--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/inspect_and_manipulate.xml	Wed Sep 11 10:21:26 2024 +0000
@@ -0,0 +1,755 @@
+<tool id="seurat_data" name="Seurat Data Management" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>- Inspect and Manipulate </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+@CMD@
+    ]]></command>
+    <configfiles>
+        <configfile name="script_file"><![CDATA[
+@CMD_imports@
+@CMD_read_inputs@
+
+#if $method.method == 'Inspect'
+    #if $method.inspect.inspect == 'General'
+        sink('inspect.txt')
+        seurat_obj
+        sink()
+
+    #else if $method.inspect.inspect == 'Features'
+        inspect<-Features(seurat_obj[['$method.inspect.assay']])
+        row.names = FALSE
+        col.names = FALSE
+        @CMD_inspect_rds_outputs@
+
+    #else if $method.inspect.inspect == 'Cells'
+        inspect<-Cells(
+            seurat_obj,
+            #if $method.layer != ''
+            layer = $method.layer
+            #end if
+        )
+        row.names = FALSE
+        col.names = FALSE
+        @CMD_inspect_rds_outputs@
+
+    #else if $method.inspect.inspect == 'Idents'
+        inspect<-Idents(seurat_obj)
+        row.names = TRUE
+        col.names = FALSE
+        @CMD_inspect_rds_outputs@
+
+    #else if $method.inspect.inspect == 'Metadata'
+        #if $method.inspect.view_metadata != ''
+        inspect<-seurat_obj[['$method.inspect.view_metadata']]
+        #else
+        inspect<-seurat_obj[[]]
+        #end if
+        row.names = TRUE
+        col.names = TRUE
+        @CMD_inspect_rds_outputs@
+
+    #else if $method.inspect.inspect == 'Matrix'
+        inspect<-LayerData(
+            seurat_obj, 
+            assay='$method.inspect.assay', 
+            layer='$method.inspect.layer'
+            )
+        row.names = TRUE
+        col.names = TRUE
+        @CMD_inspect_rds_outputs@
+
+    #end if
+
+#else if $method.method == 'Manipulate'
+    #if $method.manipulate.manipulate == 'Change_Idents'
+        Idents(seurat_obj)<- '$method.manipulate.change'
+
+    #else if $method.manipulate.manipulate == 'Rename_Idents'
+        #if $method.manipulate.stash_idents.stash_idents == 'true'
+            seurat_obj[['$method.manipulate.stash_idents.old_ident']]<-Idents(seurat_obj)
+        #end if
+        #if $method.manipulate.rename.rename_all == 'true'
+            new_names = c(unlist(strsplit(gsub(" ", "", '$method.manipulate.rename.new_names'), ",")))
+            names(new_names)<-levels(seurat_obj)
+            seurat_obj<-RenameIdents(
+                seurat_obj,
+                new_names
+            )
+        #else if $method.manipulate.rename.rename_all == 'false'
+            seurat_obj<-RenameIdents(
+                seurat_obj,
+                '$method.manipulate.rename.old_name' = '$method.manipulate.rename.new_name'
+            )
+        #end if
+
+    #else if $method.manipulate.manipulate == 'Add_Metadata'
+        meta_data<-read.table(
+            "$method.manipulate.metadata",
+            header = TRUE,
+            row.names = 1,
+            sep = "\t"
+        )
+        seurat_obj<-AddMetaData(
+            seurat_obj,
+            metadata = meta_data,
+        )
+
+    #else if $method.manipulate.manipulate == 'Merge'
+        y = list()
+        #for $file in $method.manipulate.add_seurat
+            y<-append(y, readRDS('${file}'))
+        #end for
+        seurat_obj<-merge(x = seurat_obj, y)
+
+        #if $method.manipulate.join.join == 'true'
+            seurat_obj[['$method.manipulate.join.assay']]<-JoinLayers(
+                seurat_obj[['$method.manipulate.join.assay']]
+            )
+        #end if
+
+    #else if $method.manipulate.manipulate == 'Subset_Ident'
+        seurat_obj<-subset(
+            seurat_obj,
+            idents = c(unlist(strsplit(gsub(" ", "", '$method.manipulate.idents'), ","))),
+         )
+
+    #else if $method.manipulate.manipulate == 'Subset_Group'
+        seurat_obj<-subset(
+            seurat_obj,
+            subset = $method.manipulate.grouping == '$method.manipulate.groups',
+        )
+
+    #else if $method.manipulate.manipulate == 'DietSeurat'
+
+        #if $method.manipulate.features
+        features_list<-paste(readLines('$method.manipulate.features'), collapse=",")
+        #end if
+
+        seurat_obj<-DietSeurat(
+            seurat_obj,
+            #if $method.manipulate.layers != ''
+            layers = c(unlist(strsplit(gsub(" ", "", '$method.manipulate.layers'), ","))),
+            #else if $method.manipulate.features
+            features = c(unlist(strsplit(features_list, ","))),
+            #else if $method.manipulate.assays != ''
+            assays = c(unlist(strsplit(gsub(" ", "", '$method.manipulate.assays'), ","))),
+            #else if $method.manipulate.dimreducs != ''
+            dimreducs = c(unlist(strsplit(gsub(" ", "", '$method.manipulate.dimreducs'), ","))),
+            #else if $method.manipulate.graphs != ''
+            graphs = c(unlist(strsplit(gsub(" ", "", '$method.manipulate.graphs'), ","))),
+            #else if $method.manipulate.features != ''
+            misc = $method.manipulate.misc
+            #end if
+        )
+
+    #else if $method.manipulate.manipulate == 'AggregateExpression'
+
+        #if $method.manipulate.features
+        features_list<-paste(readLines('$method.manipulate.features'), collapse=",")
+        #end if
+
+        seurat_obj<-AggregateExpression(
+            seurat_obj,
+            group.by = c(unlist(strsplit(gsub(" ", "", '$method.manipulate.group_by'), ","))),
+            #if $method.assays != ''
+            assays = c(unlist(strsplit(gsub(" ", "", '$method.manipulate.assays'), ","))),
+            #end if
+            #if $method.manipulate.features
+            features = c(unlist(strsplit(features_list, ","))),
+            #end if
+            normalization.method = '$method.manipulate.normalization_method.normalization_method',
+            #if $method.manipulate.normalization_method.normalization_method == 'CLR'
+            margin = $method.manipulate.normalization_method.margin,
+            #end if
+            scale.factor = $method.manipulate.scale_factor,
+            #if $method.manipulate.block_size
+            block.size = $method.manipulate.block_size,
+            #end if
+            return.seurat = TRUE
+        )
+
+    #else if $method.manipulate.manipulate == 'DefaultAssay'
+        DefaultAssay(object = seurat_obj)<-'$method.manipulate.default_assay'
+
+    #end if
+
+#end if
+
+@CMD_rds_write_outputs@
+
+]]></configfile>
+    </configfiles>
+    <inputs>
+        <expand macro="input_rds"/>
+        <conditional name="method">
+            <param name="method" type="select" label="Method used">
+                <option value="Inspect">Inspect Seurat Object</option>
+                <option value="Manipulate">Manipulate Seurat Object</option>
+            </param>
+            <when value="Inspect">
+                <conditional name="inspect">
+                    <param name="inspect" type="select" label="Display information about">
+                        <option value="General">General</option>
+                        <option value="Features">Features</option>
+                        <option value="Cells">Cells</option>
+                        <option value="Idents">Cell Identities</option>
+                        <option value="Metadata">Cell Metadata</option>
+                        <option value="Matrix">Matrix</option>
+                    </param>
+                    <when value="General">
+                    </when>
+                    <when value="Features">
+                        <param name="assay" type="text" value="RNA" label="Assay to display features for">
+                            <expand macro="valid_name"/>
+                        </param>
+                    </when>
+                    <when value="Cells">
+                        <expand macro="select_layer"/>
+                    </when>
+                    <when value="Idents">
+                    </when>
+                    <when value="Metadata">
+                        <param name="view_metadata" type="text" optional="true" value="" label="Metadata to view" help="leave blank to view all metadata"/>
+                    </when>
+                    <when value="Matrix">
+                        <param name="assay" type="text" value="RNA" label="Assay to display matrix for">
+                            <expand macro="valid_name"/>
+                        </param>
+                        <param name="layer" type="text" value="data" label="Layer to display matrix for">
+                            <expand macro="valid_name"/>
+                        </param>
+                    </when>
+                </conditional>
+            </when>
+            <when value="Manipulate">
+                <conditional name="manipulate">
+                    <param name="manipulate" type="select" label="Manipulation to perform">
+                        <option value="Change_Idents">Change annotation used as idents</option>
+                        <option value="Rename_Idents">Rename idents</option>
+                        <option value="Add_Metadata">Add metadata</option>
+                        <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="DietSeurat">Choose elements to keep with 'DietSeurat'</option>
+                        <option value="AggregateExpression">Pseudobulk cells with 'AggregateExpression'</option>
+                        <option value="DefaultAssay">Set default assay</option>
+                    </param>
+                    <when value="Change_Idents">
+                        <param name="change" type="text" value="" label="New annotation to use as ident"/>
+                    </when>
+                    <when value="Rename_Idents">
+                        <conditional name="rename">
+                            <param name="rename_all" type="select" label="Rename all idents">
+                                <option value="true" selected="true">Yes</option>
+                                <option value="false">No - just rename one ident</option>
+                            </param>
+                            <when value="true">
+                                <param name="new_names" type="text" value="" label="New names" help="comma-separated list, must be same as number of idents">
+                                    <expand macro="valid_list"/>
+                                </param>
+                            </when>
+                            <when value="false">
+                                <param name="old_name" type="text" value="" label="Name of ident to change"/>
+                                <param name="new_name" type="text" value="" label="New name for ident">
+                                    <expand macro="valid_name"/>
+                                </param>
+                            </when>
+                        </conditional>
+                        <conditional name="stash_idents">
+                            <param name="stash_idents" type="select" label="Save copy of old idents first">
+                                <option value="false" selected="true">No</option>
+                                <option value="true">Yes</option>
+                            </param>
+                            <when value="false">
+                            </when>
+                            <when value="true">
+                                <param name="old_ident" type="text" value="old.ident" label="Name to store old idents under"/>
+                            </when>
+                        </conditional>
+                    </when>
+                    <when value="Add_Metadata">
+                        <param name="metadata" type="data" format="tabular,tsv" label="Cell metadata to add" help="table with cell names in first column"/>
+                    </when>
+                    <when value="Merge">
+                        <param name="add_seurat" type="data" format="rds" multiple="true" label="Seurat object to merge"/>
+                        <conditional name="join">
+                            <param name="join" type="select" label="Join layers after merging">
+                                <option value="false" selected="true">No</option>
+                                <option value="true">Yes</option>
+                            </param>
+                            <when value="false">
+                            </when>
+                            <when value="true">
+                                <param argument="assay" type="text" value="RNA" label="Name of assay to join">
+                                    <expand macro="valid_name"/>
+                                </param>
+                            </when>
+                        </conditional>
+                    </when>
+                    <when value="Subset_Ident">
+                        <param name="idents" type="text" value="" label="Idents to keep" help="comma-separated list of clusters or idents">
+                            <expand macro="valid_list"/>
+                        </param>
+                    </when>
+                    <when value="Subset_Group">
+                        <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="DietSeurat">
+                        <param argument="layers" type="text" value="counts" label="Layers to keep" help="comma-separated list">
+                            <expand macro="valid_list"/>
+                        </param>
+                        <param argument="assays" type="text" value="RNA" label="Assays to keep" help="comma-separated list">
+                            <expand macro="valid_list"/>
+                        </param>
+                        <param argument="features" type="data" format="txt,tabular" optional="true" label="List of features to keep" help="text file with one feature on each line, leave blank to keep all"/>
+                        <param argument="dimreducs" type="text" optional="true" value="" label="Dimensional Reductions to keep" help="comma-separated list, leave blank to remove all">
+                            <expand macro="valid_list"/>
+                        </param>
+                        <param argument="graphs" type="text" optional="true" value="" label="Graphs to keep" help="comma-separated list, leave blank to remove all">
+                            <expand macro="valid_list"/>
+                        </param>
+                        <param argument="misc" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Keep misc slot"/>
+                    </when>
+                    <when value="AggregateExpression">
+                        <param name="group_by" type="text" value="ident" label="Aggregate expression for these categories" help="comma-separated list of group/condition names (group.by)"/>
+                        <param argument="assays" type="text" optional="true" value="" label="Assays to use" help="comma-separated list, leave blank to use all assays">
+                            <expand macro="valid_list"/>
+                        </param>
+                        <param argument="features" type="data" format="txt,tabular" optional="true" label="Features to use" help="text file with one feature on each line, leave blank to use all features"/>
+                        <expand macro="normalize"/>
+                    </when>
+                    <when value="DefaultAssay">
+                        <param name="default_assay" type="text" value="RNA" label="Assay to use as default">
+                            <expand macro="valid_name"/>
+                        </param>
+                    </when>
+                </conditional>
+            </when>
+        </conditional>
+        <expand macro="inputs_common_advanced"/>
+    </inputs>
+    <outputs>
+        <expand macro="seurat_outputs"/>
+        <expand macro="inspect_out"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <!-- test1:  Inspect General-->
+            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/integrated_umap.rds"/>
+            <conditional name="method">
+                <param name="method" value="Inspect"/>
+                <conditional name="inspect">
+                    <param name="inspect" value="General"/>
+                </conditional>
+            </conditional>
+            <section name="advanced_common">
+                <param name="show_log" value="true"/>
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="seurat_obj"/>
+                </assert_contents>
+            </output>
+            <output name="inspect_general" location="https://zenodo.org/records/13732784/files/inspect.txt" ftype="txt">
+                <assert_contents>
+                    <has_text_matching expression="An object of class Seurat"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="2">
+            <!-- test2:  Inspect Cells-->
+            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/rawdata.rds"/>
+            <conditional name="method">
+                <param name="method" value="Inspect"/>
+                <conditional name="inspect">
+                    <param name="inspect" value="Cells"/>
+                </conditional>
+            </conditional>
+            <section name="advanced_common">
+                <param name="show_log" value="true"/>
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="Cells"/>
+                </assert_contents>
+            </output>
+            <output name="inspect_tabular" location="https://zenodo.org/records/13732784/files/inspect_cells.tabular" ftype="tabular">
+                <assert_contents>
+                    <has_n_columns n="1"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="2">
+            <!-- test3:  Inspect Features-->
+            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/citeseq.rds"/>
+            <conditional name="method">
+                <param name="method" value="Inspect"/>
+                <conditional name="inspect">
+                    <param name="inspect" value="Features"/>
+                    <param name="assay" value="ADT"/>
+                </conditional>
+            </conditional>
+            <section name="advanced_common">
+                <param name="show_log" value="true"/>
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="Features"/>
+                </assert_contents>
+            </output>
+            <output name="inspect_tabular" location="https://zenodo.org/records/13732784/files/inspect_features.tabular" ftype="tabular">
+                <assert_contents>
+                    <has_n_columns n="1"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="2">
+            <!-- test4:  Inspect Metadata-->
+            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/added_metadata.rds"/>
+            <conditional name="method">
+                <param name="method" value="Inspect"/>
+                <conditional name="inspect">
+                    <param name="inspect" value="Metadata"/>
+                    <param name="view_metadata" value="Group"/>
+                </conditional>
+            </conditional>
+            <section name="advanced_common">
+                <param name="show_log" value="true"/>
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <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">
+                <assert_contents>
+                    <has_n_columns n="1"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="2">
+            <!-- test5:  Inspect Idents-->
+            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/renamed_clusters.rds"/>
+            <conditional name="method">
+                <param name="method" value="Inspect"/>
+                <conditional name="inspect">
+                    <param name="inspect" value="Idents"/>
+                </conditional>
+            </conditional>
+            <section name="advanced_common">
+                <param name="show_log" value="true"/>
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="Idents"/>
+                </assert_contents>
+            </output>
+            <output name="inspect_tabular" location="https://zenodo.org/records/13732784/files/inspect_idents.tabular" ftype="tabular">
+                <assert_contents>
+                    <has_n_columns n="2"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="2">
+            <!-- test6:  Inspect Matrix-->
+            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/clusters.rds"/>
+            <conditional name="method">
+                <param name="method" value="Inspect"/>
+                <conditional name="inspect">
+                    <param name="inspect" value="Matrix"/>
+                </conditional>
+            </conditional>
+            <section name="advanced_common">
+                <param name="show_log" value="true"/>
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <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">
+                <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"/>
+            <conditional name="method">
+                <param name="method" value="Manipulate"/>
+                <conditional name="manipulate">
+                    <param name="manipulate" value="Change_Idents"/>
+                    <param name="change" value="orig.idents"/>
+                </conditional>
+            </conditional>
+            <section name="advanced_common">
+                <param name="show_log" value="true"/>
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="Idents"/>
+                </assert_contents>
+            </output>
+            <output name="rds_out" location="https://zenodo.org/records/13732784/files/changed_idents.rds" ftype="rds"/>
+        </test>
+        <test expect_num_outputs="2">
+            <!-- test8:  Rename Idents-->
+            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/clusters.rds"/>
+            <conditional name="method">
+                <param name="method" value="Manipulate"/>
+                <conditional name="manipulate">
+                    <param name="manipulate" value="Rename_Idents"/>
+                    <conditional name="rename">
+                        <param name="rename_all" value="true"/>
+                        <param name="new_names" value="Cell A, Cell B, Cell C, Cell D"/>
+                    </conditional>
+                    <conditional name="stash_idents">
+                        <param name="stash_idents" value="true"/>
+                        <param name="old_ident" value="renamed"/>
+                    </conditional>
+                </conditional>
+            </conditional>
+            <section name="advanced_common">
+                <param name="show_log" value="true"/>
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="Idents"/>
+                </assert_contents>
+            </output>
+            <output name="rds_out" location="https://zenodo.org/records/13732784/files/renamed_clusters.rds" ftype="rds"/>
+        </test>
+        <test expect_num_outputs="2">
+            <!-- test9:  Add Metadata-->
+            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/rawdata.rds"/>
+            <conditional name="method">
+                <param name="method" value="Manipulate"/>
+                <conditional name="manipulate">
+                    <param name="manipulate" value="Add_Metadata"/>
+                    <param name="metadata" location="https://zenodo.org/records/13732784/files/metadata.tsv"/>
+                </conditional>
+            </conditional>
+            <section name="advanced_common">
+                <param name="show_log" value="true"/>
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="AddMetaData"/>
+                </assert_contents>
+            </output>
+            <output name="rds_out" location="https://zenodo.org/records/13732784/files/added_metadata.rds" ftype="rds"/>
+        </test>
+        <test expect_num_outputs="2">
+            <!-- test10:  Merge-->
+            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/subset_Group_A.rds"/>
+            <conditional name="method">
+                <param name="method" value="Manipulate"/>
+                <conditional name="manipulate">
+                    <param name="manipulate" value="Merge"/>
+                    <param name="add_seurat" location="https://zenodo.org/records/13732784/files/subset_B16.rds,https://zenodo.org/records/13732784/files/subset_B8.rds"/>
+                </conditional>
+            </conditional>
+            <section name="advanced_common">
+                <param name="show_log" value="true"/>
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="merge"/>
+                </assert_contents>
+            </output>
+            <output name="rds_out" location="https://zenodo.org/records/13736785/files/merged.rds" ftype="rds"/>
+        </test>
+        <test expect_num_outputs="2">
+            <!-- test11:  Subset Ident-->
+            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/clusters.rds"/>
+            <conditional name="method">
+                <param name="method" value="Manipulate"/>
+                <conditional name="manipulate">
+                    <param name="manipulate" value="Subset_Ident"/>
+                    <param name="idents" value="2, 3"/>
+                </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/13732784/files/subset_cluster.rds" ftype="rds"/>
+        </test>
+        <test expect_num_outputs="2">
+            <!-- test12:  Subset Group-->
+            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/added_metadata.rds"/>
+            <conditional name="method">
+                <param name="method" value="Manipulate"/>
+                <conditional name="manipulate">
+                    <param name="manipulate" value="Subset_Group"/>
+                    <param name="grouping" value="Group"/>
+                    <param name="groups" value="Group_A"/>
+                </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/13732784/files/subset_Group_A.rds" ftype="rds"/>
+        </test>
+        <test expect_num_outputs="2">
+            <!-- test13:  DietSeurat-->
+            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/integrated_umap.rds"/>
+            <conditional name="method">
+                <param name="method" value="Manipulate"/>
+                <conditional name="manipulate">
+                    <param name="manipulate" value="DietSeurat"/>
+                    <param name="assays" value="ADT"/>
+                    <param name="dimreducs" value="pca, umap"/>
+                </conditional>
+            </conditional>
+            <section name="advanced_common">
+                <param name="show_log" value="true"/>
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="DietSeurat"/>
+                </assert_contents>
+            </output>
+            <output name="rds_out" location="https://zenodo.org/records/13732784/files/diet_seurat.rds" ftype="rds"/>
+        </test>
+        <test expect_num_outputs="2">
+            <!-- test14:  AggregateExpression-->
+            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/integrated_umap.rds"/>
+            <conditional name="method">
+                <param name="method" value="Manipulate"/>
+                <conditional name="manipulate">
+                    <param name="manipulate" value="AggregateExpression"/>
+                    <param name="group_by" value="Group"/>
+                </conditional>
+            </conditional>
+            <section name="advanced_common">
+                <param name="show_log" value="true"/>
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <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"/>
+        </test>
+        <test expect_num_outputs="2">
+            <!-- test15:  Default Assay-->
+            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/citeseq.rds"/>
+            <conditional name="method">
+                <param name="method" value="Manipulate"/>
+                <conditional name="manipulate">
+                    <param name="manipulate" value="DefaultAssay"/>
+                    <param name="default_assay" value="ADT"/>
+                </conditional>
+            </conditional>
+            <section name="advanced_common">
+                <param name="show_log" value="true"/>
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="DefaultAssay"/>
+                </assert_contents>
+            </output>
+            <output name="rds_out" location="https://zenodo.org/records/13732784/files/default.rds" ftype="rds"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Seurat
+======
+
+Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. 
+
+Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data.
+
+Inspect and Manipulate
+======================
+
+A selection of essential functions to display information about a Seurat Object or make basic changes to the object.
+
+More details on these essential commands can be found in the `seurat documentation
+<https://satijalab.org/seurat/articles/essential_commands>`__
+
+Inspect
+=======
+
+General - basic information about the Seurat Object
+Features - list of features, select which assay to display features from if object contains multimodal data
+Cells - list of cell barcodes/ids, select layer to display cells for if object contains multiple layers
+Idents - list showing Ident for each cell
+Metadata - table of cell metadata
+Matrix - show the full matrix
+
+Manipulate
+==========
+
+Functions to add, change, or remove selected elements of a Seurat Object.
+
+Change Idents
+=============
+
+Change which annotation in your cell metadata is used as the Ident column.
+
+Rename Idents
+=============
+
+Rename the classes in the Ident column (e.g. to replace cluster numbers with cell types).
+
+You have the option to stash the original idents in a new column called 'old.ident' before renaming the classes in the Ident column.
+
+AddMetaData
+===========
+
+Merge
+=====
+
+Combine two Seurat Objects into a single Seurat Object. 
+Each object will be placed in a separate layer, but you can choose to run the JoinLayers function after merging to combine the objects into a single layer.
+
+Subset
+======
+
+Subset a group of cells based on their ident or another grouping in your cell metadata.
+
+DietSeurat
+==========
+
+Keep only certain aspects of the Seurat object. 
+Can be useful in functions that utilize merge as it reduces the amount of data in the merge
+
+More details on these essential commands can be found in the `seurat documentation
+<https://satijalab.org/seurat/reference/dietseurat>`__
+
+AggregateExpression
+===================
+
+Returns summed counts ("pseudobulk") for each identity class. 
+
+More details on the `seurat documentation
+<https://satijalab.org/seurat/reference/aggregateexpression>`__
+
+
+DefaultAssay
+============
+
+Set the default assay for multimodal data. 
+
+You can use the Inspect - General function to check which assay is currently active and which other assays are available.
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>