Mercurial > repos > iuc > seurat_data

--- /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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Sep 11 10:21:26 2024 +0000
@@ -0,0 +1,437 @@
+<macros>
+    <token name="@TOOL_VERSION@">5.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">23.0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">r-seurat</requirement>
+            <requirement type="package" version="1.2.1">fit-sne</requirement>
+            <requirement type="package" version="3.58.1">bioconductor-limma</requirement>
+            <requirement type="package" version="1.28.0">bioconductor-mast</requirement>
+            <requirement type="package" version="1.42.0">bioconductor-deseq2</requirement>
+            <requirement type="package" version="2.1.3">r-svglite</requirement>
+            <requirement type="package" version="1.1">r-metap</requirement>
+            <requirement type="package" version="1.14.0">bioconductor-glmGamPoi</requirement>
+            <requirement type="package" version="0.5.3">umap-learn</requirement> <!-- https://github.com/satijalab/seurat/issues/8283 -->
+            <requirement type="package" version="0.10.2">leidenalg</requirement>
+            <requirement type="package" version="1.2.0">r-harmony</requirement>
+            <requirement type="package" version="1.18.0">bioconductor-batchelor</requirement>
+            <requirement type="package" version="2.0.0">numpy</requirement>
+            <requirement type="package" version="2.2.2">pandas</requirement>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1038/s41587-023-01767-y</citation>
+        </citations>
+    </xml>
+    <xml name="sanitize_query" token_validinitial="string.printable">
+        <sanitizer>
+            <valid initial="@VALIDINITIAL@">
+                <remove value="&apos;" />
+            </valid>
+       </sanitizer>
+    </xml>
+    <xml name="sanitize_vectors" token_validinitial="string.digits">
+        <sanitizer>
+            <valid initial="@VALIDINITIAL@">
+                <add value=","/>
+            </valid>
+        </sanitizer>
+    </xml>
+    <xml name="version_command">
+        <version_command><![CDATA[
+echo $(R --version | grep version | grep -v GNU)", Seurat version" $(R --vanilla --slave -e "library(Seurat); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
+        ]]></version_command>
+    </xml>
+
+    <token name="@CMD_imports@"><![CDATA[
+library(Seurat)
+    ]]>
+    </token>
+    <token name="@reticulate_hack@"><![CDATA[
+library(reticulate)
+## HACK: CI biocontainers do not contain a useable conda binary, just the env.
+##  see: https://github.com/galaxyproject/tools-iuc/issues/5585#issuecomment-1803773923
+is_biocontainer = grepl("^# cmd: /opt/conda/bin/",
+                        paste0(reticulate:::python_info_condaenv_find("/usr/local/"),
+                               "-none"))
+if (is_biocontainer) {
+   ## conda detection false positive
+   assignInNamespace("is_conda_python", function(x) FALSE, ns="reticulate")
+   use_python("/usr/local/bin/python")
+} else {
+   conda_path = Sys.getenv("CONDA_PREFIX")
+   if (conda_path != "") {
+      ## Active conda env found
+      use_python(file.path(conda_path, "bin", "python3"))
+   } else {
+      ## Not biocontainer or conda, assume system python
+      use_python("/usr/bin/python3")
+   }
+}]]>
+    </token>
+    <xml name="input_rds">
+        <param name="seurat_rds" type="data" format="rds" label="Input file with the Seurat object"/>
+    </xml>
+    <token name="@CMD_read_inputs@"><![CDATA[
+seurat_obj = readRDS('seurat.rds')
+        ]]>
+    </token>
+    <token name="@CMD_read_expression_matrix@"><![CDATA[
+counts<-read.table("matrix.tab", header=TRUE, row.names=1, sep="\t")
+    ]]>]
+    </token>
+    <token name="@CMD@"><![CDATA[
+cp '$seurat_rds' seurat.rds &&
+cat '$script_file' > $hidden_output &&
+Rscript '$script_file' >> $hidden_output
+    ]]>
+    </token>
+    <xml name="inputs_common_advanced">
+        <section name="advanced_common" title="Advanced Output" expanded="false">
+            <param name="show_log" type="boolean" checked="false" label="Output Log?" />
+        </section>
+    </xml>
+    <xml name="outputs_common_advanced">
+        <data name="hidden_output" format="txt" label="Log file" >
+            <filter>advanced_common['show_log']</filter>
+        </data>
+    </xml>
+    <xml name="seurat_outputs">
+        <data name="rds_out" format="rds" from_work_dir="seurat.rds" label="${tool.name} (${method.method}) on ${on_string}: RDS">
+             <filter>method['method'] != 'Inspect'</filter>
+        </data>
+        <expand macro="outputs_common_advanced"/>
+    </xml>
+    <token name="@CMD_rds_write_outputs@"><![CDATA[
+saveRDS(seurat_obj, 'seurat.rds')
+        ]]>
+    </token>
+    <xml name="variable_out">
+        <data name="variable_tabular" format="txt" from_work_dir="variable_out.txt" label="${tool.name} (${method.method}) on ${on_string}: Top variable features list">
+            <filter>method['method'] == 'FindVariableFeatures' or method['method'] == 'SCTransform'</filter>
+            <filter>method['output_topN']['output_topN'] == 'true'</filter>
+        </data>
+    </xml>
+    <token name="@CMD_write_variable_tab@"><![CDATA[
+write.table(top_N, 'variable_out.txt', sep= "\t", col.names = FALSE, quote = FALSE)
+    ]]>
+    </token>
+    <xml name="markers_out">
+        <data name="markers_tabular" format="csv" from_work_dir="markers_out.csv" label="${tool.name} (${method.method}) on ${on_string}: Markers list">
+            <filter>method['method'] == 'FindAllMarkers' or method['method'] == 'FindMarkers' or method['method'] == 'FindConservedMarkers'</filter>
+        </data>
+    </xml>
+    <token name="@CMD_write_markers_tab@"><![CDATA[
+write.csv(seurat_obj, 'markers_out.csv', quote = FALSE)
+    ]]>
+    </token>
+    <xml name="print_top_pcs">
+        <data name="top_pcs" format="txt" from_work_dir="print_pcs.txt" label="${tool.name} Print PCs on ${on_string}">
+            <filter>method['method'] == 'RunPCA' and method['print_pcs']['print_pcs'] == 'true'</filter>
+        </data>
+    </xml>
+    <xml name="inspect_out">
+        <data name="inspect_tabular" format="tabular" from_work_dir="inspect_out.tab" label="${tool.name} Inspect (${method.inspect.inspect}) on ${on_string}">
+            <filter>method['method'] == 'Inspect' and method['inspect']['inspect'] != 'General'</filter>
+        </data>
+        <data name="inspect_general" format="txt" from_work_dir="inspect.txt" label="${tool.name} Inspect General on ${on_string}">
+            <filter>method['method'] == 'Inspect' and method['inspect']['inspect'] == 'General'</filter>
+        </data>
+    </xml>
+    <token name="@CMD_inspect_rds_outputs@"><![CDATA[
+write.table(inspect, 'inspect_out.tab', sep="\t", col.names = col.names, row.names = row.names, quote = FALSE)
+    ]]>
+    </token>
+    <xml name="plot_out">
+        <data name="plot_out_png" format="png" from_work_dir="plot.png" label="${tool.name} (${method.method}) on ${on_string}: png plot">
+            <filter>plot_format == 'png'</filter>
+        </data>
+        <data name="plot_out_pdf" format="pdf" from_work_dir="plot.pdf" label="${tool.name} (${method.method}) on ${on_string}: pdf plot">
+            <filter>plot_format == 'pdf'</filter>
+        </data>
+        <data name="plot_out_svg" format="svg" from_work_dir="plot.svg" label="${tool.name} (${method.method}) on ${on_string}: svg plot">
+            <filter>plot_format == 'svg'</filter>
+        </data>
+        <data name="plot_out_jpeg" format="jpeg" from_work_dir="plot.jpeg" label="${tool.name} (${method.method}) on ${on_string}: jpeg plot">
+            <filter>plot_format == 'jpeg'</filter>
+        </data>
+        <data name="plot_out_tex" format="tex" from_work_dir="plot.tex" label="${tool.name} (${method.method}) on ${on_string}: tex plot">
+            <filter>plot_format == 'tex'</filter>
+        </data>
+        <data name="plot_out_tiff" format="tiff" from_work_dir="plot.tiff" label="${tool.name} (${method.method}) on ${on_string}: tiff plot">
+            <filter>plot_format == 'tiff'</filter>
+        </data>
+        <data name="plot_out_eps" format="eps" from_work_dir="plot.eps" label="${tool.name} (${method.method}) on ${on_string}: eps plot">
+            <filter>plot_format == 'eps'</filter>
+        </data>
+    </xml>
+    <xml name="param_eps" tokens="eps_value">
+        <param argument="eps" type="float" value="@EPS_VALUE@"  label="Small number to avoid numerical errors"/>
+    </xml>
+    <xml name="valid_name">
+        <validator type="regex" message="Please only use letters, numbers, or _ - .">^[\w\-.]+$</validator>
+    </xml>
+    <xml name="valid_reduction_key">
+        <validator type="regex" message="Please only use letters and _">^[A-Za-z_]+$</validator>
+    </xml>
+    <xml name="valid_list">
+        <validator type="regex" message="Please only use letters, numbers, or _ - . ,">^[\w\-., ]+$</validator>
+    </xml>
+    <xml name="valid_cell_name">
+        <validator type="regex" message="Please only use letters, numbers, or punctuation marks">^[\w[:punct:]]+$</validator>
+    </xml>
+    <xml name="valid_cell_list">
+        <validator type="regex" message="Please only use letters, numbers, or punctuation marks">^[\w[:punct:]]+$</validator>
+    </xml>
+    <xml name="select_assay">
+        <param argument="assay" type="text" optional="true" value="" label="Name of assay to use" help="leave blank to use default assay">
+            <expand macro="valid_name"/>
+        </param>
+    </xml>
+    <xml name="select_assay_RNA">
+        <param argument="assay" type="text" value="RNA" label="Name of assay to use">
+            <expand macro="valid_name"/>
+        </param>
+    </xml>
+    <xml name="select_slot_data">
+        <param argument="slot" type="select" label="Slot to pull data from">
+                    <option value="counts">counts</option>
+                    <option value="data" selected="true">data</option>
+                    <option value="scale.data">scale.data</option>
+                    <option value="raw.data">raw.data</option>
+        </param>
+    </xml>
+    <xml name="select_slot_scale">
+        <param argument="slot" type="select" label="Slot to pull data from">
+                    <option value="counts">counts</option>
+                    <option value="data">data</option>
+                    <option value="scale.data" selected="true">scale.data</option>
+                    <option value="raw.data">raw.data</option>
+        </param>
+    </xml>
+    <xml name="select_slot_counts">
+        <param argument="slot" type="select" label="Slot to pull data from">
+                    <option value="counts" selected="true">counts</option>
+                    <option value="data">data</option>
+                    <option value="scale.data">scale.data</option>
+                    <option value="raw.data">raw.data</option>
+        </param>
+    </xml>
+    <xml name="select_layer">
+        <param argument="layer" type="text" optional="true" value="" label="Layer to pull data from" help="leave blank to use default">
+            <expand macro="valid_name"/>
+        </param>
+    </xml>
+    <xml name="select_reduction_pca">
+        <param argument="reduction" type="text" value="pca" label="Name of reduction to use" help="default is pca">
+            <expand macro="valid_name"/>
+        </param>
+    </xml>
+    <xml name="select_reduction_umap">
+        <param argument="reduction" type="text" value="umap" label="Name of reduction to use" help="first defaults to umap, then tsne, then pca">
+            <expand macro="valid_name"/>
+        </param>
+    </xml>
+    <xml name="set_topN">
+        <param name="topN" type="integer" value="10" label="Number to show"/>
+    </xml>
+    <xml name="set_dims">
+        <param argument="dims" type="integer" optional="true" value="10" label="Number of dimensions from reduction to use as input"/>
+    </xml>
+    <xml name="normalize">
+        <conditional name="normalization_method">
+                    <param name="normalization_method" type="select" label="Method for normalization" help="(normalization.method)">
+                        <option value="LogNormalize" selected="true">LogNormalize</option>
+                        <option value="CLR">CLR</option>
+                        <option value="RC">RC</option>
+                    </param>
+                    <when value="LogNormalize"></when>
+                    <when value="CLR">
+                        <param argument="margin" type="select" checked="true" label="Normalize across features (1) or cells (2)">
+                            <option value="1" selected="true">features</option>
+                            <option value="2">cells</option>
+                        </param>
+                    </when>
+                    <when value="RC"></when>
+                </conditional>
+                <param name="scale_factor" type="integer" value="10000" label="Set scale factor for normalization" help="(scale.factor)"/>
+                <param name="block_size" type="integer" optional="true" value="" label="Number of cells to run in each block" help="(block.size)"/>
+    </xml>
+    <xml name="integration_inputs">
+        <param argument="dims" type="integer" value="30" label="Number of dimensions from reduction to use for integration"/>
+        <param name="dims_to_integrate" type="integer" optional="true" value="" label="Number of dimensions to return integrated values for" help="(dims.to.integrate)"/>
+        <param name="k_weight" type="integer" value="100" label="Number of neighbors to consider when weighting anchors" help="(k.weight)"/>
+        <param name="weight_reduction" type="text" optional="true" value="" label="Name of reduction(s) to use for calculating anchor weights" help="leave blank to use full corrected space (weight.reduction)">
+            <expand macro="valid_list"/>
+        </param>
+        <param name="sd_weight" type="float" value="1" label="Controls bandwidth of Gaussian kernel for weighting"/>
+        <param name="preserve_order" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Preserve order" help="do not reorder objects based on size for each pairwise integration (preserve.order)"/>
+    </xml>
+    <xml name="markers_inputs">
+        <param argument="features" type="data" format="txt,tabular" optional="true" value="" label="Features to test" help="text file with one feature on each line, leave empty to use all genes"/>
+        <param name="logfc_threshold" type="float" value="0.1" label="Minimum log-fold difference to test" help="(logfc.threshold)"/>
+        <conditional name="test_use">
+            <param name="test_use" type="select" label="Select test to run" help="(test.use)">
+                <option value="wilcox" selected="true">wilcox</option>
+                <option value="wilcox_limma">wilcox_limma</option>
+                <option value="bimod">bimod</option>
+                <option value="roc">roc</option>
+                <option value="t">t</option>
+                <option value="negbinom">negbinom</option>
+                <option value="poisson">poisson</option>
+                <option value="LR">LR</option>
+                <option value="MAST">MAST</option>
+                <option value="DESeq2">DESeq2</option>
+            </param>
+            <when value="wilcox">
+                <expand macro="select_slot_data"/>
+            </when>
+            <when value="wilcox_limma">
+                <expand macro="select_slot_data"/>
+            </when>
+            <when value="bimod">
+                <expand macro="select_slot_data"/>
+            </when>
+            <when value="roc">
+                <expand macro="select_slot_data"/>
+                <param name="return_thresh" type="float" value="0.01" min="0.0" max="1.0" label="Only return markers with a p-value below or power above this threshold" help="(return.thresh)"/>
+            </when>
+            <when value="t">
+                <expand macro="select_slot_data"/>
+            </when>
+            <when value="negbinom">
+                <expand macro="select_slot_counts"/>
+                <param name="latent_vars" type="text" optional="true" value="" label="Select variables to test" help="(latent.vars)"/>
+                <param name="min_cells_feature" type="integer" value="3" label="Minimum number of cells expressing the feature in at least one cluster" help="(min.cells.feature)"/>
+            </when>
+            <when value="poisson">
+                <expand macro="select_slot_counts"/>
+                <param name="latent_vars" type="text" optional="true" value="" label="Select variables to test" help="(latent.vars)"/>
+                <param name="min_cells_feature" type="integer" value="3" label="Minimum number of cells expressing the feature in at least one cluster" help="(min.cells.feature)"/>
+            </when>
+            <when value="LR">
+                <expand macro="select_slot_data"/>
+                <param name="latent_vars" type="text" optional="true" value="" label="Select variables to test" help="(latent.vars)"/>
+            </when>
+            <when value="MAST">
+                <expand macro="select_slot_data"/>
+                <param name="latent_vars" type="text" optional="true" value="" label="Select variables to test" help="(latent.vars)"/>
+            </when>
+            <when value="DESeq2">
+                <expand macro="select_slot_counts"/>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="advanced_markers_inputs">
+        <expand macro="select_assay"/>
+        <param name="fc_name" type="text" optional="true" value="" label="Choose a name for the fold change, average difference, or custom function column" help="(fc.name)">
+            <expand macro="valid_name"/>
+        </param>
+        <param name="min_pct" type="float" value="0.01" min="0" max="100" label="Minimum percentage of cells genes must be present in to be tested" help="(min.pct)"/>
+        <param name="min_diff_pct" type="float" optional="true" value="" label="Minimum difference in percentage of expression between groups for genes to be tested" help="defaults to -Inf (min.diff.pct)"/>
+        <param name="only_pos" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Only return positive markers" help="(only.pos)"/>
+        <param name="max_cells_per_ident" type="integer" optional="true" value="" label="Downsample each identity class to a max number of cells" help="defaults to Inf for no downsampling (max.cells.per.ident)"/>
+        <param name="random_seed" type="integer" optional = "true" value="1" label="Set a random seed for downsampling" help="(random.seed)"/>
+        <param name="min_cells_group" type="integer" value="3" label="Minimum number of cells in one group" help="(min.cells.group)"/>
+        <param argument="densify" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Convert to dense matrix before running DE test"/>
+    </xml>
+    <xml name="plot_types">
+        <param name="plot_format" type="select" label="Format of plot to produce">
+        <option value="png">png</option>
+        <option value="pdf">pdf</option>
+        <option value="svg">svg</option>
+        <option value="jpeg">jpeg</option>
+        <option value="tex">tex</option>
+        <option value="tiff">tiff</option>
+        <option value="eps">eps</option>
+        </param>
+    </xml>
+    <xml name="plot_sizes">
+        <conditional name="resize">
+        <param name="resize" type="select" label="Change size of plot">
+            <option value="false" selected="true">No</option>
+            <option value="true">Yes</option>
+        </param>
+        <when value="false"></when>
+        <when value="true">
+            <param argument="width" type="integer" value="2100" label="Width of plot in pixels"/>
+            <param argument="height" type="integer" value="2100" label="Height of plot in pixels"/>
+        </when>
+        </conditional>
+    </xml>
+    <xml name="plot_cols">
+        <param argument="cols" type="text" optional="true" value="" label="Colours to use for plotting" help="comma separated list">
+            <expand macro="valid_list"/>
+        </param>
+    </xml>
+    <xml name="plot_log_scale">
+        <param argument="log" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Plot on a log scale"/>
+    </xml>
+    <xml name="plot_2_dims">
+        <param name="dims_1" type="integer" value="1" label="Dimension to plot on x axis"/>
+        <param name="dims_2" type="integer" value="2" label="Dimension to plot on y axis"/>
+    </xml>
+    <xml name="plot_projected_and_balanced">
+        <param argument="projected" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Use reduction values for full dataset" help="i.e. projected dimensional reduction values"/>
+        <param argument="balanced" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Return an equal number of genes with + and - scores"/>
+    </xml>
+    <xml name="plot_disp_min_max">
+        <param name="disp_min" type="float" optional="true" value="-2.5" label="Minimum display value" help="all values below are clipped (disp.min)"/>
+        <param name="disp_max" type="float" optional="true" value="" label="Maximum display value" help="all values above are clipped. Defaults to 2.5 if slot is scale.data, otherwise defaults to 6 (disp.max)"/>
+    </xml>
+    <xml name="plot_shuffle_and_seed">
+        <conditional name="shuffle">
+            <param argument="shuffle" type="select" label="Randomly shuffle order of points" help="can help with crowded plots if points of interest are hidden">
+                <option value="TRUE">Yes</option>
+                <option value="FALSE" selected="true">No</option>
+            </param>
+            <when value="TRUE">
+                <param argument="seed" type="integer" value="1" label="Set random seed for shuffling"/>
+            </when>
+            <when value="FALSE"></when>
+        </conditional>
+    </xml>
+    <xml name="plot_order">
+        <param argument="order" type="text" optional="true" value="" label="Specify the order of plotting for the idents" help="a full comma-separated list or the ident to be plotted last on the top">
+            <expand macro="valid_list"/>
+        </param>
+    </xml>
+    <xml name="plot_group_by">
+        <param name="group_by" type="text" optional="true" value="" label="Factor to group cells by" help="(group.by)"/>
+    </xml>
+    <xml name="plot_split_by">
+        <param name="split_by" type="text" optional="true" value="" label="Factor or identity to split the plot by" help="(split.by)"/>
+    </xml>
+    <xml name="plot_alpha">
+        <param argument="alpha" type="integer" value="1" label="Alpha value for points"/>
+    </xml>
+    <xml name="plot_pt_size">
+        <param name="pt_size" type="float" optional="true" value="" label="Point size for plot" help="(pt.size)"/>
+    </xml>
+    <xml name="plot_smooth">
+        <param argument="smooth" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Smooth the graph"/>
+    </xml>
+    <xml name="plot_ncol">
+        <param argument="ncol" type="integer" optional="true" value="" label="Number of columns to display"/>
+    </xml>
+    <xml name="raster_select">
+        <conditional name="raster">
+            <param argument="raster" type="select" label="Convert points to raster format" help="NULL will automatically use raster if more than 100,000 points plotted">
+                <option value="NULL" selected="true">NULL</option>
+                <option value="TRUE">TRUE</option>
+                <option value="FALSE">FALSE</option>
+            </param>
+            <when value="NULL"></when>
+            <when value="TRUE">
+                <param name="raster_x" type="integer" value="512" label="Horizontal length of raster plot (pixels)"/>
+                <param name="raster_y" type="integer" value="512" label="Vertical height of raster plot (pixels)"/>
+            </when>
+            <when value="FALSE"></when>
+        </conditional>
+    </xml>
+    <xml name="raster_boolean">
+        <param argument="raster" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Convert to raster format"/>
+    </xml>
+</macros>