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Merge pull request #16885 from bernt-matthias/topic/dynamic-multiple

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Add test and doc showing how dynamic selects are used
This commit is contained in:
Marius van den Beek
2024-03-05 16:25:14 +01:00
committed by GitHub
parent fb30ddf12a 6c63958bea
commit eeb2d04c78
3 changed files with 85 additions and 3 deletions
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lib/galaxy/tool_util/xsd/galaxy.xsd
+5 -3
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@@ -4273,10 +4273,12 @@ Galaxy-aware URI for the default file for collection element.
<xs:complexType name="ParamOptions">
<xs:annotation>
<xs:documentation xml:lang="en"><![CDATA[
This tag set is optionally contained within the ``<param>`` tag when the
``type`` attribute value is ``select`` or ``data`` and used to dynamically
generated lists of options.
See [/tools/extract/liftOver_wrapper.xml](https://github.com/galaxyproject/galaxy/blob/dev/tools/extract/liftOver_wrapper.xml)
for an example of how to use this tag set. This tag set is optionally contained
within the ``<param>`` tag when the ``type`` attribute value is ``select`` or
``data`` and used to dynamically generated lists of options.
and [test/functional/tools/select_dynamic.xml](https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/select_dynamic.xml)
for an examples of how to use this tag set.
For data parameters this tag can be used to restrict possible input datasets to datasets that match the ``dbkey`` of another data input by including a ``data_meta`` filter. See for
instance here: [/tools/maf/interval2maf.xml](https://github.com/galaxyproject/galaxy/blob/dev/tools/maf/interval2maf.xml)
test/functional/tools/sample_tool_conf.xml
+1
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@@ -137,6 +137,7 @@
<tool file="column_param_list.xml" />
<tool file="column_multi_param.xml" />
<tool file="select_optional.xml"/>
<tool file="select_dynamic.xml"/>
<tool file="hidden_param.xml" />
<tool file="special_params.xml" />
<tool file="section.xml" />
test/functional/tools/select_dynamic.xml
+79
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@@ -0,0 +1,79 @@
<!-- test how dynamic selects are used in the command section -->
<tool id="select_dynamic" name="Dynamic select" version="1.0.0" profile="22.05">
<command><![CDATA[
echo "select $select" >> '$output1' &&
echo "select path $select.fields.path" >> '$output1' &&
## direct access to the select parameter gives a comma sepated list of the `value`s
echo "select_mult $select_mult" >> '$output1'
## looping over the select parameter gives the `value`s
#for i, o in enumerate($select_mult)
&& echo "select_mult $i $o" >> '$output1'
#end for
## acessing fields gives comma separated properties
## and in case nothing is selected empty string
&& echo "select_mult real_value $select_mult.fields.real_value" >> '$output1'
&& echo "select_mult dbkey $select_mult.fields.dbkey" >> '$output1'
&& echo "select_mult name $select_mult.fields.name" >> '$output1'
&& echo "select_mult path $select_mult.fields.path" >> '$output1'
&& echo "select_mult value $select_mult.fields.value" >> '$output1'
]]></command>
<inputs>
<param name="select" type="select" optional="true">
<options from_data_table="test_fasta_indexes">
</options>
</param>
<param name="select_mult" type="select" optional="true" multiple="true">
<options from_data_table="test_fasta_indexes">
<!-- all columns that should be accessible via the fields attribute need to be included
since the for loop should iterate over the paths column 3 is names value here
and the actual value column (0) is "renamed" to real_value -->
<column name="real_value" index="0"/>
<column name="dbkey" index="1"/>
<column name="name" index="2"/>
<column name="value" index="3"/>
<!-- same column can be accessible via multiple names-->
<column name="path" index="3"/>
</options>
</param>
</inputs>
<outputs>
<data name="output1" format="tabular" />
</outputs>
<tests>
<test>
<param name="select" value="hg19_name"/>
<param name="select_mult" value="hg19_name,hg18_name"/>
<output name="output1">
<assert_contents>
<has_line line="select hg19_value" />
<has_line line="select path hg19_path" />
<has_line line="select_mult hg19_path,hg18_path" />
<has_line line="select_mult 0 hg19_path" />
<has_line line="select_mult 1 hg18_path" />
<has_line line="select_mult real_value hg19_value,hg18_value" />
<has_line line="select_mult dbkey hg19,hg18" />
<has_line line="select_mult name hg19_name,hg18_name" />
<has_line line="select_mult path hg19_path,hg18_path" />
<has_line line="select_mult value hg19_path,hg18_path" />
<has_n_lines n="10"/>
</assert_contents>
</output>
</test>
<test>
<output name="output1">
<assert_contents>
<has_line line="select None" />
<has_line line="select path " />
<has_line line="select_mult None" />
<has_line line="select_mult real_value " />
<has_line line="select_mult dbkey " />
<has_line line="select_mult name " />
<has_line line="select_mult path " />
<has_line line="select_mult value " />
<has_n_lines n="8" />
</assert_contents>
</output>
</test>
</tests>
</tool>