--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Sep 11 10:20:51 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>