filter_from_file.xml

<tool id="__FILTER_FROM_FILE__"
      name="Filter collection"
      version="1.0.0"
      tool_type="filter_from_file">
    <description></description>
    <type class="FilterFromFileTool" 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" name="input" label="Input Collection" help="A collection whose elements will be filtered."/>
        <conditional name="how">
            <param type="select" name="how_filter" label="How should the elements to remove be determined?">
                <option value="remove_if_absent" selected="true">Remove if identifiers are ABSENT from file</option>
                <option value="remove_if_present">Remove if identifiers are PRESENT in file</option>
            </param>
            <when value="remove_if_absent">
                <param type="data" name="filter_source" format="txt" label="Filter out identifiers absent from" />
            </when>
            <when value="remove_if_present">
                <param type="data" name="filter_source" format="txt" label="Filter out identifiers present in" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <collection name="output_filtered" format_source="input" type_source="input" label="${on_string} (filtered)" >
        </collection>
        <collection name="output_discarded" format_source="input" type_source="input" label="${on_string} (discarded)" >
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="input">
                <collection type="list">
                    <element name="i1" value="simple_line.txt" />
                    <element name="i2" value="simple_line_alternative.txt" />
                </collection>
            </param>
            <param name="how_filter" value="remove_if_present" />
            <param name="filter_source" value="filter_labels_1.txt" ftype="txt" />
            <output_collection name="output_filtered" type="list">
                <element name="i1">
                  <assert_contents>
                    <has_text_matching expression="^This is a line of text.\n$" />
                  </assert_contents>
                </element>
            </output_collection>
            <output_collection name="output_discarded" type="list">
                <element name="i2">
                  <assert_contents>
                    <has_text_matching expression="^This is a different line of text.\n$" />
                  </assert_contents>
                </element>
            </output_collection>
        </test>
        <test>
            <param name="input">
                <collection type="list">
                    <element name="i1" value="simple_line.txt" />
                    <element name="i2" value="simple_line_alternative.txt" />
                </collection>
            </param>
            <param name="how_filter" value="remove_if_absent" />
            <param name="filter_source" value="filter_labels_1.txt" ftype="txt" />
            <output_collection name="output_filtered" type="list">
                <element name="i2">
                  <assert_contents>
                    <has_text_matching expression="^This is a different line of text.\n$" />
                  </assert_contents>
                </element>
            </output_collection>
            <output_collection name="output_discarded" type="list">
                <element name="i1">
                  <assert_contents>
                    <has_text_matching expression="^This is a line of text.\n$" />
                  </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[

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

Filters elements from a collection using a list supplied in a file.

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

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:

**Remove if identifiers are ABSENT from file**

Given a collection::

 Collection: [Dataset A] 
             [Dataset B] 
             [Dataset X]

and a text file::

             A
             B
             Z

the tool will return two collections::

 (filtered):  [Dataset A]
              [Dataset B]

 (discarded): [Dataset X]

------

**Remove if identifiers are PRESENT in file**

Given a collection::

 Collection: [Dataset A] 
             [Dataset B] 
             [Dataset X]

and a text file::

             A
             B
             Z

the tool will return two collections::

 (filtered):  [Dataset X]

 (discarded): [Dataset A]
              [Dataset B]

.. class:: warningmark

**Note** how the tool deals with the ``Z`` entry.

.. class:: infomark


This tool will create new history datasets from your collection but your quota usage will not increase.
    ]]></help>
</tool>