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Add ImageDimPlot, ImageFeaturePlot to Seurat Visualize #7501

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4066582
add ImageDimPlot, ImageFeaturePlot
khaled196 Dec 2, 2025
a6f5d12
add ImageDimPlot, ImageFeaturePlot
khaled196 Dec 2, 2025
1bfc882
adjost lines
khaled196 Dec 2, 2025
52b93ce
adjost the parameters and fix the cinfig
khaled196 Dec 2, 2025
dbbac01
Merge branch 'galaxyproject:main' into seurat
khaled196 Dec 3, 2025
59fe0ca
update plot.xml
khaled196 Dec 3, 2025
2de8cc2
update plot.xml
khaled196 Dec 3, 2025
14900f6
Merge branch 'seurat' of https://github.com/bioinfbrad/tools-iuc into…
khaled196 Dec 3, 2025
1862960
update
khaled196 Dec 3, 2025
3eb93f4
adjost the mol_alpha location
khaled196 Dec 3, 2025
981b867
fix issues
khaled196 Dec 3, 2025
c10112c
fix indentations
khaled196 Dec 3, 2025
105a693
add help label
khaled196 Dec 3, 2025
c2a073d
add imagedimplot and imagefeatureplot
khaled196 Dec 3, 2025
8cecec4
fix conda hell
khaled196 Dec 3, 2025
6259b27
update seurate version, add creators and update test outptus
khaled196 Dec 4, 2025
1f3879b
fix errors
khaled196 Dec 9, 2025
90451a8
fix identation and add subset_logic
khaled196 Dec 9, 2025
6d295e2
fix tests
khaled196 Dec 9, 2025
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11 changes: 6 additions & 5 deletions tools/seurat/create_seurat.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
<expand macro="bio_tools"/>
<expand macro="requirements"/>
<expand macro="version_command"/>
<expand macro="creators"/>
<command detect_errors="exit_code"><![CDATA[
#if str($method.method) == 'CreateSeuratObject':
#if str($method.input_type.input_type) == 'mtx':
Expand Down Expand Up @@ -350,7 +351,7 @@ seurat_obj[['$method.col_name']]<-PercentageFeatureSet(
<has_text_matching expression="CreateSeuratObject"/>
</assert_contents>
</output>
<output name="rds_out" location="https://zenodo.org/records/13732784/files/rawdata.rds" ftype="rds"/>
<output name="rds_out" location="https://zenodo.org/records/17817806/files/rawdata.rds" ftype="rds"/>
</test>
<test expect_num_outputs="2">
<!-- test2: CreateSeuratObject from tabular -->
Expand All @@ -370,7 +371,7 @@ seurat_obj[['$method.col_name']]<-PercentageFeatureSet(
<has_text_matching expression="CreateSeuratObject"/>
</assert_contents>
</output>
<output name="rds_out" location="https://zenodo.org/records/13732784/files/rawdata2.rds" ftype="rds"/>
<output name="rds_out" location="https://zenodo.org/records/17817806/files/rawdata2.rds" ftype="rds"/>
</test>
<test expect_num_outputs="2">
<!-- test3: CreateSeuratObject with CITE-Seq -->
Expand All @@ -395,7 +396,7 @@ seurat_obj[['$method.col_name']]<-PercentageFeatureSet(
<has_text_matching expression="CreateSeuratObject"/>
</assert_contents>
</output>
<output name="rds_out" location="https://zenodo.org/records/13732784/files/citeseq.rds" ftype="rds"/>
<output name="rds_out" location="https://zenodo.org/records/17817806/files/citeseq.rds" ftype="rds" compare="sim_size"/>
</test>
<test expect_num_outputs="2">
<!-- test4: Add_QC_Metrics -->
Expand All @@ -417,7 +418,7 @@ seurat_obj[['$method.col_name']]<-PercentageFeatureSet(
<has_text_matching expression="percent.ribo"/>
</assert_contents>
</output>
<output name="rds_out" location="https://zenodo.org/records/13732784/files/ribodata.rds" ftype="rds"/>
<output name="rds_out" location="https://zenodo.org/records/17817806/files/ribodata.rds" ftype="rds"/>
</test>
<test expect_num_outputs="2">
<!-- test5: FilterCells -->
Expand All @@ -440,7 +441,7 @@ seurat_obj[['$method.col_name']]<-PercentageFeatureSet(
<has_text_matching expression="subset"/>
</assert_contents>
</output>
<output name="rds_out" location="https://zenodo.org/records/13732784/files/filtered.rds" ftype="rds"/>
<output name="rds_out" location="https://zenodo.org/records/17817806/files/filtered.rds" ftype="rds" compare="sim_size"/>
</test>
</tests>
<help><![CDATA[
Expand Down
117 changes: 100 additions & 17 deletions tools/seurat/inspect_and_manipulate.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
<expand macro="bio_tools"/>
<expand macro="requirements"/>
<expand macro="version_command"/>
<expand macro="creators"/>
<command detect_errors="exit_code"><![CDATA[
@CMD@
]]></command>
Expand Down Expand Up @@ -123,7 +124,51 @@
seurat_obj,
subset = $method.manipulate.grouping == '$method.manipulate.groups',
)


#else if $method.manipulate.manipulate == 'Subset_Logical'

colname_raw <- "$method.manipulate.column"
operator_code <- "$method.manipulate.operator"
value_str <- "$method.manipulate.value"

# Map operator codes to actual operators
operator_map <- c(
"gt" = ">",
"lt" = "<",
"gte" = ">=",
"lte" = "<=",
"eq" = "==",
"ne" = "!="
)
operator <- operator_map[operator_code]

# Wrap column name in backticks if it contains special characters
# Check for non-alphanumeric characters (except underscore and dot)
if (grepl("[^A-Za-z0-9_.]", colname_raw) || grepl("^[0-9]", colname_raw)) {
colname <- paste0("`", colname_raw, "`")
} else {
colname <- colname_raw
}

# Convert value to numeric if possible
value_num <- suppressWarnings(as.numeric(value_str))
if (!is.na(value_num)) {
value <- value_num
} else {
# If value is a string, wrap it in quotes
value <- paste0('"', value_str, '"')
}

# Build expression string
expr_text <- paste0(colname, " ", operator, " ", value)

# Parse and evaluate the expression
library(rlang)
expr <- rlang::parse_expr(expr_text)

# Subset Seurat object
seurat_obj <- subset(seurat_obj, subset = !!expr)

#else if $method.manipulate.manipulate == 'DietSeurat'

#if $method.manipulate.features
Expand Down Expand Up @@ -235,6 +280,7 @@
<option value="Merge">Merge Seurat Objects</option>
<option value="Subset_Ident">Subset by Ident</option>
<option value="Subset_Group">Subset by Group</option>
<option value="Subset_Logical">Subset Seurat Logic</option>
<option value="DietSeurat">Choose elements to keep with 'DietSeurat'</option>
<option value="AggregateExpression">Pseudobulk cells with 'AggregateExpression'</option>
<option value="DefaultAssay">Set default assay</option>
Expand Down Expand Up @@ -300,6 +346,20 @@
<param name="grouping" type="text" value="" label="Grouping to use to select cells" help="from the object metadata e.g. batch, donor"/>
<param name="groups" type="text" value="" label="Group to keep" help="enter a single category from the grouping"/>
</when>
<when value="Subset_Logical">
<param name="column" type="text" value="" label="Metadata column"
help="Column in Seurat object metadata to filter on (e.g. nCount_Spatial, percent.mt)"/>
<param name="operator" type="select" value="gt"
label="Operator" help="Logical operator for filtering">
<option value="gt">&gt; (greater than)</option>
<option value="lt">&lt; (less than)</option>
<option value="gte">&gt;= (greater than or equal)</option>
<option value="lte">&lt;= (less than or equal)</option>
<option value="eq">== (equal)</option>
<option value="ne">!= (not equal)</option>
</param>
<param name="value" type="text" value="" label="Value" help="Value to compare against"/>
</when>
<when value="DietSeurat">
<param argument="layers" type="text" value="counts" label="Layers to keep" help="comma-separated list">
<expand macro="valid_list"/>
Expand Down Expand Up @@ -356,7 +416,7 @@
<has_text_matching expression="seurat_obj"/>
</assert_contents>
</output>
<output name="inspect_general" location="https://zenodo.org/records/13732784/files/inspect.txt" ftype="txt">
<output name="inspect_general" location="https://zenodo.org/records/17817806/files/inspect.txt" ftype="txt">
<assert_contents>
<has_text_matching expression="An object of class Seurat"/>
</assert_contents>
Expand All @@ -379,7 +439,7 @@
<has_text_matching expression="Cells"/>
</assert_contents>
</output>
<output name="inspect_tabular" location="https://zenodo.org/records/13732784/files/inspect_cells.tabular" ftype="tabular">
<output name="inspect_tabular" location="https://zenodo.org/records/17817806/files/inspect_cells.tabular" ftype="tabular">
<assert_contents>
<has_n_columns n="1"/>
</assert_contents>
Expand All @@ -403,7 +463,7 @@
<has_text_matching expression="Features"/>
</assert_contents>
</output>
<output name="inspect_tabular" location="https://zenodo.org/records/13732784/files/inspect_features.tabular" ftype="tabular">
<output name="inspect_tabular" location="https://zenodo.org/records/17817806/files/inspect_features.tabular" ftype="tabular">
<assert_contents>
<has_n_columns n="1"/>
</assert_contents>
Expand All @@ -427,7 +487,7 @@
<has_text_matching expression="seurat_obj"/>
</assert_contents>
</output>
<output name="inspect_tabular" location="https://zenodo.org/records/13732784/files/inspect_metadata_group.tabular" ftype="tabular">
<output name="inspect_tabular" location="https://zenodo.org/records/17817806/files/inspect_metadata_group.tabular" ftype="tabular">
<assert_contents>
<has_n_columns n="1"/>
</assert_contents>
Expand All @@ -450,7 +510,7 @@
<has_text_matching expression="Idents"/>
</assert_contents>
</output>
<output name="inspect_tabular" location="https://zenodo.org/records/13732784/files/inspect_idents.tabular" ftype="tabular">
<output name="inspect_tabular" location="https://zenodo.org/records/17817806/files/inspect_idents.tabular" ftype="tabular">
<assert_contents>
<has_n_columns n="2"/>
</assert_contents>
Expand All @@ -473,15 +533,15 @@
<has_text_matching expression="seurat_obj"/>
</assert_contents>
</output>
<output name="inspect_tabular" location="https://zenodo.org/records/13732784/files/inspect_matrix.tabular" ftype="tabular">
<output name="inspect_tabular" location="https://zenodo.org/records/17817806/files/inspect_matrix.tabular" ftype="tabular">
<assert_contents>
<has_n_columns n="249"/>
</assert_contents>
</output>
</test>
<test expect_num_outputs="2">
<!-- test7: Change Idents-->
<param name="seurat_rds" location="https://zenodo.org/records/13732784/files/clusters.rds"/>
<param name="seurat_rds" location="https://zenodo.org/records/17817806/files/clusters.rds"/>
<conditional name="method">
<param name="method" value="Manipulate"/>
<conditional name="manipulate">
Expand All @@ -497,7 +557,7 @@
<has_text_matching expression="Idents"/>
</assert_contents>
</output>
<output name="rds_out" location="https://zenodo.org/records/13732784/files/changed_idents.rds" ftype="rds"/>
<output name="rds_out" location="https://zenodo.org/records/17817806/files/changed_idents.rds" ftype="rds" compare="sim_size"/>
</test>
<test expect_num_outputs="2">
<!-- test8: Rename Idents-->
Expand All @@ -524,7 +584,7 @@
<has_text_matching expression="Idents"/>
</assert_contents>
</output>
<output name="rds_out" location="https://zenodo.org/records/13732784/files/renamed_clusters.rds" ftype="rds"/>
<output name="rds_out" location="https://zenodo.org/records/17817806/files/renamed_clusters.rds" ftype="rds"/>
</test>
<test expect_num_outputs="2">
<!-- test9: Add Metadata-->
Expand All @@ -544,7 +604,7 @@
<has_text_matching expression="AddMetaData"/>
</assert_contents>
</output>
<output name="rds_out" location="https://zenodo.org/records/13732784/files/added_metadata.rds" ftype="rds"/>
<output name="rds_out" location="https://zenodo.org/records/17817806/files/added_metadata.rds" ftype="rds"/>
</test>
<test expect_num_outputs="2">
<!-- test10: Merge-->
Expand All @@ -564,7 +624,7 @@
<has_text_matching expression="merge"/>
</assert_contents>
</output>
<output name="rds_out" location="https://zenodo.org/records/13736785/files/merged.rds" ftype="rds"/>
<output name="rds_out" location="https://zenodo.org/records/17817806/files/merged.rds" ftype="rds"/>
</test>
<test expect_num_outputs="2">
<!-- test11: Subset Ident-->
Expand All @@ -584,7 +644,7 @@
<has_text_matching expression="subset"/>
</assert_contents>
</output>
<output name="rds_out" location="https://zenodo.org/records/13732784/files/subset_cluster.rds" ftype="rds"/>
<output name="rds_out" location="https://zenodo.org/records/17817806/files/subset_cluster.rds" ftype="rds"/>
</test>
<test expect_num_outputs="2">
<!-- test12: Subset Group-->
Expand All @@ -605,7 +665,7 @@
<has_text_matching expression="subset"/>
</assert_contents>
</output>
<output name="rds_out" location="https://zenodo.org/records/13732784/files/subset_Group_A.rds" ftype="rds"/>
<output name="rds_out" location="https://zenodo.org/records/17817806/files/subset_Group_A.rds" ftype="rds"/>
</test>
<test expect_num_outputs="2">
<!-- test13: DietSeurat-->
Expand All @@ -626,7 +686,7 @@
<has_text_matching expression="DietSeurat"/>
</assert_contents>
</output>
<output name="rds_out" location="https://zenodo.org/records/13732784/files/diet_seurat.rds" ftype="rds"/>
<output name="rds_out" location="https://zenodo.org/records/17817806/files/diet_seurat.rds" ftype="rds"/>
</test>
<test expect_num_outputs="2">
<!-- test14: AggregateExpression-->
Expand All @@ -646,7 +706,7 @@
<has_text_matching expression="AggregateExpression"/>
</assert_contents>
</output>
<output name="rds_out" location="https://zenodo.org/records/13732784/files/aggregated.rds" ftype="rds" compare="sim_size"/>
<output name="rds_out" location="https://zenodo.org/records/17817806/files/aggregated.rds" ftype="rds" compare="sim_size"/>
</test>
<test expect_num_outputs="2">
<!-- test15: Default Assay-->
Expand All @@ -666,7 +726,30 @@
<has_text_matching expression="DefaultAssay"/>
</assert_contents>
</output>
<output name="rds_out" location="https://zenodo.org/records/13732784/files/default.rds" ftype="rds"/>
<output name="rds_out" location="https://zenodo.org/records/17817806/files/default.rds" ftype="rds"/>
</test>
<test expect_num_outputs="2">
<!-- test16: Subset Logical -->
<param name="seurat_rds" location="https://zenodo.org/records/17817806/files/test_seurat_spatial.rds"/>
<conditional name="method">
<param name="method" value="Manipulate"/>
<conditional name="manipulate">
<param name="manipulate" value="Subset_Logical"/>
<!-- Split expression into column/operator/value -->
<param name="column" value="nCount_Spatial"/>
<param name="operator" value="gt"/>
<param name="value" value="0"/>
</conditional>
</conditional>
<section name="advanced_common">
<param name="show_log" value="true"/>
</section>
<output name="hidden_output">
<assert_contents>
<has_text_matching expression="subset"/>
</assert_contents>
</output>
<output name="rds_out" location="https://zenodo.org/records/17817806/files/test_seurat_spatial.rds" ftype="rds" compare="sim_size"/>
</test>
</tests>
<help><![CDATA[
Expand Down
11 changes: 6 additions & 5 deletions tools/seurat/integrate.xml
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
<expand macro="bio_tools"/>
<expand macro="requirements"/>
<expand macro="version_command"/>
<expand macro="creators"/>
<command detect_errors="exit_code"><![CDATA[
@CMD@
]]></command>
Expand Down Expand Up @@ -230,7 +231,7 @@
<has_text_matching expression="split"/>
</assert_contents>
</output>
<output name="rds_out" location="https://zenodo.org/records/13732784/files/splitdata.rds" ftype="rds"/>
<output name="rds_out" location="https://zenodo.org/records/17817806/files/splitdata.rds" ftype="rds"/>
</test>
<test expect_num_outputs="2">
<!-- test2: IntegrateLayers-->
Expand All @@ -251,7 +252,7 @@
<has_text_matching expression="IntegrateLayers"/>
</assert_contents>
</output>
<output name="rds_out" location="https://zenodo.org/records/13732784/files/cca_integrated.rds" ftype="rds"/>
<output name="rds_out" location="https://zenodo.org/records/17817806/files/cca_integrated.rds" ftype="rds"/>
</test>
<test expect_num_outputs="2">
<!-- test3: IntegrateLayers - Harmony Installed-->
Expand All @@ -272,7 +273,7 @@
<has_text_matching expression="IntegrateLayers"/>
</assert_contents>
</output>
<output name="rds_out" location="https://zenodo.org/records/13732784/files/harm_integrated.rds" ftype="rds" compare="sim_size"/>
<output name="rds_out" location="https://zenodo.org/records/17817806/files/harm_integrated.rds" ftype="rds" compare="sim_size"/>
</test>
<test expect_num_outputs="2">
<!-- test4: JoinLayers-->
Expand All @@ -288,7 +289,7 @@
<has_text_matching expression="JoinLayers"/>
</assert_contents>
</output>
<output name="rds_out" location="https://zenodo.org/records/13732784/files/joined.rds" ftype="rds"/>
<output name="rds_out" location="https://zenodo.org/records/17817806/files/joined.rds" ftype="rds"/>
</test>
<test expect_num_outputs="2">
<!-- test5: PrepSCTFindMarkers-->
Expand All @@ -304,7 +305,7 @@
<has_text_matching expression="PrepSCTFindMarkers"/>
</assert_contents>
</output>
<output name="rds_out" location="https://zenodo.org/records/13732784/files/PrepSCTFindMarkers.rds" ftype="rds"/>
<output name="rds_out" location="https://zenodo.org/records/17817806/files/PrepSCTFindMarkers.rds" ftype="rds"/>
</test>
</tests>
<help><![CDATA[
Expand Down
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