filter_failed_collection.xml

<tool id="__FILTER_FAILED_DATASETS__"
      name="Filter failed datasets"
      version="1.0.0"
      tool_type="filter_failed_datasets_collection">
    <description></description>
    <type class="FilterFailedDatasetsTool" module="galaxy.tools" />
    <action module="galaxy.tools.actions.model_operations"
            class="ModelOperationToolAction"/>
    <edam_operations>
        <edam_operation>operation_3695</edam_operation>
    </edam_operations>
    <inputs>
        <param type="data_collection" collection_type="list,list:paired" name="input" label="Input Collection" />
    </inputs>
    <outputs>
        <collection name="output" format_source="input" type_source="input" label="${on_string} (filtered failed datasets)" >
        </collection>
    </outputs>
    <tests>
        <!-- Test framework has no way of creating a collection with
             failed elements, so best we can do is verify identity on
             an okay collection. API tests verify this tool works
             though.
        -->
        <test>
            <param name="input">
                <collection type="list">
                    <element name="e1" value="simple_line.txt" />
                </collection>
            </param>
            <output_collection name="output" type="list">
                <element name="e1">
                  <assert_contents>
                      <has_text_matching expression="^This is a line of text.\n$" />
                  </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[

========
Synopsis
========

Removes datasets in error (red) from a collection.

===========
Description
===========

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.

.. image:: ${static_path}/images/tools/collection_ops/filter_error.svg
  :width: 500
  :alt: Filter failed datasets

-----

.. class:: infomark

This tool will create new history datasets from your collection but your quota usage will not increase.

      ]]></help>
</tool>