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Keep old and new version
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mvdbeek
@@ -11,7 +11,6 @@
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</edam_operations>
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<inputs>
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<param type="data_collection" collection_type="list,list:paired" name="input" label="Input Collection" />
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<param type="data" name="replacement" optional="true" label="Replace empty elements with this dataset" help="If provided, empty elements will be replaced with this dataset"/>
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</inputs>
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<outputs>
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<collection name="output" format_source="input" type_source="input" label="${on_string} (filtered empty datasets)" >
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@@ -0,0 +1,57 @@
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<tool id="__FILTER_EMPTY_DATASETS__"
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name="Filter empty datasets"
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version="1.1.0"
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tool_type="filter_empty_datasets_collection">
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<description></description>
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<type class="FilterEmptyDatasetsTool" module="galaxy.tools" />
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<action module="galaxy.tools.actions.model_operations"
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class="ModelOperationToolAction"/>
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<edam_operations>
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<edam_operation>operation_3695</edam_operation>
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</edam_operations>
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<inputs>
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<param type="data_collection" collection_type="list,list:paired" name="input" label="Input Collection" />
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<param type="data" name="replacement" optional="true" label="Replace empty elements with this dataset" help="If provided, empty elements will be replaced with this dataset"/>
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</inputs>
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<outputs>
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<collection name="output" format_source="input" type_source="input" label="${on_string} (filtered empty datasets)" >
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</collection>
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</outputs>
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<tests>
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<test>
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<param name="input">
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<collection type="list">
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<element name="e1" value="simple_line.txt" />
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</collection>
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</param>
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<output_collection name="output" type="list" count="1">
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<element name="e1">
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<assert_contents>
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<has_text_matching expression="^This is a line of text.\n$" />
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</assert_contents>
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</element>
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</output_collection>
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</test>
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</tests>
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<help><![CDATA[
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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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This tool will create new history datasets from your collection but your quota usage will not increase.
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]]></help>
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</tool>
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@@ -0,0 +1,150 @@
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<tool id="__FILTER_FROM_FILE__"
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name="Filter collection"
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version="1.1.0"
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tool_type="filter_from_file">
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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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<edam_operations>
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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 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 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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</when>
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<when value="remove_if_present">
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<param type="data" name="filter_source" format="txt" label="Filter out identifiers present in" />
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</when>
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</conditional>
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</inputs>
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<outputs>
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<collection name="output_filtered" format_source="input" type_source="input" label="${on_string} (filtered)" >
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</collection>
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<collection name="output_discarded" format_source="input" type_source="input" label="${on_string} (discarded)" >
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</collection>
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</outputs>
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<tests>
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<test>
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<param name="input">
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<collection type="list">
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<element name="i1" value="simple_line.txt" />
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<element name="i2" value="simple_line_alternative.txt" />
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</collection>
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</param>
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<param name="how_filter" value="remove_if_present" />
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<param name="filter_source" value="filter_labels_1.txt" ftype="txt" />
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<output_collection name="output_filtered" type="list">
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<element name="i1">
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<assert_contents>
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<has_text_matching expression="^This is a line of text.\n$" />
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</assert_contents>
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</element>
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</output_collection>
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<output_collection name="output_discarded" type="list">
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<element name="i2">
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<assert_contents>
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<has_text_matching expression="^This is a different line of text.\n$" />
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</assert_contents>
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</element>
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</output_collection>
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</test>
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<test>
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<param name="input">
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<collection type="list">
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<element name="i1" value="simple_line.txt" />
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<element name="i2" value="simple_line_alternative.txt" />
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</collection>
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</param>
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<param name="how_filter" value="remove_if_absent" />
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<param name="filter_source" value="filter_labels_1.txt" ftype="txt" />
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<output_collection name="output_filtered" type="list">
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<element name="i2">
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<assert_contents>
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<has_text_matching expression="^This is a different line of text.\n$" />
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</assert_contents>
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</element>
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</output_collection>
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<output_collection name="output_discarded" type="list">
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<element name="i1">
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<assert_contents>
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<has_text_matching expression="^This is a line of text.\n$" />
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</assert_contents>
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</element>
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</output_collection>
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</test>
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</tests>
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<help><![CDATA[
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========
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Synopsis
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========
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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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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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**Remove if identifiers are PRESENT in 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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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 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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This tool will create new history datasets from your collection but your quota usage will not increase.
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]]></help>
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</tool>
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@@ -7,7 +7,6 @@
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</edam_operations>
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<inputs>
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<param type="data_collection" collection_type="list,list:paired" name="input" label="Input Collection"/>
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<param type="data" name="replacement" optional="true" label="Replace null elements with this dataset" help="If provided, null elements will be replaced with this dataset"/>
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</inputs>
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<outputs>
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<collection name="output" format_source="input" type_source="input" label="${on_string} (without null datasets)">
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@@ -0,0 +1,47 @@
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<tool id="__FILTER_NULL__" name="Filter null elements" version="1.1.0" tool_type="filter_null">
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<description/>
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<type class="FilterNullTool" module="galaxy.tools"/>
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<action module="galaxy.tools.actions.model_operations" class="ModelOperationToolAction"/>
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<edam_operations>
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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" collection_type="list,list:paired" name="input" label="Input Collection"/>
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<param type="data" name="replacement" optional="true" label="Replace null elements with this dataset" help="If provided, null elements will be replaced with this dataset"/>
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</inputs>
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<outputs>
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<collection name="output" format_source="input" type_source="input" label="${on_string} (without null datasets)">
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</collection>
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</outputs>
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<tests>
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<test>
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<param name="input">
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<collection type="list">
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<element name="e1" value="simple_line.txt"/>
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</collection>
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</param>
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<output_collection name="output" type="list" count="1">
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<element name="e1">
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<assert_contents>
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<has_text_matching expression="^This is a line of text.\n$"/>
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</assert_contents>
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</element>
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</output_collection>
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</test>
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</tests>
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<help><![CDATA[
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========
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Synopsis
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========
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Removes null elements from a collection.
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This tool takes a dataset collection and filters out nulls. This is useful for removing elements that resulted from conditional execution of jobs.
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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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]]></help>
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</tool>
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@@ -11,7 +11,6 @@
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</edam_operations>
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<inputs>
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<param type="data_collection" collection_type="list,list:paired" name="input" label="Input Collection" />
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<param type="data" name="replacement" optional="true" label="Replace unsuccessful elements with this dataset" help="If provided, unsuccessful elements will be replaced with this dataset"/>
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</inputs>
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<outputs>
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<collection name="output" format_source="input" type_source="input" label="${on_string} (only successed datasets)" >
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@@ -0,0 +1,65 @@
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<tool id="__KEEP_SUCCESS_DATASETS__"
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name="Keep success"
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version="1.1.0"
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tool_type="keep_success_datasets_collection">
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<description></description>
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<type class="KeepSuccessDatasetsTool" module="galaxy.tools" />
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<action module="galaxy.tools.actions.model_operations"
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class="ModelOperationToolAction"/>
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<edam_operations>
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<edam_operation>operation_3695</edam_operation>
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</edam_operations>
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<inputs>
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<param type="data_collection" collection_type="list,list:paired" name="input" label="Input Collection" />
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<param type="data" name="replacement" optional="true" label="Replace unsuccessful elements with this dataset" help="If provided, unsuccessful elements will be replaced with this dataset"/>
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</inputs>
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<outputs>
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<collection name="output" format_source="input" type_source="input" label="${on_string} (only successed datasets)" >
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</collection>
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</outputs>
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<tests>
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<!-- Test framework has no way of creating a collection with
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unsuccess elements, so best we can do is verify identity on
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an okay collection.
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-->
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<test>
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<param name="input">
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<collection type="list">
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<element name="e1" value="simple_line.txt" />
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</collection>
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</param>
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<output_collection name="output" type="list">
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<element name="e1">
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<assert_contents>
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<has_text_matching expression="^This is a line of text.\n$" />
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</assert_contents>
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</element>
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</output_collection>
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</test>
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</tests>
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<help><![CDATA[
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========
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Synopsis
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========
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Keep datasets in success (green) from a collection.
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===========
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Description
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===========
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This tool takes a dataset collection and filters in (keep) datasets in the success (green) state. This is useful for continuing a multi-sample analysis when one of more of the samples fails or is in paused state.
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.. image:: ${static_path}/images/tools/collection_ops/keep_success.svg
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:width: 500
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:alt: Keep success datasets
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-----
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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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]]></help>
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</tool>
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