Repository 'seurat_data'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/seurat_data

Changeset 0:50c5abeb08ba (2024-09-11)
Next changeset 1:4ec52a83ec82 (2024-11-05)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat_v5 commit a9214c07b0cc929a51fd92a369bb89c675b6c88d
added:
inspect_and_manipulate.xml
macros.xml
b
diff -r 000000000000 -r 50c5abeb08ba inspect_and_manipulate.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/inspect_and_manipulate.xml Wed Sep 11 10:21:26 2024 +0000
[
b'@@ -0,0 +1,755 @@\n+<tool id="seurat_data" name="Seurat Data Management" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+    <description>- Inspect and Manipulate </description>\n+    <macros>\n+        <import>macros.xml</import>\n+    </macros>\n+    <expand macro="requirements"/>\n+    <expand macro="version_command"/>\n+    <command detect_errors="exit_code"><![CDATA[\n+@CMD@\n+    ]]></command>\n+    <configfiles>\n+        <configfile name="script_file"><![CDATA[\n+@CMD_imports@\n+@CMD_read_inputs@\n+\n+#if $method.method == \'Inspect\'\n+    #if $method.inspect.inspect == \'General\'\n+        sink(\'inspect.txt\')\n+        seurat_obj\n+        sink()\n+\n+    #else if $method.inspect.inspect == \'Features\'\n+        inspect<-Features(seurat_obj[[\'$method.inspect.assay\']])\n+        row.names = FALSE\n+        col.names = FALSE\n+        @CMD_inspect_rds_outputs@\n+\n+    #else if $method.inspect.inspect == \'Cells\'\n+        inspect<-Cells(\n+            seurat_obj,\n+            #if $method.layer != \'\'\n+            layer = $method.layer\n+            #end if\n+        )\n+        row.names = FALSE\n+        col.names = FALSE\n+        @CMD_inspect_rds_outputs@\n+\n+    #else if $method.inspect.inspect == \'Idents\'\n+        inspect<-Idents(seurat_obj)\n+        row.names = TRUE\n+        col.names = FALSE\n+        @CMD_inspect_rds_outputs@\n+\n+    #else if $method.inspect.inspect == \'Metadata\'\n+        #if $method.inspect.view_metadata != \'\'\n+        inspect<-seurat_obj[[\'$method.inspect.view_metadata\']]\n+        #else\n+        inspect<-seurat_obj[[]]\n+        #end if\n+        row.names = TRUE\n+        col.names = TRUE\n+        @CMD_inspect_rds_outputs@\n+\n+    #else if $method.inspect.inspect == \'Matrix\'\n+        inspect<-LayerData(\n+            seurat_obj, \n+            assay=\'$method.inspect.assay\', \n+            layer=\'$method.inspect.layer\'\n+            )\n+        row.names = TRUE\n+        col.names = TRUE\n+        @CMD_inspect_rds_outputs@\n+\n+    #end if\n+\n+#else if $method.method == \'Manipulate\'\n+    #if $method.manipulate.manipulate == \'Change_Idents\'\n+        Idents(seurat_obj)<- \'$method.manipulate.change\'\n+\n+    #else if $method.manipulate.manipulate == \'Rename_Idents\'\n+        #if $method.manipulate.stash_idents.stash_idents == \'true\'\n+            seurat_obj[[\'$method.manipulate.stash_idents.old_ident\']]<-Idents(seurat_obj)\n+        #end if\n+        #if $method.manipulate.rename.rename_all == \'true\'\n+            new_names = c(unlist(strsplit(gsub(" ", "", \'$method.manipulate.rename.new_names\'), ",")))\n+            names(new_names)<-levels(seurat_obj)\n+            seurat_obj<-RenameIdents(\n+                seurat_obj,\n+                new_names\n+            )\n+        #else if $method.manipulate.rename.rename_all == \'false\'\n+            seurat_obj<-RenameIdents(\n+                seurat_obj,\n+                \'$method.manipulate.rename.old_name\' = \'$method.manipulate.rename.new_name\'\n+            )\n+        #end if\n+\n+    #else if $method.manipulate.manipulate == \'Add_Metadata\'\n+        meta_data<-read.table(\n+            "$method.manipulate.metadata",\n+            header = TRUE,\n+            row.names = 1,\n+            sep = "\\t"\n+        )\n+        seurat_obj<-AddMetaData(\n+            seurat_obj,\n+            metadata = meta_data,\n+        )\n+\n+    #else if $method.manipulate.manipulate == \'Merge\'\n+        y = list()\n+        #for $file in $method.manipulate.add_seurat\n+            y<-append(y, readRDS(\'${file}\'))\n+        #end for\n+        seurat_obj<-merge(x = seurat_obj, y)\n+\n+        #if $method.manipulate.join.join == \'true\'\n+            seurat_obj[[\'$method.manipulate.join.assay\']]<-JoinLayers(\n+                seurat_obj[[\'$method.manipulate.join.assay\']]\n+            )\n+        #end if\n+\n+    #else if $method.manipulate.manipulate == \'Subset_Ident\'\n+        seurat_obj<-subset(\n+            seurat_obj,\n+            idents = c(unlist(strsplit(gsub(" ", "", \'$method.manipulate.idents\'), ","))),\n+         )\n+\n+    #else if $meth'..b'              <assert_contents>\n+                    <has_text_matching expression="AggregateExpression"/>\n+                </assert_contents>\n+            </output>\n+            <output name="rds_out" location="https://zenodo.org/records/13732784/files/aggregated.rds" ftype="rds" compare="sim_size"/>\n+        </test>\n+        <test expect_num_outputs="2">\n+            <!-- test15:  Default Assay-->\n+            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/citeseq.rds"/>\n+            <conditional name="method">\n+                <param name="method" value="Manipulate"/>\n+                <conditional name="manipulate">\n+                    <param name="manipulate" value="DefaultAssay"/>\n+                    <param name="default_assay" value="ADT"/>\n+                </conditional>\n+            </conditional>\n+            <section name="advanced_common">\n+                <param name="show_log" value="true"/>\n+            </section>\n+            <output name="hidden_output">\n+                <assert_contents>\n+                    <has_text_matching expression="DefaultAssay"/>\n+                </assert_contents>\n+            </output>\n+            <output name="rds_out" location="https://zenodo.org/records/13732784/files/default.rds" ftype="rds"/>\n+        </test>\n+    </tests>\n+    <help><![CDATA[\n+Seurat\n+======\n+\n+Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. \n+\n+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.\n+\n+Inspect and Manipulate\n+======================\n+\n+A selection of essential functions to display information about a Seurat Object or make basic changes to the object.\n+\n+More details on these essential commands can be found in the `seurat documentation\n+<https://satijalab.org/seurat/articles/essential_commands>`__\n+\n+Inspect\n+=======\n+\n+General - basic information about the Seurat Object\n+Features - list of features, select which assay to display features from if object contains multimodal data\n+Cells - list of cell barcodes/ids, select layer to display cells for if object contains multiple layers\n+Idents - list showing Ident for each cell\n+Metadata - table of cell metadata\n+Matrix - show the full matrix\n+\n+Manipulate\n+==========\n+\n+Functions to add, change, or remove selected elements of a Seurat Object.\n+\n+Change Idents\n+=============\n+\n+Change which annotation in your cell metadata is used as the Ident column.\n+\n+Rename Idents\n+=============\n+\n+Rename the classes in the Ident column (e.g. to replace cluster numbers with cell types).\n+\n+You have the option to stash the original idents in a new column called \'old.ident\' before renaming the classes in the Ident column.\n+\n+AddMetaData\n+===========\n+\n+Merge\n+=====\n+\n+Combine two Seurat Objects into a single Seurat Object. \n+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.\n+\n+Subset\n+======\n+\n+Subset a group of cells based on their ident or another grouping in your cell metadata.\n+\n+DietSeurat\n+==========\n+\n+Keep only certain aspects of the Seurat object. \n+Can be useful in functions that utilize merge as it reduces the amount of data in the merge\n+\n+More details on these essential commands can be found in the `seurat documentation\n+<https://satijalab.org/seurat/reference/dietseurat>`__\n+\n+AggregateExpression\n+===================\n+\n+Returns summed counts ("pseudobulk") for each identity class. \n+\n+More details on the `seurat documentation\n+<https://satijalab.org/seurat/reference/aggregateexpression>`__\n+\n+\n+DefaultAssay\n+============\n+\n+Set the default assay for multimodal data. \n+\n+You can use the Inspect - General function to check which assay is currently active and which other assays are available.\n+\n+    ]]></help>\n+    <expand macro="citations"/>\n+</tool>\n'
b
diff -r 000000000000 -r 50c5abeb08ba macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Sep 11 10:21:26 2024 +0000
[
b'@@ -0,0 +1,437 @@\n+<macros>\n+    <token name="@TOOL_VERSION@">5.0</token>\n+    <token name="@VERSION_SUFFIX@">0</token>\n+    <token name="@PROFILE@">23.0</token>\n+    <xml name="requirements">\n+        <requirements>\n+            <requirement type="package" version="@TOOL_VERSION@">r-seurat</requirement>\n+            <requirement type="package" version="1.2.1">fit-sne</requirement>\n+            <requirement type="package" version="3.58.1">bioconductor-limma</requirement>\n+            <requirement type="package" version="1.28.0">bioconductor-mast</requirement>\n+            <requirement type="package" version="1.42.0">bioconductor-deseq2</requirement>\n+            <requirement type="package" version="2.1.3">r-svglite</requirement>\n+            <requirement type="package" version="1.1">r-metap</requirement>\n+            <requirement type="package" version="1.14.0">bioconductor-glmGamPoi</requirement>\n+            <requirement type="package" version="0.5.3">umap-learn</requirement> <!-- https://github.com/satijalab/seurat/issues/8283 -->\n+            <requirement type="package" version="0.10.2">leidenalg</requirement>\n+            <requirement type="package" version="1.2.0">r-harmony</requirement>\n+            <requirement type="package" version="1.18.0">bioconductor-batchelor</requirement>\n+            <requirement type="package" version="2.0.0">numpy</requirement>\n+            <requirement type="package" version="2.2.2">pandas</requirement>\n+        </requirements>\n+    </xml>\n+    <xml name="citations">\n+        <citations>\n+            <citation type="doi">10.1038/s41587-023-01767-y</citation>\n+        </citations>\n+    </xml>\n+    <xml name="sanitize_query" token_validinitial="string.printable">\n+        <sanitizer>\n+            <valid initial="@VALIDINITIAL@">\n+                <remove value="&apos;" />\n+            </valid>\n+       </sanitizer>\n+    </xml>\n+    <xml name="sanitize_vectors" token_validinitial="string.digits">\n+        <sanitizer>\n+            <valid initial="@VALIDINITIAL@">\n+                <add value=","/>\n+            </valid>\n+        </sanitizer>\n+    </xml>\n+    <xml name="version_command">\n+        <version_command><![CDATA[\n+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: ")\n+        ]]></version_command>\n+    </xml>\n+\n+    <token name="@CMD_imports@"><![CDATA[\n+library(Seurat)\n+    ]]>\n+    </token>\n+    <token name="@reticulate_hack@"><![CDATA[\n+library(reticulate)\n+## HACK: CI biocontainers do not contain a useable conda binary, just the env.\n+##  see: https://github.com/galaxyproject/tools-iuc/issues/5585#issuecomment-1803773923\n+is_biocontainer = grepl("^# cmd: /opt/conda/bin/",\n+                        paste0(reticulate:::python_info_condaenv_find("/usr/local/"),\n+                               "-none"))\n+if (is_biocontainer) {\n+   ## conda detection false positive\n+   assignInNamespace("is_conda_python", function(x) FALSE, ns="reticulate")\n+   use_python("/usr/local/bin/python")\n+} else {\n+   conda_path = Sys.getenv("CONDA_PREFIX")\n+   if (conda_path != "") {\n+      ## Active conda env found\n+      use_python(file.path(conda_path, "bin", "python3"))\n+   } else {\n+      ## Not biocontainer or conda, assume system python\n+      use_python("/usr/bin/python3")\n+   }\n+}]]>\n+    </token>\n+    <xml name="input_rds">\n+        <param name="seurat_rds" type="data" format="rds" label="Input file with the Seurat object"/>\n+    </xml>\n+    <token name="@CMD_read_inputs@"><![CDATA[\n+seurat_obj = readRDS(\'seurat.rds\')\n+        ]]>\n+    </token>\n+    <token name="@CMD_read_expression_matrix@"><![CDATA[\n+counts<-read.table("matrix.tab", header=TRUE, row.names=1, sep="\\t")\n+    ]]>]\n+    </token>\n+    <token name="@CMD@"><![CDATA[\n+cp \'$seurat_rds\' seurat.rds &&\n+cat \'$script_file\' > $hidden_output &&\n+Rscript \'$script_file\' >> $hidden_output\n+    ]]>\n+    </token>\n+ '..b'le"/>\n+    </xml>\n+    <xml name="plot_2_dims">\n+        <param name="dims_1" type="integer" value="1" label="Dimension to plot on x axis"/>\n+        <param name="dims_2" type="integer" value="2" label="Dimension to plot on y axis"/>\n+    </xml>\n+    <xml name="plot_projected_and_balanced">\n+        <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"/>\n+        <param argument="balanced" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Return an equal number of genes with + and - scores"/>\n+    </xml>\n+    <xml name="plot_disp_min_max">\n+        <param name="disp_min" type="float" optional="true" value="-2.5" label="Minimum display value" help="all values below are clipped (disp.min)"/>\n+        <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)"/>\n+    </xml>\n+    <xml name="plot_shuffle_and_seed">\n+        <conditional name="shuffle">\n+            <param argument="shuffle" type="select" label="Randomly shuffle order of points" help="can help with crowded plots if points of interest are hidden">\n+                <option value="TRUE">Yes</option>\n+                <option value="FALSE" selected="true">No</option>\n+            </param>\n+            <when value="TRUE">\n+                <param argument="seed" type="integer" value="1" label="Set random seed for shuffling"/>\n+            </when>\n+            <when value="FALSE"></when>\n+        </conditional>\n+    </xml>\n+    <xml name="plot_order">\n+        <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">\n+            <expand macro="valid_list"/>\n+        </param>\n+    </xml>\n+    <xml name="plot_group_by">\n+        <param name="group_by" type="text" optional="true" value="" label="Factor to group cells by" help="(group.by)"/>\n+    </xml>\n+    <xml name="plot_split_by">\n+        <param name="split_by" type="text" optional="true" value="" label="Factor or identity to split the plot by" help="(split.by)"/>\n+    </xml>\n+    <xml name="plot_alpha">\n+        <param argument="alpha" type="integer" value="1" label="Alpha value for points"/>\n+    </xml>\n+    <xml name="plot_pt_size">\n+        <param name="pt_size" type="float" optional="true" value="" label="Point size for plot" help="(pt.size)"/>\n+    </xml>\n+    <xml name="plot_smooth">\n+        <param argument="smooth" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Smooth the graph"/>\n+    </xml>\n+    <xml name="plot_ncol">\n+        <param argument="ncol" type="integer" optional="true" value="" label="Number of columns to display"/>\n+    </xml>\n+    <xml name="raster_select">\n+        <conditional name="raster">\n+            <param argument="raster" type="select" label="Convert points to raster format" help="NULL will automatically use raster if more than 100,000 points plotted">\n+                <option value="NULL" selected="true">NULL</option>\n+                <option value="TRUE">TRUE</option>\n+                <option value="FALSE">FALSE</option>\n+            </param>\n+            <when value="NULL"></when>\n+            <when value="TRUE">\n+                <param name="raster_x" type="integer" value="512" label="Horizontal length of raster plot (pixels)"/>\n+                <param name="raster_y" type="integer" value="512" label="Vertical height of raster plot (pixels)"/>\n+            </when>\n+            <when value="FALSE"></when>\n+        </conditional>\n+    </xml>\n+    <xml name="raster_boolean">\n+        <param argument="raster" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Convert to raster format"/>\n+    </xml>\n+</macros>\n'