Mercurial > repos > ebi-gxa > seurat_find_clusters

--- a/README	Wed Mar 13 12:51:22 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-Seurat tools
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extra/macro_mapper_seurat.yaml	Sun Oct 01 09:06:23 2023 +0000
@@ -0,0 +1,90 @@
+---
+- option_group:
+    - input-object-file
+    - input-format
+  pre_command_macros:
+    - INPUT_OBJ_PREAMBLE
+  post_command_macros:
+    - INPUT_OBJECT
+  input_declaration_macros:
+    - input_object_params
+- option_group:
+    - output-object-file
+    - output-format
+  post_command_macros:
+    - OUTPUT_OBJECT
+  input_declaration_macros:
+    - output_object_params
+  output_declaration_macros:
+    - output_files
+- option_group:
+    - input-object-files
+    - input-format
+  pre_command_macros:
+    - INPUT_OBJS_PREAMBLE
+  post_command_macros:
+    - INPUT_OBJECTS
+  input_declaration_macros:
+    - input_object_params:
+        multiple: true
+- option_group:
+    - reference-object-files
+    - reference-format
+  pre_command_macros:
+    - REFERENCE_OBJS_PREAMBLE
+  post_command_macros:
+    - REFERENCE_OBJECTS
+  input_declaration_macros:
+    - input_object_params:
+        varname: reference
+        multiple: true
+        optional: true
+- option_group:
+    - reference-object-file
+    - reference-format
+  pre_command_macros:
+    - REFERENCE_OBJ_PREAMBLE
+  post_command_macros:
+    - REFERENCE_OBJECT
+  input_declaration_macros:
+    - input_object_params:
+        varname: reference
+- option_group:
+    - anchors-object-file
+    - anchors-format
+  pre_command_macros:
+    - ANCHORS_OBJ_PREAMBLE
+  post_command_macros:
+    - ANCHORS_OBJECT
+  input_declaration_macros:
+    - input_object_params:
+        varname: anchors
+- option_group:
+    - query-object-file
+    - query-format
+  pre_command_macros:
+    - QUERY_OBJ_PREAMBLE
+  post_command_macros:
+    - QUERY_OBJECT
+  input_declaration_macros:
+    - input_object_params:
+        varname: query
+- option_group:
+    - plot-out
+  post_command_macros:
+    - OUTPUT_PLOT
+  output_declaration_macros:
+    - plot_output_files_format:
+        format: png
+    - plot_output_files_format:
+        format: pdf
+    - plot_output_files_format:
+        format: eps
+    - plot_output_files_format:
+        format: jpg
+    - plot_output_files_format:
+        format: ps
+    - plot_output_files_format:
+        format: tiff
+    - plot_output_files_format:
+        format: svg
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_test_data.sh	Sun Oct 01 09:06:23 2023 +0000
@@ -0,0 +1,77 @@
+#!/usr/bin/env bash
+
+BASENAME_FILE='E-MTAB-6077-3k_features_90_cells'
+
+MTX_LINK='https://drive.google.com/uc?export=download&id=1-1ejn7scP80xsbrG0FtWzsozjg0hhc23'
+RDS_LINK='https://drive.google.com/uc?export=download&id=1KW_GX6xznSUpWRWUykpNaSbAhyClf7_n'
+NORM_LINK='https://drive.google.com/uc?export=download&id=1mvo3ENkBvEAOyWG6ejApzQTPDLX5yBKU'
+FVG_LINK='https://drive.google.com/uc?export=download&id=13Fhruuj-vEEo1WM138ahtAYqfHc7LsaZ'
+SCALED_LINK='https://drive.google.com/uc?export=download&id=18TK8us235LWNajarWDBAtASUXMYAxvw0'
+PCA_LINK='https://drive.google.com/uc?export=download&id=1gf3BTB4dygDsom1TzjsBfgZnZepcoG5c'
+NEIGHBOURS_LINK='https://drive.google.com/uc?export=download&id=1N2lHoKRBZ7pmAYGfghLWB9KUrLA5WoNX'
+CLUSTERS_LINK='https://drive.google.com/uc?export=download&id=1HWxZWHbNUNo4z__9PhhL_CJOLzec_ETa'
+TSNE_LINK='https://drive.google.com/uc?export=download&id=1qsvMr_GkCSp1dyTJt1BZ6cElJwFFX2zO'
+MARKERS_LINK='https://drive.google.com/uc?export=download&id=18OmWNc7mF-4pzH6DQkPp1eKunN4BfvxD'
+
+LOOM_LINK='https://drive.google.com/uc?export=download&id=1qNk5cg8hJG3Nv1ljTKmUEnxTOf11EEZX'
+H5AD_LINK='https://drive.google.com/uc?export=download&id=1YpE0H_t_dkh17P-WBhPijKvRiGP0BlBz'
+
+H5AD_SC182_LINK='https://drive.google.com/uc?export=download&id=16PUJ2KAkXT8F1UkfqU-9LWoOJUkUG1rp'
+SCE_LINK='https://drive.google.com/uc?export=download&id=1UKdyf3M01uAt7oBg93JfmRvNVB_jlUKe'
+
+# Seurat v4 exclusives
+IFNB_BASE_FILE='ifnb_'
+
+IFNB_CTRL_INT_LINK='https://drive.google.com/uc?export=download&id=15E_MLz-UclJYInNaA7YKLhLo5W-qlykL'
+IFNB_STIM_INT_LINK='https://drive.google.com/uc?export=download&id=14iKgCJGPk16dEmpJJF-Gp_lBDcOdo-54'
+
+## Classify and UMAP mapping
+CLASSIFY_QUERY_LINK='https://drive.google.com/uc?export=download&id=1RFsHa_1EFD_n-19JH_cHGqxwO66QdmXN'
+CLASSIFY_RESULTS_ANCHORS_OBJECT_LINK='https://drive.google.com/uc?export=download&id=1Xtv4K_CxIU1cJ8RjJ7NTvzLQkLvc8a3i'
+# UMAP_RESULT_OBJECT_LINK='https://oc.ebi.ac.uk/s/k4MdM07y9DAnurp/download'
+UMAP_RESULT_OBJECT_LINK='https://oc.ebi.ac.uk/s/D1z4z2ef1e3dyc3/download'
+
+
+function get_data {
+  local link=$1
+  local fname=$2
+
+  if [ ! -f $fname ]; then
+    echo "$fname not available locally, downloading.."
+    wget -O $fname --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 -t 3 $link
+  fi
+}
+
+# get matrix data
+mkdir -p test-data
+pushd test-data
+get_data $MTX_LINK mtx.zip
+unzip mtx.zip
+rm -f mtx.zip
+
+get_data $RDS_LINK $BASENAME_FILE".rds"
+get_data $NORM_LINK $BASENAME_FILE"-normalised.rds"
+get_data $FVG_LINK $BASENAME_FILE"-fvg.rds"
+get_data $SCALED_LINK $BASENAME_FILE"-scaled.rds"
+get_data $PCA_LINK $BASENAME_FILE"-pca.rds"
+get_data $NEIGHBOURS_LINK $BASENAME_FILE"-neighbours.rds"
+get_data $CLUSTERS_LINK $BASENAME_FILE"-clusters.rds"
+get_data $TSNE_LINK $BASENAME_FILE"-tsne.rds"
+get_data $MARKERS_LINK $BASENAME_FILE"-markers.csv.zip"
+
+unzip $BASENAME_FILE"-markers.csv.zip"
+rm -f $BASENAME_FILE"-markers.csv.zip"
+
+get_data $LOOM_LINK $BASENAME_FILE"_loom.h5"
+get_data $SCE_LINK $BASENAME_FILE"_sce.rds"
+get_data $H5AD_LINK $BASENAME_FILE".h5ad"
+
+get_data $H5AD_SC182_LINK $BASENAME_FILE"_sc182.h5ad"
+
+get_data $IFNB_CTRL_INT_LINK $IFNB_BASE_FILE"ctrl_norm_fvg.rds"
+get_data $IFNB_STIM_INT_LINK $IFNB_BASE_FILE"stim_norm_fvg.rds"
+
+get_data $CLASSIFY_QUERY_LINK "Classify_query.rds"
+get_data $CLASSIFY_RESULTS_ANCHORS_OBJECT_LINK "Classify_anchors.rds"
+get_data $UMAP_RESULT_OBJECT_LINK "UMAP_result_integrated.rds"
+
--- a/seurat_find_clusters.xml	Wed Mar 13 12:51:22 2019 -0400
+++ b/seurat_find_clusters.xml	Sun Oct 01 09:06:23 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="seurat_find_clusters" name="Seurat FindClusters" version="2.3.1+galaxy1">
+<tool id="seurat_find_clusters" name="Seurat FindClusters" profile="18.01" version="@SEURAT_VERSION@+galaxy0">
     <description>find clusters of cells</description>
     <macros>
         <import>seurat_macros.xml</import>
@@ -8,30 +8,10 @@
     <command detect_errors="exit_code"><![CDATA[
         seurat-find-clusters.R

-        --input-object-file '$input'
-        --output-object-file '$output'
+        @INPUT_OBJECT@
+        @OUTPUT_OBJECT@
         --output-text-file output_tab

-        #if $genes_use:
-          --genes-use '$genes_use'
-        #end if
-
-        #if str($adv.reduction_type):
-          --reduction-type '$adv.reduction_type'
-        #end if
-
-        #if str($adv.dims_use):
-          --dims-use \$(seq -s , 1 '$adv.dims_use')
-        #end if
-
-        #if str($adv.k_num_clusters):
-          --k-param '$adv.k_num_clusters'
-        #end if
-
-        #if str($adv.prune_snn):
-          --prune-snn '$adv.prune_snn'
-        #end if
-
         #if str($adv.resolution):
           --resolution '$adv.resolution'
         #end if
@@ -40,39 +20,75 @@
           --algorithm '$adv.algorithm'
         #end if

+        #if str($adv.modularity_fxn):
+          --modularity-fxn '$adv.modularity_fxn'
+        #end if
+
+        #if str($adv.method):
+          --method '$adv.method'
+        #end if
+
+        #if str($adv.graph_name):
+          --graph-name '$adv.graph_name'
+        #end if
+
+        #if str($adv.nrandom_starts):
+          --nrandom-starts '$adv.nrandom_starts'
+        #end if
+
+        $adv.group_singletons
+
+
+
   ## TODO add pdf support as optional
   ]]></command>

       <inputs>
-        <param name="input" argument="--input-object-file" type="data" format="rdata" label="Seurat RDS object" help="Seurat object produced by Seurat run PCA or other." />
-        <expand macro="genes-use-input"/>
+        <expand macro="input_object_params"/>
+        <expand macro="output_object_params"/>
           <section name="adv" title="Advanced Options">
-            <param name="reduction_type" argument="--reduction-type" optional="true" type="select" label="Dimensional reduction type" help="dimensional reduction technique to use in construction of SNN graph. (e.g. 'pca', 'ica'). PCA by default.">
-              <option value="pca" selected="true">PCA</option>
-              <option value="ica">ICA</option>
-            </param>
-            <expand macro="dims-use-input"/>
-            <param name="k_num_clusters" argument="--k-param" optional="true" type="integer" label="Number of clusters (k) to compute" help="Defines k for the k-nearest neighbor algorithm."/>
-            <param name="prune_snn" argument="--prune-snn" optional="true" type="float" label="Prune SNN cutoff" help="Sets the cutoff for acceptable Jaccard distances when computing the neighborhood overlap for the SNN construction. Any edges with values less than or equal to this will be set to 0 and removed from the SNN graph. Essentially sets the strigency of pruning (0 — no pruning, 1 — prune everything). Defaults to 1/15."/>
             <param name="resolution" argument="--resolution" optional="true" type="float" label="Resolution" help="Value of the resolution parameter, use a value above (below) 1.0 if you want to obtain a larger (smaller) number of communities. Defaults to 0.8."/>
             <param name="algorithm" argument="--algorithm" optional="true" type="select" label="Modularity organization algorithm">
               <option value="1" selected="true">Louvain</option>
               <option value="2">Louvain algorithm with multilevel refinement</option>
               <option value="3">SLM algorithm</option>
+              <option value="4">Leiden</option>
             </param>
+            <param name="modularity_fxn" argument="--modularity-fxn" optional="true" type="select" label="Modularity function">
+              <option value="1" selected="true">Standard</option>
+              <option value="2">Alternative</option>
+            </param>
+            <param name="method" argument="--method" type="select" label="Method for Leiden" help="Method for leiden  (defaults to matrix which is fast for small datasets). Select iGraph to avoid casting large data to a dense matrix.">
+              <option value="matrix" selected="true">Matrix</option>
+              <option value="igraph">iGraph</option>
+            </param>
+            <param name="graph_name" argument="--graph-name" type="text" value="RNA_nn" label="Graph Name" help="Name of graph to use for the clustering algorith."/>
+            <param name="nrandom_starts" argument="--nrandom-starts" type="integer" optional="true" label="Random starts" help="Number of random starts, 10 by default."/>
+            <param name="group_singletons" argument="--group-singletons" type="boolean" truevalue="--group-singletons" falsevalue="" checked="false" label="Group singletons" help="Group singletons into nearest cluster. If FALSE, assign all singletons to a 'singleton' group."/>
+            <param name="random_seed" argument="--random-seed" type="integer" optional="true" label="Random seed" help="Seed of the random number generator"/>
           </section>
+
       </inputs>
       <outputs>
           <!-- <data name="out_pdf" format="pdf" from_work_dir="out.pdf" label="${tool.name} on ${on_string}: Plots" /> -->
-          <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: Seurat RDS"/>
+          <expand macro="output_files"/>
           <data name="output_tab" format="csv" from_work_dir="output_tab" label="${tool.name} on ${on_string}: CSV Seurat Clusters"/>
       </outputs>

     <tests>
         <!-- Ensure count matrix input works -->
         <test>
-            <param name="input" ftype="rdata" value="out_runpca.rds"/>
-            <output name="output" ftype="rdata" value="out_findclust.rds" compare="sim_size"/>
+            <param name="rds_seurat_file" ftype="rdata" value="E-MTAB-6077-3k_features_90_cells-neighbours.rds"/>
+            <output name="rds_seurat_file" ftype="rdata" >
+              <assert_contents>
+                <has_size value="5064329" delta="200000"/>
+              </assert_contents>
+            </output>
+            <output name="output_tab" >
+              <assert_contents>
+                <has_n_lines n="92" />
+              </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[
@@ -80,16 +96,14 @@

 **What it does**

-Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data.
-It is developed and maintained by the `Satija Lab`_ at NYGC. 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.
+Identify clusters of cells by a shared nearest neighbor (SNN) modularity optimization
+based clustering algorithm. First calculate k-nearest neighbors and construct t
+he SNN graph (using Seurat find neighbours).
+Then optimize the modularity function to determine clusters.
+For a full description of the algorithms, see Waltman and van Eck (2013)
+The European Physical Journal B.

-Seurat clustering use SNN method to determine different clusters in your dataset. In order to construct a
-SNN graph, you must have perform a PCA before launch this tool (you can use Seurat dimensional reduction).
-It will search k (30) nearest neighbors for each cells and link cells to each other if they shared the
-same neighbors. You can modulate the resolution in order to get larger (resolution superior to 1) or smaller
-(inferior to 1) clusters.
+@SEURAT_INTRO@

 -----
--- a/seurat_macros.xml	Wed Mar 13 12:51:22 2019 -0400
+++ b/seurat_macros.xml	Sun Oct 01 09:06:23 2023 +0000
@@ -1,39 +1,343 @@
 <?xml version="1.0"?>
 <macros>
-
-    <token name="@VERSION@">0.0.5</token>
-
+    <token name="@VERSION@">4.0.0</token>
+    <token name="@SEURAT_VERSION@">4.0.4</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">seurat-scripts</requirement>
         </requirements>
     </xml>
-
     <xml name="version">
     	<version_command><![CDATA[
 echo $(R --version | grep version | grep -v GNU)", seurat version" $(R --vanilla --slave -e "library(seurat); cat(sessionInfo()\$otherPkgs\$seurat\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
     ]]></version_command>
     </xml>

+   <xml name="input_object_params" token_multiple="False" token_varname="input" token_optional="False">
+     <conditional name="@VARNAME@" label="Input format">
+       <param type="select" name="format" label="Choose the format of the @VARNAME@" help="Seurat RDS, Seurat H5, Single Cell Experiment RDS, Loom or AnnData">
+         <option value="rds_seurat" selected="true">RDS with a Seurat object</option>
+         <option value="loom">Loom</option>
+         <option value="h5seurat">Seurat HDF5</option>
+         <option value="anndata">AnnData</option>
+         <option value="rds_sce">RDS with a Single Cell Experiment object</option>
+       </param>
+       <when value="anndata">
+         <param type="data" name="anndata_file" multiple="@MULTIPLE@" optional="@OPTIONAL@" label="AnnData file" help="Select AnnData files for @VARNAME@" format="h5,h5ad"/>
+       </when>
+       <when value="loom">
+         <param type="data" name="loom_file" multiple="@MULTIPLE@" optional="@OPTIONAL@" label="Loom file" help="Select Loom file(s) for @VARNAME@" format="h5,h5loom"/>
+       </when>
+       <when value="rds_seurat">
+         <param type="data" name="rds_seurat_file" multiple="@MULTIPLE@" optional="@OPTIONAL@" label="RDS file" help="Select RDS file(s) with Seurat object for @VARNAME@" format="rdata"/>
+       </when>
+       <when value="rds_sce">
+         <param type="data" name="rds_sce_file" multiple="@MULTIPLE@" optional="@OPTIONAL@" label="RDS file" help="Select RDS file(s) with Single Cell Experiment object for @VARNAME@" format="rdata"/>
+       </when>
+       <when value="h5seurat">
+         <param type="data" name="h5seurat_file" multiple="@MULTIPLE@" optional="@OPTIONAL@" label="Seurat HDF5" help="Select Seurat HDF5 file(s) for @VARNAME" format="h5"/>
+       </when>
+     </conditional>
+   </xml>
+
+   <token name="@INPUT_OBJ_PREAMBLE@">
+     #if $input.format == 'loom'
+     ln -s '$input.loom_file' input.loom;
+     #else if $input.format == 'h5seurat'
+     ln -s '$input.h5seurat_file' input.h5seurat;
+     #else if $input.format == 'anndata'
+     ## it complains when using links for AnnData...
+     cp '$input.anndata_file' input.h5ad;
+     #end if
+   </token>
+
+   <token name="@INPUT_OBJECT@">
+    #if $input.format == "anndata"
+        --input-object-file input.h5ad --input-format anndata
+    #else if $input.format == "loom"
+        --input-object-file input.loom --input-format loom
+    #else if $input.format == "rds_seurat"
+        --input-object-file '$input.rds_seurat_file' --input-format seurat
+    #else if $input.format == "rds_sce"
+        --input-object-file '$input.rds_sce_file' --input-format singlecellexperiment
+    #else if $input.format == "h5seurat"
+        --input-object-file input.h5seurat --input-format h5seurat
+    #end if
+   </token>
+
+   <token name="@QUERY_OBJ_PREAMBLE@">
+     #if $query.format == 'loom'
+     ln -s '$query.loom_file' query.loom;
+     #else if $query.format == 'h5seurat'
+     ln -s '$query.h5seurat_file' query.h5seurat;
+     #else if $query.format == 'anndata'
+     ## it complains when using links for AnnData...
+     cp '$query.anndata_file' query.h5ad;
+     #end if
+   </token>
+
+   <token name="@QUERY_OBJECT@">
+    #if $query.format == "anndata"
+        --query-object-file query.h5ad --query-format anndata
+    #else if $query.format == "loom"
+        --query-object-file query.loom --query-format loom
+    #else if $query.format == "rds_seurat"
+        --query-object-file '$query.rds_seurat_file' --query-format seurat
+    #else if $query.format == "rds_sce"
+        --query-object-file '$query.rds_sce_file' --query-format singlecellexperiment
+    #else if $query.format == "h5seurat"
+        --query-object-file query.h5seurat --query-format h5seurat
+    #end if
+  </token>
+
+  <token name="@ANCHORS_OBJ_PREAMBLE@">
+    #if $anchors.format == 'loom'
+    ln -s '$anchors.loom_file' anchors.loom;
+    #else if $anchors.format == 'h5seurat'
+    ln -s '$anchors.h5seurat_file' anchors.h5seurat;
+    #else if $anchors.format == 'anndata'
+    ## it complains when using links for AnnData...
+    cp '$anchors.anndata_file' anchors.h5ad;
+    #end if
+  </token>
+
+  <token name="@ANCHORS_OBJECT@">
+   #if $anchors.format == "anndata"
+       --anchors-object-file anchors.h5ad --anchors-format anndata
+   #else if $anchors.format == "loom"
+       --anchors-object-file anchors.loom --anchors-format loom
+   #else if $anchors.format == "rds_seurat"
+       --anchors-object-file '$anchors.rds_seurat_file' --anchors-format seurat
+   #else if $anchors.format == "rds_sce"
+       --anchors-object-file '$anchors.rds_sce_file' --anchors-format singlecellexperiment
+   #else if $anchors.format == "h5seurat"
+       --anchors-object-file anchors.h5seurat --anchors-format h5seurat
+   #end if
+ </token>
+
+ <token name="@REFERENCE_OBJ_PREAMBLE@">
+   #if $reference.format == 'loom'
+   ln -s '$reference.loom_file' reference.loom;
+   #else if $reference.format == 'h5seurat'
+   ln -s '$reference.h5seurat_file' reference.h5seurat;
+   #else if $reference.format == 'anndata'
+   ## it complains when using links for AnnData...
+   cp '$reference.anndata_file' reference.h5ad;
+   #end if
+ </token>
+
+ <token name="@REFERENCE_OBJECT@">
+  #if $reference.format == "anndata"
+      --reference-object-file reference.h5ad --reference-format anndata
+  #else if $reference.format == "loom"
+      --reference-object-file reference.loom --reference-format loom
+  #else if $reference.format == "rds_seurat"
+      --reference-object-file '$reference.rds_seurat_file' --reference-format seurat
+  #else if $reference.format == "rds_sce"
+      --reference-object-file '$reference.rds_sce_file' --reference-format singlecellexperiment
+  #else if $reference.format == "h5seurat"
+      --reference-object-file reference.h5seurat --reference-format h5seurat
+  #end if
+ </token>
+
+   <token name="@INPUT_OBJS_PREAMBLE@">
+     #if $input.format == 'loom'
+     #for $i, $fh in enumerate($input.loom_file):
+        ln -s '$fh' input.${i}.loom;
+     #end for
+     #else if $input.format == 'h5seurat'
+     #for $i, $fh in enumerate($input.h5seurat_file):
+        ln -s '$fh' input.${i}.h5seurat;
+     #end for
+     #else if $input.format == 'anndata'
+     ## it complains when using links for AnnData...
+     #for $i, $fh in enumerate($input.anndata_file):
+        cp '$fh' input.${i}.h5ad;
+     #end for
+     #end if
+   </token>
+
+   <token name="@INPUT_OBJECTS@">
+    #if $input.format == "anndata"
+        --input-object-files
+    #set file_array = [ "input."+str($i)+".h5ad" for $i, $fh in enumerate($input.anndata_file)]
+    #set files = ",".join($file_array)
+        ${files}
+         --input-format anndata
+    #else if $input.format == "loom"
+        --input-object-files
+    #set file_array = [ "input."+str($i)+".loom" for $i, $fh in enumerate($input.loom_file)]
+    #set files = ",".join($file_array)
+        ${files}
+         --input-format loom
+    #else if $input.format == "rds_seurat"
+        --input-object-files
+    #set file_array = $input.rds_seurat_file
+    #set files = ",".join([ str($fh) for $fh in $file_array ])
+        ${files}
+        --input-format seurat
+    #else if $input.format == "rds_sce"
+        --input-object-files
+    #set file_array = $input.rds_sce_file
+    #set files = ",".join([ str($fh) for $fh in $file_array ])
+        ${files}
+        --input-format singlecellexperiment
+    #else if $input.format == "h5seurat"
+        --input-object-files
+    #set file_array = [ "input."+str($i)+".h5seurat" for $i, $fh in enumerate($input.h5seurat)]
+    #set files = ",".join($file_array)
+        ${files}
+        --input-format h5seurat
+    #end if
+   </token>
+
+   <token name="@REFERENCE_OBJS_PREAMBLE@">
+     #if $reference.format == 'loom'
+     #for $i, $fh in enumerate($reference.loom_file):
+        ln -s '$fh' reference.${i}.loom;
+     #end for
+     #else if $reference.format == 'h5seurat'
+     #for $i, $fh in enumerate($reference.h5seurat_file):
+        ln -s '$fh' reference.${i}.h5seurat;
+     #end for
+     #else if $reference.format == 'anndata'
+     ## it complains when using links for AnnData...
+     #for $i, $fh in enumerate($reference.anndata_file):
+        cp '$fh' reference.${i}.h5ad;
+     #end for
+     #end if
+   </token>
+
+   <token name="@REFERENCE_OBJECTS@">
+    #if $reference.format == "anndata" and $reference.anndata_file:
+        --reference-object-files
+    #set file_array = [ "reference."+str($i)+".h5ad" for $i, $fh in enumerate($reference.anndata_file)]
+    #set files = ",".join($file_array)
+        ${files}
+         --reference-format anndata
+    #else if $reference.format == "loom" and $reference.loom_file:
+        --reference-object-files
+    #set file_array = [ "reference."+str($i)+".loom" for $i, $fh in enumerate($reference.loom_file)]
+    #set files = ",".join($file_array)
+        ${files}
+         --reference-format loom
+    #else if $reference.format == "rds_seurat" and $reference.rds_seurat_file:
+        --reference-object-files
+    #set files = ",".join([ str($fh) for $fh in $reference.rds_seurat_file ])
+        ${files}
+        --reference-format seurat
+    #else if $reference.format == "rds_sce" and $reference.rds_sce_file:
+        --reference-object-files
+    #set files = ",".join([ str($fh) for $fh in $reference.rds_sce_file ])
+        ${files}
+        --reference-format singlecellexperiment
+    #else if $reference.format == "h5seurat" and $reference.h5seurat:
+        --reference-object-files
+    #set file_array = [ "reference."+str($i)+".h5seurat" for $i, $fh in enumerate($reference.h5seurat)]
+    #set files = ",".join($file_array)
+        ${files}
+        --reference-format h5seurat
+    #end if
+   </token>
+
+   <xml name="output_object_params">
+     <param type="select" name="format" label="Choose the format of the output" help="Seurat, Single Cell Experiment, AnnData or Loom">
+       <option value="rds_seurat" selected="true">RDS with a Seurat object</option>
+       <option value="anndata">AnnData written by Seurat</option>
+       <option value="loom">Loom</option>
+       <option value="rds_sce">RDS with a Single Cell Experiment object</option>
+     </param>
+   </xml>
+
+   <xml name="output_files">
+    <data name="loom_file" from_work_dir="seurat_obj.loom" format="h5" label="${tool.name} on ${on_string}: Seurat Loom">
+      <filter>format == 'loom'</filter>
+    </data>
+    <data name="rds_seurat_file" format="rdata" label="${tool.name} on ${on_string}: Seurat RDS">
+      <filter>format == 'rds_seurat'</filter>
+    </data>
+    <data name="anndata_file" format="h5ad" label="${tool.name} on ${on_string}: AnnData from Seurat">
+        <filter>format == 'anndata'</filter>
+    </data>
+    <data name="rds_sce_file" format="rdata" label="${tool.name} on ${on_string}: Seurat Single Cell Experiment RDS">
+      <filter>format == 'rds_sce'</filter>
+    </data>
+   </xml>
+
+   <token name="@OUTPUT_OBJECT@">
+    #if $format == "anndata"
+        --output-object-file '$anndata_file' --output-format anndata
+    #else if $format == "loom"
+        --output-object-file seurat_obj.loom --output-format loom
+    #else if $format == "rds_seurat"
+        --output-object-file '$rds_seurat_file' --output-format seurat
+    #else if $format == "rds_sce"
+        --output-object-file '$rds_sce_file' --output-format singlecellexperiment
+    #end if
+   </token>
+
+   <xml name="plot_output_files_format" token_format="png">
+     <data label="Seurat ${plot_type.plot_type_selector} on ${on_string}: @FORMAT@ plot" name="plot_out_@FORMAT@" format='@FORMAT@' >
+       <filter>plot_format == '@FORMAT@'</filter>
+     </data>
+   </xml>
+
+   <token name="@OUTPUT_PLOT@">
+    #if $plot_format == "png"
+        --plot-out '$plot_out_png'
+    #else if $plot_format == "pdf"
+        --plot-out '$plot_out_pdf'
+    #else if $plot_format == "eps"
+        --plot-out '$plot_out_eps'
+    #else if $plot_format == "ps"
+        --plot-out '$plot_out_ps'
+    #else if $plot_format == "jpg"
+        --plot-out '$plot_out_jpg'
+    #else if $plot_format == "tiff"
+        --plot-out '$plot_out_tiff'
+    #else if $plot_format == "svg"
+        --plot-out '$plot_out_svg'
+    #end if
+   </token>
+
     <xml name="genes-use-input">
-      <param name="genes_use" argument="--genes-use" optional="true" type="data" format="tsv, txt" label="Genes to use" help="A file with gene names to use in construction of SNN graph if building directly based on expression data rather than a dimensionally reduced representation (i.e. PCs)."/>
+      <param name="genes_use" argument="--genes-use" optional="true" type="data" format="tsv,txt,tabular" label="Genes to use" help="A file with gene names to use in construction of SNN graph if building directly based on expression data rather than a dimensionally reduced representation (i.e. PCs)."/>
     </xml>
     <xml name="dims-use-input">
       <param name="dims_use" argument="--dims-use" min="1" optional="true" type="integer" label="PCA Dimensions to use" help="Number of PCs (dimensions) to use in construction of the SNN graph."/>
     </xml>

+    <token name="@SEURAT_INTRO@"><![CDATA[
+Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data.
+It is developed and maintained by the `Satija Lab`_ at NYGC. 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.
+      ]]></token>
+
     <token name="@VERSION_HISTORY@"><![CDATA[
 **Version history**
+4.0.0: Moves to Seurat 4.0.0, introducing a number of methods for merging datasets, plus the whole suite of Seurat plots. Pablo Moreno with funding from AstraZeneca.

-0.0.1: Initial contribution. Maria Doyle, https://github.com/mblue9.
+3.2.3+galaxy0: Moves to Seurat 3.2.3 and introduce convert method, improving format interconversion support.
+
+3.1.2_0.0.8: Update metadata parsing
+
+3.1.1_0.0.7: Exposes perplexity and enables tab input.
+
+3.1.1_0.0.6+galaxy0: Moved to Seurat 3.
+
+  Find clusters: removed dims-use, k-param, prune-snn.

 2.3.1+galaxy0: Improved documentation and further exposition of all script's options. Pablo Moreno, Jonathan Manning and Ni Huang, Expression Atlas team https://www.ebi.ac.uk/gxa/home  at
-EMBL-EBI https://www.ebi.ac.uk/. Parts obtained from wrappers from Christophe Antoniewski(https://github.com/drosofff) and Lea Bellenger(https://github.com/bellenger-l).
+EMBL-EBI https://www.ebi.ac.uk/. Parts obtained from wrappers from Christophe Antoniewski (GitHub drosofff) and Lea Bellenger (GitHub bellenger-l).
+
+0.0.1: Initial contribution. Maria Doyle (GitHub mblue9).
       ]]></token>


     <xml name="citations">
         <citations>
+            <citation type="doi">10.1038/s41592-021-01102-w</citation>
             <citation type="doi">10.1038/nbt.4096</citation>
             <citation type="bibtex">
               @misc{r-seurat-scripts.git,