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data_meta: add docs and test
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M Bernt
@@ -3677,6 +3677,23 @@ is the ``none`` preset.</xs:documentation>
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``<options>`` tag set - modify (e.g. remove, add, sort, ...) the list of values obtained from a locally stored file (e.g.
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a tool data table) or a dataset in the current history.
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Currently the following filters are defined:
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* ``static_value`` filter options for which the entry in a given ``column`` of the referenced file based on equality to the ``value`` attribute of the filter.
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* ``regexp`` similar to the ``static_value`` filter, but checks if the regular expression given by ``value`` matches the entry.
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* ``param_value`` filter options for which the entry in a given ``column`` of the referenced file based on properties of another input parameter specified by ``ref``. This property is by default the value of the parameter, but also the values of another attribute (``ref_attribute``) of the parameter can be used, e.g. the extension of a data input.
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* ``data_meta`` populate or filter options based on the metadata of another input parameter specified by ``ref``. If a ``column`` is given options are filtered for which the entry in this column ``column`` is equal to metadata of the input parameter specified by ``ref``.
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If no ``column`` is given the metadata value of the referenced input is added to the options list (in this case the corresponding ``options`` tag must not have the ``from_data_table`` or ``from_dataset`` attributes).
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In both cases the desired metadata is selected by ``key``.
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The ``static_value`` and ``regexp`` filters can be inverted by setting ``keep`` to true.
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* ``add_value``: add an option with a given ``name`` and ``value`` to the options. By default the new option is appended, with ``index`` the insertion position can be specified.
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* ``remove_value``: remove a value from the options. Either specified explicitly with ``value``, the value of another input specifified with ``ref``, or the metatdata ``key`` of another input ``meta_ref``.
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* ``unique_value``: remove options that have duplicate entries in the given ``column``.
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* ``sort_by``: sort options by the entries of a given ``column``.
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* ``multiple_splitter``: split the entries of the specified ``column``(s) in the referenced file using a ``separator``. Thereby the number of columns is increased.
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### Examples
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The following example from Mothur's
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@@ -3777,28 +3794,8 @@ demonstrates splitting up strings into multiple values.
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<xs:attribute name="type" type="FilterType" use="required">
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<xs:annotation>
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<xs:documentation xml:lang="en"><
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in the ``filter_types`` dictionary.
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Currently the filters in the ``filter_types`` dictionary in the module
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[/lib/galaxy/tools/parameters/dynamic_options.py](https://github.com/galaxyproject/galaxy/blob/master/lib/galaxy/tools/parameters/dynamic_options.py) are defined.
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Deprecated filter types:
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@@ -1,5 +1,5 @@
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<tool id="dbkey_filter_collection_input" name="dbkey_filter_multi_input" version="0.1.0">
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<description>Filter select on dbkey of multiple inputs</description>
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<tool id="dbkey_filter_collection_input" name="dbkey_filter_collection_input" version="0.1.0">
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<description>Filter select on dbkey of collection inputs</description>
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<command><![CDATA[
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#for $input in $inputs#
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cat $input >> $output;
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@@ -15,6 +15,12 @@
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<validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
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</options>
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</param>
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<param name="index_multi" type="select" multiple="true" label="Using reference genome">
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<options from_data_table="test_fasta_indexes">
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<filter type="data_meta" ref="inputs" key="dbkey" column="1" />
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<validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
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</options>
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</param>
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</inputs>
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<outputs>
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@@ -22,47 +28,66 @@
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</outputs>
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<tests>
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<!-- note: in the following tests two different files are needed
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because otherwise only the later dbkey is uses. apparently
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the two data sets would be considered as the same data set -->
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<!-- can choose a dbkey if it matches input -->
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<test>
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<param name="inputs" >
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<collection type="paired">
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<collection type="list">
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<element name="e1" value="simple_line.txt" dbkey="hg19"/>
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<element name="e2" value="simple_line.txt" dbkey="hg19"/>
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<element name="e2" value="same_simple_line.txt" dbkey="hg19"/>
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</collection>
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</param>
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<param name="index" value="hg19" />
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<param name="index_multi" value="hg19" />
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<output name="output" file="simple_line_x2.txt"/>
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</test>
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<!-- can choose any dbkey if none specified in reference -->
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<test>
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<param name="inputs" >
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<collection type="paired">
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<collection type="list">
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<element name="e1" value="simple_line.txt"/>
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<element name="e2" value="simple_line.txt"/>
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<element name="e2" value="same_simple_line.txt"/>
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</collection>
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</param>
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<param name="index" value="hg19" />
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<param name="index_multi" value="hg18,hg19" />
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<output name="output" file="simple_line_x2.txt"/>
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</test>
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<!-- can choose any dbkey specified in reference -->
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<test>
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<param name="inputs" >
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<collection type="paired">
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<element name="e1" value="simple_line.txt" dbkey="hg18"/>
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<element name="e2" value="simple_line.txt" dbkey="hg19"/>
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<collection type="list">
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<element name="e1" value="simple_line.txt" dbkey="hg19"/>
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<element name="e2" value="same_simple_line.txt" dbkey="hg18"/>
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</collection>
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</param>
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<param name="index" value="hg18" />
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<param name="index_multi" value="hg18,hg19" />
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<output name="output" file="simple_line_x2.txt"/>
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</test>
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<test>
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<param name="inputs" >
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<collection type="paired">
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<element name="e1" value="simple_line.txt" dbkey="hg18"/>
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<element name="e2" value="simple_line.txt" dbkey="hg19"/>
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<collection type="list">
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<element name="e1" value="simple_line.txt" dbkey="hg19"/>
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<element name="e2" value="same_simple_line.txt" dbkey="hg18"/>
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</collection>
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</param>
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<param name="index" value="hg19" />
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<param name="index_multi" value="hg18,hg19" />
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<output name="output" file="simple_line_x2.txt"/>
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</test>
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<!-- cant choose a dkkey different from reference -->
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<test expect_failure="true">
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<param name="inputs" >
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<collection type="list">
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<element name="e1" value="simple_line.txt" dbkey="hg19"/>
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<element name="e2" value="same_simple_line.txt" dbkey="hg19"/>
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</collection>
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</param>
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<param name="index" value="hg18" />
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<param name="index_multi" value="hg18" />
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<output name="output" file="simple_line_x2.txt"/>
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</test>
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</tests>
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@@ -46,6 +46,7 @@
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<tool file="filter_static_regexp.xml" />
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<tool file="dbkey_filter_input.xml" />
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<tool file="dbkey_filter_multi_input.xml" />
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<tool file="dbkey_filter_collection.xml" />
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<tool file="dbkey_output_action.xml" />
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<tool file="composite_output.xml" />
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<tool file="composite_output_tests.xml" />
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