mule176]
|
||||
|
||||
and a file specifying sort order::
|
||||
|
||||
Donkey543
|
||||
Horse123
|
||||
Mule176
|
||||
|
||||
the output will predictably look like this::
|
||||
|
||||
Collection: [Donkey543]
|
||||
[Horse123]
|
||||
[Mule176]
|
||||
|
||||
-------
|
||||
|
||||
.. class:: infomark
|
||||
|
||||
|
||||
@@ -1,8 +1,8 @@
|
||||
<tool id="__TAG_FROM_FILE__"
|
||||
name="Tag elements from file"
|
||||
name="Tag elements"
|
||||
version="1.0.0"
|
||||
tool_type="tag_from_file">
|
||||
<description>from contents of a file</description>
|
||||
<description></description>
|
||||
<type class="TagFromFileTool" module="galaxy.tools" />
|
||||
<action module="galaxy.tools.actions.model_operations"
|
||||
class="ModelOperationToolAction"/>
|
||||
@@ -80,21 +80,30 @@
|
||||
</tests>
|
||||
<help><![CDATA[
|
||||
|
||||
.. class:: infomark
|
||||
========
|
||||
Synopsis
|
||||
========
|
||||
|
||||
This tool will take an input collection and a tabular file,
|
||||
where the first column indicates an element identifier and the
|
||||
remaining columns contains the new tags. This file may contain
|
||||
less entries than elements in the collection.
|
||||
In that case only matching list identifiers will be tagged.
|
||||
Adds tags (including name: and group: tags) to collection elements.
|
||||
|
||||
This tool will create new history datasets from your collection
|
||||
but your quota usage will not increase.
|
||||
===========
|
||||
Description
|
||||
===========
|
||||
|
||||
The relationship between element names and tags is specified in a two column tab-delimited file. This file may contain less entries than elements in the collection. In that case only matching list identifiers will be tagged.
|
||||
|
||||
To create name: or group: tags prepend them with ``#`` (you can also use ``name:``) or ``group:``, respectively.
|
||||
|
||||
===============
|
||||
More about tags
|
||||
===============
|
||||
|
||||
Galaxy allows tagging datasets to facilitate analyses. There are several types of tags including simple tags, name tags, and group tags. **Simple** tags allow you to attach an alternative label to a dataset, which will make it easier to find it later. **Name** tags allow you to track propagation of a dataset through the analyses: all datasets derived from the initial dataset labeled with a name tag will inherit it. Finally, **group** tags allow you to label group of datasets. This is useful. for example, for differential expression analysis where you can have two groups of datasets labeled as "treatment" and "control".
|
||||
|
||||
To learn mote about tags go to `our training site`_.
|
||||
|
||||
.. _our training site: https://training.galaxyproject.org/training-material/search?query=tags
|
||||
|
||||
In order to create
|
||||
|
||||
- name tags prefix the tag name with "#" or "name:"
|
||||
- group tags prefix the tag name with "group:"
|
||||
|
||||
|
||||
]]></help>
|
||||
|
||||
@@ -1,7 +1,8 @@
|
||||
<tool id="__UNZIP_COLLECTION__"
|
||||
name="Unzip Collection"
|
||||
name="Unzip collection"
|
||||
version="1.0.0"
|
||||
tool_type="unzip_collection">
|
||||
<description></description>
|
||||
<type class="UnzipCollectionTool" module="galaxy.tools" />
|
||||
<action module="galaxy.tools.actions.model_operations"
|
||||
class="ModelOperationToolAction"/>
|
||||
@@ -9,7 +10,7 @@
|
||||
<edam_operation>operation_3359</edam_operation>
|
||||
</edam_operations>
|
||||
<inputs>
|
||||
<param type="data_collection" collection_type="paired" name="input" label="Input Paired Dataset" />
|
||||
<param type="data_collection" collection_type="paired" name="input" label="Paired input to unzip" />
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data name="forward" label="${on_string} (forward)" format_source="input"/>
|
||||
@@ -17,13 +18,24 @@
|
||||
</outputs>
|
||||
<help><
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|
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|
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|
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Reference in New Issue
Block a user