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Merge branch 'release_23.1' into release_23.2

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mvdbeek
2024-01-15 12:05:09 +01:00
parent 8ae1db1c9e 5ba634b08c
commit a2cb91487a
6 changed files with 127 additions and 6 deletions
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lib/galaxy/config/sample/datatypes_conf.xml.sample
+3
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@@ -216,6 +216,9 @@
<display file="igv/interval_as_bed.xml" inherit="true"/>
</datatype>
<datatype extension="jellyfish" type="galaxy.datatypes.binary:Binary" subclass="true" display_in_upload="true" description="Jellyfish database files are k-mer counts in binary format with a readable head. They are operated on and converted to human-readable text through jellyfish commands." />
<datatype extension="ktab" type="galaxy.datatypes.binary:Binary" subclass="true" description="A table of canonical k‑mers and their counts for the fastk toolkit." display_in_upload="true" description_url="https://github.com/thegenemyers/FASTK?tab=readme-ov-file#file-encodings"/>
<datatype extension="hist" type="galaxy.datatypes.binary:Binary" subclass="true" description="A binary histogram file of kmers and frequencies for the fastk toolkit." display_in_upload="true" description_url="https://github.com/thegenemyers/FASTK?tab=readme-ov-file#file-encodings"/>
<datatype extension="prof" type="galaxy.datatypes.binary:Binary" subclass="true" description="Read profile file for the fastk toolkit." display_in_upload="true" description_url="https://github.com/thegenemyers/FASTK?tab=readme-ov-file#file-encodings"/>
<!-- ISA data types -->
<datatype extension="isa-tab" type="galaxy.datatypes.isa:IsaTab" mimetype="application/isa-tools" display_in_upload="true" description="ISA-Tab data type." description_url="https://isa-tools.org"/>
lib/galaxy/config/sample/tool_conf.xml.sample
+1
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@@ -79,6 +79,7 @@
<tool file="filters/bed_to_bigbed.xml" />
</section>
<section id="filter" name="Filter and Sort">
<tool file="stats/filtering_1_1_0.xml" />
<tool file="stats/filtering.xml" />
<tool file="filters/sorter.xml" />
<tool file="filters/grep.xml" />
lib/galaxy/tool_util/toolbox/views/static.py
+1 -1
View File
@@ -105,7 +105,7 @@ class StaticToolPanelView(ToolPanelView):
f"Failed to find matching section for (id, name) = ({section_def.id}, {section_def.name})"
)
continue
section = closest_section.copy()
section = closest_section.copy(merge_tools=True)
if section_def.id is not None:
section.id = section_def.id
if section_def.name is not None:
lib/galaxy/workflow/modules.py
+6 -5
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@@ -126,6 +126,8 @@ class ConditionalStepWhen(BooleanToolParameter):
def to_cwl(value, hda_references, step):
element_identifier = None
if isinstance(value, model.HistoryDatasetCollectionAssociation):
value = value.collection
if isinstance(value, model.DatasetCollectionElement) and value.hda:
element_identifier = value.element_identifier
value = value.hda
@@ -155,14 +157,13 @@ def to_cwl(value, hda_references, step):
properties, value.dataset.created_from_basename or element_identifier or value.name
)
return properties
elif hasattr(value, "collection"):
collection = value.collection
if collection.collection_type == "list":
return [to_cwl(dce, hda_references=hda_references, step=step) for dce in collection.dataset_elements]
elif isinstance(value, model.DatasetCollection):
if value.collection_type == "list":
return [to_cwl(dce, hda_references=hda_references, step=step) for dce in value.dataset_elements]
else:
# Could be record or nested lists
rval = {}
for element in collection.elements:
for element in value.elements:
rval[element.element_identifier] = to_cwl(
element.element_object, hda_references=hda_references, step=step
)