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Add hint to the tool schema about runtime conditional changes #18996

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Nov 1, 2024
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Add hint to the tool schema about runtime conditional changes #18996

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7cda336
add a hint to tool schema
martenson Oct 15, 2024
c6ead00
run make config-revuild
martenson Oct 15, 2024
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5 changes: 1 addition & 4 deletions doc/source/admin/galaxy_options.rst
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Expand Up @@ -5124,7 +5124,7 @@
'deferred' are "materialized" (or undeferred) by the workflow
scheduler. This might be a lengthy process. Setting this to 'True'
will place the invocation back in the queue after materialization
before scheduling the workflow so it is less likely to starve
before scheduling the workflow so it is less likely to starve
other workflow scheduling. Ideally, Galaxy would allow more fine
grain control of handlers but until then, this provides a way to
tip the balance between "doing more work" and "being more fair".
Expand Down Expand Up @@ -5658,6 +5658,3 @@
to the user. Currently only affects s3fs file sources.
:Default: ``60``
:Type: int



5 changes: 2 additions & 3 deletions lib/galaxy/config/sample/galaxy.yml.sample
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Expand Up @@ -191,7 +191,7 @@ gravity:

# Routes file to monitor.
# Should be set to the same path as ``interactivetools_map`` in the ``galaxy:`` section. This is ignored if
# ``interactivetools_map is set.
# ``interactivetools_map is set``.
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galaxyproject/gravity#121

# sessions: database/interactivetools_map.sqlite

# Include verbose messages in gx-it-proxy
Expand Down Expand Up @@ -2752,7 +2752,7 @@ galaxy:
# 'deferred' are "materialized" (or undeferred) by the workflow
# scheduler. This might be a lengthy process. Setting this to 'True'
# will place the invocation back in the queue after materialization
# before scheduling the workflow so it is less likely to starve other
# before scheduling the workflow so it is less likely to starve other
# workflow scheduling. Ideally, Galaxy would allow more fine grain
# control of handlers but until then, this provides a way to tip the
# balance between "doing more work" and "being more fair". The default
Expand Down Expand Up @@ -3006,4 +3006,3 @@ galaxy:
# but outdated contents might be displayed to the user. Currently only
# affects s3fs file sources.
#file_source_listings_expiry_time: 60

4 changes: 3 additions & 1 deletion lib/galaxy/config/sample/tool_shed.yml.sample
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Expand Up @@ -54,6 +54,9 @@ tool_shed:
# options.
#whoosh_index_dir: database/toolshed_whoosh_indexes

# Cache directory for Pydantic model objects.
#model_cache_dir: database/model_cache

# For searching repositories at /api/repositories:
#repo_name_boost: 0.9

Expand Down Expand Up @@ -426,4 +429,3 @@ tool_shed:
# The value of this option will be resolved with respect to
# <config_dir>.
#datatypes_config_file: datatypes_conf.xml

16 changes: 9 additions & 7 deletions lib/galaxy/tool_util/xsd/galaxy.xsd
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Expand Up @@ -312,8 +312,6 @@ A generalisation for macro tokens, templates and xml macros, i.e.
`<macro name="an_xml_macro" type="xml">` is identical to `<xml name="an_xml_macro">`,
`<macro name="a_template" type="template">` is identical to `<template name="a_template">`, and
`<macro name="a_token" type="xml">` is identical to `<token name="a_token">`.

Note that
]]></xs:documentation>
</xs:annotation>
</xs:element>
Expand Down Expand Up @@ -3499,9 +3497,13 @@ Data source HTTP action (e.g. ``get`` or ``put``) to use.</xs:documentation>
<xs:annotation>
<xs:documentation xml:lang="en"><![CDATA[

This is a container for conditional parameters in the tool (must contain 'when'
tag sets) - the command line (or portions thereof) are then wrapped in an if-else
statement. A good example tool that demonstrates many conditional parameters is
This is a container for conditional parameters in the tool (must contain ``when``
tag sets) - the command line is then wrapped in an if-else statement.

Note that value of a conditional cannot be changed on the workflow run form.
If you expect users to interact with the element during runtime consider using ``sections`` instead.

An example tool that demonstrates conditional parameters is
[biom_convert.xml](https://github.com/galaxyproject/tools-iuc/blob/main/tools/biom_format/biom_convert.xml).

```xml
Expand Down Expand Up @@ -3608,7 +3610,7 @@ Referenced parameter to pass method.]]></xs:documentation>
<xs:annotation>
<xs:documentation xml:lang="en"><![CDATA[Infrequently used option to dynamically access Galaxy internals, this should be avoided.

Is referenced parameter is the same group.]]></xs:documentation>
Is referenced parameter in the same group.]]></xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="label" type="xs:string">
Expand Down Expand Up @@ -6286,7 +6288,7 @@ Therefore a filter for such a variable looks like the following example.
<xs:documentation xml:lang="en"><![CDATA[
A string `[reverse_][SORT_COMP_]SORTBY` describing the desired sort order of the collection elements.
`SORTBY` can be `filename`, `name`, `designation`, `dbkey` and the optional `SORT_COMP` can be either
`lexical` or `numeric`. Default is lexical sorting by filename.
`lexical` or `numeric`. Default is lexical sorting by filename.
Note that lexical sorting is case sensitive, i.e. upper case characters come before lower case characters (e.g. "Apple" < "Banana" < "apple" < "banana").
]]></xs:documentation>
</xs:annotation>
Expand Down
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