From 812fd5b5e7a90fb968f1fc22190df3501602d821 Mon Sep 17 00:00:00 2001
From: Wendi Bacon <44605769+nomadscientist@users.noreply.github.com>
Date: Tue, 5 Nov 2024 18:17:49 +0100
Subject: [PATCH] fix order and add to more tools

---
 .../ct_build_cell_ontology_dict.xml           |  7 ++--
 .../cell-types-analysis/ct_check_labels.xml   |  9 ++---
 .../ct_combine_tool_outputs.xml               |  5 +--
 .../ct_downsample_cells.xml                   |  3 +-
 .../ct_get_consensus_outputs.xml              |  9 ++---
 .../ct_get_empirical_dist.xml                 |  5 +--
 .../ct_get_tool_perf_table.xml                | 13 +++----
 .../cell-types-analysis/ct_get_tool_pvals.xml |  3 +-
 .../cell-types-analysis/ct_macros.xml         |  7 +++-
 .../data-hca/matrix-service.xml               |  3 ++
 .../data-scxa/retrieve-scxa.xml               |  3 ++
 .../garnett/garnett_check_markers.xml         |  2 +-
 .../garnett/garnett_classify_cells.xml        |  2 +-
 .../garnett/garnett_get_feature_genes.xml     |  2 +-
 .../garnett/garnett_get_std_output.xml        |  2 +-
 .../garnett/garnett_train_classifier.xml      |  2 +-
 .../garnett/garnett_transform_markers.xml     |  2 +-
 .../garnett/update_marker_file.xml            |  2 +-
 .../monocle3/monocle3-create.xml              |  2 +-
 .../monocle3/monocle3-diffExp.xml             |  2 +-
 .../monocle3/monocle3-learnGraph.xml          |  2 +-
 .../monocle3/monocle3-orderCells.xml          |  2 +-
 .../monocle3/monocle3-partition.xml           |  2 +-
 .../monocle3/monocle3-preprocess.xml          |  2 +-
 .../monocle3/monocle3-reduceDim.xml           |  2 +-
 tools/tertiary-analysis/pyscenic/macros.xml   |  2 +-
 .../pyscenic/pyscenic_aucell.xml              | 34 +++++++++----------
 .../pyscenic/pyscenic_binarize_aucell.xml     |  4 +--
 .../pyscenic/pyscenic_ctx.xml                 | 16 ++++-----
 .../pyscenic/pyscenic_grn.xml                 | 10 +++---
 .../sc3/sc3-calc-biology.xml                  |  2 +-
 .../sc3/sc3-calc-consens.xml                  |  2 +-
 .../tertiary-analysis/sc3/sc3-calc-dists.xml  |  2 +-
 .../sc3/sc3-calc-transfs.xml                  |  2 +-
 .../tertiary-analysis/sc3/sc3-estimate-k.xml  |  2 +-
 tools/tertiary-analysis/sc3/sc3-kmeans.xml    |  2 +-
 tools/tertiary-analysis/sc3/sc3-prepare.xml   |  2 +-
 .../scater/scater-calculate-cpm.xml           |  2 +-
 .../scater/scater-calculate-qc-metrics.xml    |  2 +-
 .../scater/scater-filter.xml                  |  2 +-
 .../scater/scater-is-outlier.xml              |  2 +-
 .../scater/scater-normalize.xml               |  2 +-
 .../scater/scater-read-10x-results.xml        |  2 +-
 tools/tertiary-analysis/sccaf/run_sccaf.xml   |  1 +
 tools/tertiary-analysis/sccaf/sccaf_asses.xml |  1 +
 .../sccaf/sccaf_asses_merger.xml              |  3 +-
 .../tertiary-analysis/sccaf/sccaf_macros.xml  |  5 +++
 .../sccaf/sccaf_regress_out.xml               |  1 +
 .../sceasy/sceasy_convert.xml                 |  2 +-
 .../scmap/scmap_get_std_output.xml            | 12 +++----
 .../scmap/scmap_index_cell.xml                |  8 ++---
 .../scmap/scmap_index_cluster.xml             |  6 ++--
 .../scmap/scmap_preprocess_sce.xml            |  4 +--
 .../scmap/scmap_scmap_cell.xml                |  2 +-
 .../scmap/scmap_scmap_cluster.xml             |  4 +--
 .../scmap/scmap_select_features.xml           | 10 +++---
 .../scpred/scpred_get_feature_space.xml       | 16 ++++-----
 .../scpred/scpred_get_std_output.xml          |  8 ++---
 .../scpred/scpred_predict.xml                 |  8 ++---
 .../scpred/scpred_train_model.xml             | 18 +++++-----
 .../ucsc-cell-browser/cell-browser.xml        |  3 ++
 61 files changed, 164 insertions(+), 135 deletions(-)

diff --git a/tools/tertiary-analysis/cell-types-analysis/ct_build_cell_ontology_dict.xml b/tools/tertiary-analysis/cell-types-analysis/ct_build_cell_ontology_dict.xml
index d0ac51e1..b6b08336 100644
--- a/tools/tertiary-analysis/cell-types-analysis/ct_build_cell_ontology_dict.xml
+++ b/tools/tertiary-analysis/cell-types-analysis/ct_build_cell_ontology_dict.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>ct_macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         mkdir -p input_dir;
@@ -12,7 +13,7 @@
 
         build_cell_ontology_dict.R --input-dir input_dir  --output-dict-path "${output_dict_path}" --output-text-path "${output_txt_path}"
         #if $condensed_sdrf
-        --condensed-sdrf "${condensed_sdrf}" 
+        --condensed-sdrf "${condensed_sdrf}"
         #end if
         #if $barcode_col_name
         --barcode-col-name "${barcode_col_name}"
@@ -21,7 +22,7 @@
         --cell-label-col-name "${cell_label_col_name}"
         #end if
         #if $cell_ontology_col_name
-        --cell-ontology-col-name "${cell_ontology_col_name}" 
+        --cell-ontology-col-name "${cell_ontology_col_name}"
         #end if
          ]]></command>
     <inputs>
@@ -50,7 +51,7 @@
     </tests>
     <help><![CDATA[
     @HELP@
-    
+
     @VERSION_HISTORY@
     ]]></help>
     <expand macro="citations" />
diff --git a/tools/tertiary-analysis/cell-types-analysis/ct_check_labels.xml b/tools/tertiary-analysis/cell-types-analysis/ct_check_labels.xml
index 9a8d97c2..a223b1b2 100644
--- a/tools/tertiary-analysis/cell-types-analysis/ct_check_labels.xml
+++ b/tools/tertiary-analysis/cell-types-analysis/ct_check_labels.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>ct_macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
 
@@ -14,15 +15,15 @@
 
         ]]></command>
         <inputs>
-            
+
             <param type="data" name="input_file" label="Input File" multiple="true" format="txt" help="Input metadta file" />
             <param type="text" name="label_field" label="Label Field" optional="true" help="Name of label field in metadata file">
                 <expand macro="sanitize_strings" />
             </param>
-            <param type="boolean" name="condensed" checked="false" label="Condensed Metadata File" help="Are the supplied metadata files of condensed format?" /> 
+            <param type="boolean" name="condensed" checked="false" label="Condensed Metadata File" help="Are the supplied metadata files of condensed format?" />
             <param type="integer" name="attribute_type_col_num" value='5' label="Number of Attribute Type Column" help="Number of the attribute type field in condensed metadata file. Default: 5" />
             <param type="integer" name="variable_col_num" value='6' label="Number of Label Column" help="Number of the label field in condensed metadata file. Default: 6" />
-            <param type="boolean" name="avoid_lowercase" checked="false" label="Avoid Lowercaase" help="Should setting the labels to lowercase be skipped? Default: False" /> 
+            <param type="boolean" name="avoid_lowercase" checked="false" label="Avoid Lowercaase" help="Should setting the labels to lowercase be skipped? Default: False" />
 
         </inputs>
         <outputs>
@@ -38,7 +39,7 @@
     </tests>
         <help><![CDATA[
     @HELP@
-    
+
     @VERSION_HISTORY@
     ]]></help>
     <expand macro="citations" />
diff --git a/tools/tertiary-analysis/cell-types-analysis/ct_combine_tool_outputs.xml b/tools/tertiary-analysis/cell-types-analysis/ct_combine_tool_outputs.xml
index baf62756..c5c2d95e 100644
--- a/tools/tertiary-analysis/cell-types-analysis/ct_combine_tool_outputs.xml
+++ b/tools/tertiary-analysis/cell-types-analysis/ct_combine_tool_outputs.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>ct_macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         mkdir -p input_dir;
@@ -10,7 +11,7 @@
           cp '$table' input_dir/;
         #end for
 
-        combine_tool_outputs.R --input-dir input_dir --top-labels-num "${top_labels_num}" --scores "${scores}" --output-table "${output_table}" 
+        combine_tool_outputs.R --input-dir input_dir --top-labels-num "${top_labels_num}" --scores "${scores}" --output-table "${output_table}"
 
         #if $exclusions
         --exclusions "${exclusions}"
@@ -35,7 +36,7 @@
     </tests>
     <help><![CDATA[
     @HELP@
-    
+
     @VERSION_HISTORY@
     ]]></help>
     <expand macro="citations" />
diff --git a/tools/tertiary-analysis/cell-types-analysis/ct_downsample_cells.xml b/tools/tertiary-analysis/cell-types-analysis/ct_downsample_cells.xml
index c6f27b8c..cc02a309 100644
--- a/tools/tertiary-analysis/cell-types-analysis/ct_downsample_cells.xml
+++ b/tools/tertiary-analysis/cell-types-analysis/ct_downsample_cells.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>ct_macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         ln -s "${matrix}" matrix.mtx &&
@@ -53,7 +54,7 @@
 
     <help><![CDATA[
     @HELP@
-    
+
     @VERSION_HISTORY@
     ]]></help>
     <expand macro="citations" />
diff --git a/tools/tertiary-analysis/cell-types-analysis/ct_get_consensus_outputs.xml b/tools/tertiary-analysis/cell-types-analysis/ct_get_consensus_outputs.xml
index d2bb6517..03cefa95 100644
--- a/tools/tertiary-analysis/cell-types-analysis/ct_get_consensus_outputs.xml
+++ b/tools/tertiary-analysis/cell-types-analysis/ct_get_consensus_outputs.xml
@@ -3,13 +3,14 @@
     <macros>
         <import>ct_macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         mkdir -p input_dir;
         #for $table in $input_tables:
           cp '$table' input_dir/;
         #end for
-        
+
         get_consensus_output.R --input-dir input_dir --parallel "TRUE" --num-cores \${GALAXY_SLOTS:-1} --cl-dictionary "${lab_cl_mapping}"   --summary-table-output-path "${summary_table_output_path}" --raw-table-output-path "${raw_table_output_path}" --tmpdir ./
         #if $tool_table
         --tool-table "${tool_table}"
@@ -27,10 +28,10 @@
         --exclusions "${exclusions}"
         #end if
         #if $sem_siml_metric
-        --semantic-sim-metric "${sem_siml_metric}" 
+        --semantic-sim-metric "${sem_siml_metric}"
         #end if
         #if $true_labels
-        --true-labels "${true_labels}" 
+        --true-labels "${true_labels}"
         #end if
          ]]></command>
     <inputs>
@@ -60,7 +61,7 @@
     </tests>
     <help><![CDATA[
     @HELP@
-    
+
     @VERSION_HISTORY@
     ]]></help>
     <expand macro="citations" />
diff --git a/tools/tertiary-analysis/cell-types-analysis/ct_get_empirical_dist.xml b/tools/tertiary-analysis/cell-types-analysis/ct_get_empirical_dist.xml
index ee986192..a93f10d2 100644
--- a/tools/tertiary-analysis/cell-types-analysis/ct_get_empirical_dist.xml
+++ b/tools/tertiary-analysis/cell-types-analysis/ct_get_empirical_dist.xml
@@ -3,14 +3,15 @@
     <macros>
         <import>ct_macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
 
-        get_empirical_dist.R --input-ref-file "${input_ref_file}" --label-column-ref "${label_col_ref}" --lab-cl-mapping "${lab_cl_mapping}" --num-iterations "${num_iter}"  --parallel "TRUE" --num-cores \${GALAXY_SLOTS:-1} --tmpdir ./  --output-path "${output_list_path}" 
+        get_empirical_dist.R --input-ref-file "${input_ref_file}" --label-column-ref "${label_col_ref}" --lab-cl-mapping "${lab_cl_mapping}" --num-iterations "${num_iter}"  --parallel "TRUE" --num-cores \${GALAXY_SLOTS:-1} --tmpdir ./  --output-path "${output_list_path}"
 
         #if $ontology_graph
         --ontology-graph "${ontology_graph}"
-        #end if 
+        #end if
         #if $sample_labs
         --sample-labs "${sample_labs}"
         #end if
diff --git a/tools/tertiary-analysis/cell-types-analysis/ct_get_tool_perf_table.xml b/tools/tertiary-analysis/cell-types-analysis/ct_get_tool_perf_table.xml
index 236dab6a..0c540c3c 100644
--- a/tools/tertiary-analysis/cell-types-analysis/ct_get_tool_perf_table.xml
+++ b/tools/tertiary-analysis/cell-types-analysis/ct_get_tool_perf_table.xml
@@ -3,6 +3,7 @@
     <macros>
          <import>ct_macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         mkdir -p input_dir;
@@ -10,7 +11,7 @@
           cp '$input_file' input_dir/;
         #end for
 
-        get_tool_performance_table.R --input-dir input_dir --ref-file "${ref_file}" --parallel "TRUE" --num-cores \${GALAXY_SLOTS:-1} --lab-cl-mapping "${lab_cl_mapping}" --output-path "${output_path}" --tmpdir ./  
+        get_tool_performance_table.R --input-dir input_dir --ref-file "${ref_file}" --parallel "TRUE" --num-cores \${GALAXY_SLOTS:-1} --lab-cl-mapping "${lab_cl_mapping}" --output-path "${output_path}" --tmpdir ./
 
         #if $exclusions
         --exclusions "${exclusions}"
@@ -28,13 +29,13 @@
         --barcode-col-pred "${barcode_col_pred}"
         #end if
         #if $label_col_ref
-        --label-column-ref "${label_col_ref}" 
+        --label-column-ref "${label_col_ref}"
         #end if
         #if $label_col_pred
-        --label-column-pred "${label_col_pred}" 
+        --label-column-pred "${label_col_pred}"
         #end if
         #if $sem_siml_metric
-        --semantic-sim-metric "${sem_siml_metric}" 
+        --semantic-sim-metric "${sem_siml_metric}"
         #end if
 
          ]]></command>
@@ -77,8 +78,8 @@
     </tests>
     <help><![CDATA[
     @HELP@
-    
+
     @VERSION_HISTORY@
     ]]></help>
     <expand macro="citations" />
-</tool> 
+</tool>
diff --git a/tools/tertiary-analysis/cell-types-analysis/ct_get_tool_pvals.xml b/tools/tertiary-analysis/cell-types-analysis/ct_get_tool_pvals.xml
index 0ed0da33..0db07b98 100644
--- a/tools/tertiary-analysis/cell-types-analysis/ct_get_tool_pvals.xml
+++ b/tools/tertiary-analysis/cell-types-analysis/ct_get_tool_pvals.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>ct_macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         get_tool_pvals.R --input-table "${input_table}" --emp-dist-list "${emp_dist_list}" --output-table "${output_table}" ]]></command>
@@ -22,7 +23,7 @@
     </tests>
     <help><![CDATA[
     @HELP@
-    
+
     @VERSION_HISTORY@
     ]]></help>
     <expand macro="citations" />
diff --git a/tools/tertiary-analysis/cell-types-analysis/ct_macros.xml b/tools/tertiary-analysis/cell-types-analysis/ct_macros.xml
index dbfd0438..f3549bb3 100644
--- a/tools/tertiary-analysis/cell-types-analysis/ct_macros.xml
+++ b/tools/tertiary-analysis/cell-types-analysis/ct_macros.xml
@@ -2,6 +2,11 @@
     <token name="@TOOL_VERSION@">1.1.1</token>
     <token name="@HELP@">More information can be found at https://github.com/ebi-gene-expression-group/cell-types-analysis</token>
     <token name="@PROFILE@">18.01</token>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">cell_types_analysis</xref>
+        </xrefs>
+    </xml>
     <xml name="requirements">
       <requirements>
         <requirement type="package" version="0.1.9">cell-types-analysis</requirement>
@@ -17,7 +22,7 @@
 **Version history**
 0.1.6+galaxy0: Add removing non-alphanumeric characters from labels in metadata files
 0.0.5+galaxy0: Initial contribution. Andrey Solovyev, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/.
-0.0.5+galaxy1: Standardise input/output format into .txt. 
+0.0.5+galaxy1: Standardise input/output format into .txt.
     ]]></token>
     <xml name="sem_siml_options">
       <param type="select" name="sem_siml_metric" label="Semantic similarity metric"  help="What semantic similarity metric should be used? NB: if include-sem-siml is set to True, make sure to use a metric that is in the [0;1] interval. See https://www.bioconductor.org/packages/release/bioc/html/Onassis.html for more detail.">
diff --git a/tools/tertiary-analysis/data-hca/matrix-service.xml b/tools/tertiary-analysis/data-hca/matrix-service.xml
index 28e7e7a1..d7dddb35 100644
--- a/tools/tertiary-analysis/data-hca/matrix-service.xml
+++ b/tools/tertiary-analysis/data-hca/matrix-service.xml
@@ -1,6 +1,9 @@
 <?xml version="1.0" encoding="utf-8"?>
 <tool id="hca_matrix_downloader" name="Human Cell Atlas Matrix Downloader" version="v0.0.4+galaxy0">
   <description>retrieves expression matrices and metadata from the Human Cell Atlas.</description>
+  <xrefs>
+      <xref type="bio.tools">human_cell_atlas_matrix_downloader</xref>
+  </xrefs>
   <requirements>
     <requirement type="package" version="0.0.4">hca-matrix-downloader</requirement>
   </requirements>
diff --git a/tools/tertiary-analysis/data-scxa/retrieve-scxa.xml b/tools/tertiary-analysis/data-scxa/retrieve-scxa.xml
index 595337d1..4f032888 100644
--- a/tools/tertiary-analysis/data-scxa/retrieve-scxa.xml
+++ b/tools/tertiary-analysis/data-scxa/retrieve-scxa.xml
@@ -1,6 +1,9 @@
 <?xml version="1.0" encoding="utf-8"?>
 <tool id="retrieve_scxa" name="EBI SCXA Data Retrieval" version="v0.0.2+galaxy2">
   <description>Retrieves expression matrixes and metadata from EBI Single Cell Expression Atlas (SCXA)</description>
+  <xrefs>
+      <xref type="bio.tools">ebi_scxa_data_retrieval</xref>
+  </xrefs>
   <requirements>
     <requirement type="package" version="1.20.1">wget</requirement>
   </requirements>
diff --git a/tools/tertiary-analysis/garnett/garnett_check_markers.xml b/tools/tertiary-analysis/garnett/garnett_check_markers.xml
index 121d1d5b..04f882f6 100644
--- a/tools/tertiary-analysis/garnett/garnett_check_markers.xml
+++ b/tools/tertiary-analysis/garnett/garnett_check_markers.xml
@@ -3,8 +3,8 @@
     <macros>
         <import>garnett_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
     <expand macro="xrefs"/>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         garnett_check_markers.R --cds-object '${cds_object}' --marker-file-path '${marker_file_path}' --database '${database}' --marker-output-path '${marker_output_path}'
 
diff --git a/tools/tertiary-analysis/garnett/garnett_classify_cells.xml b/tools/tertiary-analysis/garnett/garnett_classify_cells.xml
index 383110c6..f29c83f8 100644
--- a/tools/tertiary-analysis/garnett/garnett_classify_cells.xml
+++ b/tools/tertiary-analysis/garnett/garnett_classify_cells.xml
@@ -3,8 +3,8 @@
     <macros>
         <import>garnett_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
     <expand macro="xrefs"/>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         garnett_classify_cells.R --cds-object '${cds_object}' --classifier-object '${classifier_object}' --database '${database}' --cds-output-obj '${cds_output_obj}'
 
diff --git a/tools/tertiary-analysis/garnett/garnett_get_feature_genes.xml b/tools/tertiary-analysis/garnett/garnett_get_feature_genes.xml
index 729e1f1d..7d0c8810 100644
--- a/tools/tertiary-analysis/garnett/garnett_get_feature_genes.xml
+++ b/tools/tertiary-analysis/garnett/garnett_get_feature_genes.xml
@@ -3,8 +3,8 @@
     <macros>
         <import>garnett_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
     <expand macro="xrefs"/>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         garnett_get_feature_genes.R --classifier-object '${classifier_object}'  --database '${database}' --output-path '${output_path}'
 
diff --git a/tools/tertiary-analysis/garnett/garnett_get_std_output.xml b/tools/tertiary-analysis/garnett/garnett_get_std_output.xml
index 326abd26..887a8344 100644
--- a/tools/tertiary-analysis/garnett/garnett_get_std_output.xml
+++ b/tools/tertiary-analysis/garnett/garnett_get_std_output.xml
@@ -3,8 +3,8 @@
     <macros>
         <import>garnett_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
     <expand macro="xrefs"/>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         garnett_get_std_output.R --input-object '${input_object}' --classifier '${classifier}' --output-file-path '${output_file_path}'
     ]]></command>
diff --git a/tools/tertiary-analysis/garnett/garnett_train_classifier.xml b/tools/tertiary-analysis/garnett/garnett_train_classifier.xml
index a8896397..da735ad2 100644
--- a/tools/tertiary-analysis/garnett/garnett_train_classifier.xml
+++ b/tools/tertiary-analysis/garnett/garnett_train_classifier.xml
@@ -3,8 +3,8 @@
     <macros>
         <import>garnett_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
     <expand macro="xrefs"/>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         garnett_train_classifier.R --cds-object '${cds_object}' --marker-file-path '${marker_file_path}' --database '${database}' --cores \${GALAXY_SLOTS:-1} --output-path '${output_classifier_path}'
         #if $train_id
diff --git a/tools/tertiary-analysis/garnett/garnett_transform_markers.xml b/tools/tertiary-analysis/garnett/garnett_transform_markers.xml
index fe5edeec..00158a06 100644
--- a/tools/tertiary-analysis/garnett/garnett_transform_markers.xml
+++ b/tools/tertiary-analysis/garnett/garnett_transform_markers.xml
@@ -3,8 +3,8 @@
     <macros>
         <import>garnett_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
     <expand macro="xrefs"/>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         transform_marker_file.R --input-marker-file '${input_marker_file}' --marker-list '${marker_list}'  --garnett-marker-file '${garnett_marker_file}'
 
diff --git a/tools/tertiary-analysis/garnett/update_marker_file.xml b/tools/tertiary-analysis/garnett/update_marker_file.xml
index 967984b8..e59d4a9f 100644
--- a/tools/tertiary-analysis/garnett/update_marker_file.xml
+++ b/tools/tertiary-analysis/garnett/update_marker_file.xml
@@ -3,8 +3,8 @@
    <macros>
         <import>garnett_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
     <expand macro="xrefs"/>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         update_marker_file.R --marker-list-obj '${marker_list_obj}' --marker-check-file '${marker_check_file}'    --updated-marker-file '${updated_marker_file}'
 
diff --git a/tools/tertiary-analysis/monocle3/monocle3-create.xml b/tools/tertiary-analysis/monocle3/monocle3-create.xml
index e9318e1a..547ea5ed 100644
--- a/tools/tertiary-analysis/monocle3/monocle3-create.xml
+++ b/tools/tertiary-analysis/monocle3/monocle3-create.xml
@@ -4,8 +4,8 @@
   <macros>
     <import>monocle3-macros.xml</import>
   </macros>
-  <expand macro="requirements"/>
   <expand macro="xrefs"/>
+  <expand macro="requirements"/>
   <command detect_errors="exit_code"><![CDATA[
 ln -s '${expression_matrix}' expression_matrix.'${expression_matrix_format}' &&
 #if $cell_metadata
diff --git a/tools/tertiary-analysis/monocle3/monocle3-diffExp.xml b/tools/tertiary-analysis/monocle3/monocle3-diffExp.xml
index 72c2e4c9..c91978cb 100644
--- a/tools/tertiary-analysis/monocle3/monocle3-diffExp.xml
+++ b/tools/tertiary-analysis/monocle3/monocle3-diffExp.xml
@@ -4,8 +4,8 @@
   <macros>
     <import>monocle3-macros.xml</import>
   </macros>
-  <expand macro="requirements"/>
   <expand macro="xrefs"/>
+  <expand macro="requirements"/>
   <command detect_errors="exit_code"><![CDATA[
 LANG=en_US.UTF-8 monocle3 diffExp
     --neighbor-graph '$(neighbor_graph)'
diff --git a/tools/tertiary-analysis/monocle3/monocle3-learnGraph.xml b/tools/tertiary-analysis/monocle3/monocle3-learnGraph.xml
index 189fa9da..da68da4d 100644
--- a/tools/tertiary-analysis/monocle3/monocle3-learnGraph.xml
+++ b/tools/tertiary-analysis/monocle3/monocle3-learnGraph.xml
@@ -4,8 +4,8 @@
   <macros>
     <import>monocle3-macros.xml</import>
   </macros>
-  <expand macro="requirements"/>
   <expand macro="xrefs"/>
+  <expand macro="requirements"/>
   <command detect_errors="exit_code"><![CDATA[
 LANG=en_US.UTF-8 monocle3 learnGraph
 #if $no_partition
diff --git a/tools/tertiary-analysis/monocle3/monocle3-orderCells.xml b/tools/tertiary-analysis/monocle3/monocle3-orderCells.xml
index f1f285d3..f0404a84 100644
--- a/tools/tertiary-analysis/monocle3/monocle3-orderCells.xml
+++ b/tools/tertiary-analysis/monocle3/monocle3-orderCells.xml
@@ -4,8 +4,8 @@
   <macros>
     <import>monocle3-macros.xml</import>
   </macros>
-  <expand macro="requirements"/>
   <expand macro="xrefs"/>
+  <expand macro="requirements"/>
   <command detect_errors="exit_code"><![CDATA[
 LANG=en_US.UTF-8 monocle3 orderCells
     --reduction-method '${reduction_method}'
diff --git a/tools/tertiary-analysis/monocle3/monocle3-partition.xml b/tools/tertiary-analysis/monocle3/monocle3-partition.xml
index ddbaed0a..065f3be7 100644
--- a/tools/tertiary-analysis/monocle3/monocle3-partition.xml
+++ b/tools/tertiary-analysis/monocle3/monocle3-partition.xml
@@ -4,8 +4,8 @@
   <macros>
     <import>monocle3-macros.xml</import>
   </macros>
-  <expand macro="requirements"/>
   <expand macro="xrefs"/>
+  <expand macro="requirements"/>
   <command detect_errors="exit_code"><![CDATA[
 LANG=en_US.UTF-8 monocle3 partition
     --reduction-method '${reduction_method}'
diff --git a/tools/tertiary-analysis/monocle3/monocle3-preprocess.xml b/tools/tertiary-analysis/monocle3/monocle3-preprocess.xml
index 43acbf8c..6435ef41 100644
--- a/tools/tertiary-analysis/monocle3/monocle3-preprocess.xml
+++ b/tools/tertiary-analysis/monocle3/monocle3-preprocess.xml
@@ -4,8 +4,8 @@
   <macros>
     <import>monocle3-macros.xml</import>
   </macros>
-  <expand macro="requirements"/>
   <expand macro="xrefs"/>
+  <expand macro="requirements"/>
   <command detect_errors="exit_code"><![CDATA[
 LANG=en_US.UTF-8 monocle3 preprocess
     --method '${method}'
diff --git a/tools/tertiary-analysis/monocle3/monocle3-reduceDim.xml b/tools/tertiary-analysis/monocle3/monocle3-reduceDim.xml
index b2686b1f..420a3391 100644
--- a/tools/tertiary-analysis/monocle3/monocle3-reduceDim.xml
+++ b/tools/tertiary-analysis/monocle3/monocle3-reduceDim.xml
@@ -4,8 +4,8 @@
   <macros>
     <import>monocle3-macros.xml</import>
   </macros>
-  <expand macro="requirements"/>
   <expand macro="xrefs"/>
+  <expand macro="requirements"/>
   <command detect_errors="exit_code"><![CDATA[
 LANG=en_US.UTF-8 monocle3 reduceDim
 #if $max_components
diff --git a/tools/tertiary-analysis/pyscenic/macros.xml b/tools/tertiary-analysis/pyscenic/macros.xml
index 921e3bea..86bd80bf 100644
--- a/tools/tertiary-analysis/pyscenic/macros.xml
+++ b/tools/tertiary-analysis/pyscenic/macros.xml
@@ -2,7 +2,7 @@
     <token name="@TOOL_VERSION@">0.12.1</token>
     <xml name="xrefs">
         <xrefs>
-            <xref type="bio.tools">maaslin2</xref>
+            <xref type="bio.tools">scenic</xref>
         </xrefs>
     </xml>
     <xml name="requirements">
diff --git a/tools/tertiary-analysis/pyscenic/pyscenic_aucell.xml b/tools/tertiary-analysis/pyscenic/pyscenic_aucell.xml
index 108a6f6e..4b860ee5 100644
--- a/tools/tertiary-analysis/pyscenic/pyscenic_aucell.xml
+++ b/tools/tertiary-analysis/pyscenic/pyscenic_aucell.xml
@@ -3,8 +3,8 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
     <expand macro="xrefs"/>
+    <expand macro="requirements"/>
     <command><![CDATA[
         ln -s '${expression_mtx_fname}' expr_mat.loom &&
         ln -s '${signatures_fname}' regulons.tsv &&
@@ -67,37 +67,37 @@
     <help>
         <![CDATA[
           Run PySCENIC aucell command to analyze single-cell gene expression data.
-    
+
           **Input Parameters:**
-    
+
           - **expression_mtx_fname**: The name of the file that contains the expression matrix for the single cell experiment. Two file formats are supported: csv (rows=cells x columns=genes) or loom (rows=genes x columns=cells).
-    
+
           - **signatures_fname**: The name of the file that contains the gene signatures. Three file formats are supported: gmt, yaml, or dat (pickle).
-    
+
           **Options:**
-    
+
           - **-o, --output**: Output file/stream, a matrix of AUC values. Two file formats are supported: csv or loom. If loom file is specified, it will contain the original expression matrix and the calculated AUC values as extra column attributes.
-    
+
           - **-t, --transpose**: Transpose the expression matrix if supplied as csv (rows=genes x columns=cells).
-    
+
           - **-w, --weights**: Use weights associated with genes in recovery analysis. Is only relevant when gene signatures are supplied as json format.
-    
+
           - **--seed**: Seed for the expression matrix ranking step. The default is to use a random seed.
-    
+
           **Motif Enrichment Arguments:**
-    
+
           - **--rank_threshold**: The rank threshold used for deriving the target genes of an enriched motif (default: 5000).
-    
+
           - **--auc_threshold**: The threshold used for calculating the AUC of a feature as fraction of ranked genes (default: 0.05).
-    
+
           - **--nes_threshold**: The Normalized Enrichment Score (NES) threshold for finding enriched features (default: 3.0).
-    
+
           **Loom File Arguments:**
-    
+
           - **--cell_id_attribute**: The name of the column attribute that specifies the identifiers of the cells in the loom file.
-    
+
           - **--gene_attribute**: The name of the row attribute that specifies the gene symbols in the loom file.
-    
+
           - **--sparse**: If set, load the expression data as a sparse matrix. Currently applies to the grn inference step only.
         ]]>
       </help>
diff --git a/tools/tertiary-analysis/pyscenic/pyscenic_binarize_aucell.xml b/tools/tertiary-analysis/pyscenic/pyscenic_binarize_aucell.xml
index 084d1f39..3047c096 100644
--- a/tools/tertiary-analysis/pyscenic/pyscenic_binarize_aucell.xml
+++ b/tools/tertiary-analysis/pyscenic/pyscenic_binarize_aucell.xml
@@ -3,8 +3,8 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
     <expand macro="xrefs"/>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code">
         <![CDATA[
         ln -s $input_file aucell.tsv &&
@@ -51,7 +51,7 @@
         <![CDATA[
         **What it does**
 
-        This tool binarizes an AUC matrix using the `binarize` function from the `pySCENIC` package. 
+        This tool binarizes an AUC matrix using the `binarize` function from the `pySCENIC` package.
         It produces a classification of the cell per given AUCell into passing or not passing an
         automatically defined threshold, through binarization (when possible) of the AUCell distribution.
         See the SCENIC paper or the PySCENIC notebooks for more details.
diff --git a/tools/tertiary-analysis/pyscenic/pyscenic_ctx.xml b/tools/tertiary-analysis/pyscenic/pyscenic_ctx.xml
index b1d6ece5..db4c1ab3 100644
--- a/tools/tertiary-analysis/pyscenic/pyscenic_ctx.xml
+++ b/tools/tertiary-analysis/pyscenic/pyscenic_ctx.xml
@@ -5,15 +5,15 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
     <expand macro="xrefs"/>
+    <expand macro="requirements"/>
     <command><![CDATA[
     #set PySCENIC_DB = "db.genes_vs_motifs.rankings.feather"
     ln -s '${module_fname}' tf2targets.tsv &&
     ln -s '${expression_mtx}' expr_mat.loom &&
     ln -s '${database_fname}' ${PySCENIC_DB} &&
 
-    pyscenic ctx tf2targets.tsv ${PySCENIC_DB} 
+    pyscenic ctx tf2targets.tsv ${PySCENIC_DB}
         --expression_mtx_fname expr_mat.loom
     --output regulons.tsv
 $no_pruning
@@ -103,19 +103,19 @@ $sparse
     <help><![CDATA[
         .. class:: infomark
            :name: warning
-        
+
            **pySCENIC ctx: Contextualize GRN**
-        
+
         This tool refines gene regulatory networks (GRNs) by pruning targets that do not have an enrichment for a corresponding motif of the transcription factor (TF). This process effectively separates direct from indirect targets based on the presence of cis-regulatory footprints.
-        
+
         **Inputs:**
-        
+
         - **Module File**: A file containing the signature or co-expression modules. Supported formats include CSV, TSV (adjacencies), YAML, GMT, and DAT (modules).
         - **Database Files**: One or more regulatory feature databases. Supported formats include feather or db (legacy).
         - **Annotations File**: A file containing the motif annotations to use.
-        
+
         **Optional Parameters:**
-        
+
         - **No Pruning**: Do not perform pruning, i.e., find enriched motifs.
         - **Chunk Size**: The size of the module chunks assigned to a node in the dask graph (default: 100).
         - **Mode**: The mode to be used for computing (default: custom_multiprocessing).
diff --git a/tools/tertiary-analysis/pyscenic/pyscenic_grn.xml b/tools/tertiary-analysis/pyscenic/pyscenic_grn.xml
index 7d2141d9..df1fe4cb 100644
--- a/tools/tertiary-analysis/pyscenic/pyscenic_grn.xml
+++ b/tools/tertiary-analysis/pyscenic/pyscenic_grn.xml
@@ -3,16 +3,16 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
     <expand macro="xrefs"/>
+    <expand macro="requirements"/>
     <command detect_errors="exit_code">
         <![CDATA[
-            ln -s '${expression_mtx}' expr_mat.loom && 
+            ln -s '${expression_mtx}' expr_mat.loom &&
             ln -s '${tfs_fname}' tfs.txt &&
             #if $use_arboretum
                 arboreto_with_multiprocessing.py
             #else
-                pyscenic grn 
+                pyscenic grn
             #end if
             -o tf2targets.tsv
             $transpose
@@ -30,7 +30,7 @@
             --gene_attribute '${gene_attribute}'
             #end if
             $sparse
-            
+
             expr_mat.loom tfs.txt &&
             mv tf2targets.tsv '${tf2targets}'
         ]]>
@@ -82,7 +82,7 @@
 
         - Expression Matrix File: Loom file containing the expression matrix, (rows=genes x columns=cells)
         - Transcription Factors File: TXT file with a list of transcription factors.
-        
+
         **Options:**
 
         - Output File: Path to the output file (CSV format).
diff --git a/tools/tertiary-analysis/sc3/sc3-calc-biology.xml b/tools/tertiary-analysis/sc3/sc3-calc-biology.xml
index f565e6c2..1729d5e1 100644
--- a/tools/tertiary-analysis/sc3/sc3-calc-biology.xml
+++ b/tools/tertiary-analysis/sc3/sc3-calc-biology.xml
@@ -4,8 +4,8 @@
   <macros>
     <import>sc3-macros.xml</import>
   </macros>
-  <expand macro="requirements" />
   <expand macro="xrefs"/>
+  <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
 sc3-sc3-calc-biology.R -i '${sc3_consensus}' -o '${sc3_biology_markers}' -t '${sc3_biology_markers_tsv}' -k '${ks}' -r '${regime}'
   ]]></command>
diff --git a/tools/tertiary-analysis/sc3/sc3-calc-consens.xml b/tools/tertiary-analysis/sc3/sc3-calc-consens.xml
index 47b76efa..7134eb16 100644
--- a/tools/tertiary-analysis/sc3/sc3-calc-consens.xml
+++ b/tools/tertiary-analysis/sc3/sc3-calc-consens.xml
@@ -4,8 +4,8 @@
   <macros>
     <import>sc3-macros.xml</import>
   </macros>
-  <expand macro="requirements" />
   <expand macro="xrefs"/>
+  <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
 sc3-sc3-calc-consens.R -i '${sc3_kmeans}' -t '${clusters}' -o '${sc3_consensus}'
   ]]></command>
diff --git a/tools/tertiary-analysis/sc3/sc3-calc-dists.xml b/tools/tertiary-analysis/sc3/sc3-calc-dists.xml
index f604c030..5a047e21 100644
--- a/tools/tertiary-analysis/sc3/sc3-calc-dists.xml
+++ b/tools/tertiary-analysis/sc3/sc3-calc-dists.xml
@@ -4,8 +4,8 @@
   <macros>
     <import>sc3-macros.xml</import>
   </macros>
-  <expand macro="requirements" />
   <expand macro="xrefs"/>
+  <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
 sc3-sc3-calc-dists.R -i '${sc3_prepared}' -o '${sc3_distances}'
   ]]></command>
diff --git a/tools/tertiary-analysis/sc3/sc3-calc-transfs.xml b/tools/tertiary-analysis/sc3/sc3-calc-transfs.xml
index 9e350863..aa7cf4e2 100644
--- a/tools/tertiary-analysis/sc3/sc3-calc-transfs.xml
+++ b/tools/tertiary-analysis/sc3/sc3-calc-transfs.xml
@@ -4,8 +4,8 @@
   <macros>
     <import>sc3-macros.xml</import>
   </macros>
-  <expand macro="requirements" />
   <expand macro="xrefs"/>
+  <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
 sc3-sc3-calc-transfs.R -i '${sc3_distances}' -o '${sc3_transformed}'
   ]]></command>
diff --git a/tools/tertiary-analysis/sc3/sc3-estimate-k.xml b/tools/tertiary-analysis/sc3/sc3-estimate-k.xml
index 961febf9..064aec3a 100644
--- a/tools/tertiary-analysis/sc3/sc3-estimate-k.xml
+++ b/tools/tertiary-analysis/sc3/sc3-estimate-k.xml
@@ -4,8 +4,8 @@
   <macros>
     <import>sc3-macros.xml</import>
   </macros>
-  <expand macro="requirements" />
   <expand macro="xrefs"/>
+  <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
 sc3-sc3-estimate-k.R -i '${sc3_prepared}' -t '${sc3_estimated_k}' -o sc3_estimated.rds &&
 
diff --git a/tools/tertiary-analysis/sc3/sc3-kmeans.xml b/tools/tertiary-analysis/sc3/sc3-kmeans.xml
index 68fb2f96..2dcc9698 100644
--- a/tools/tertiary-analysis/sc3/sc3-kmeans.xml
+++ b/tools/tertiary-analysis/sc3/sc3-kmeans.xml
@@ -4,8 +4,8 @@
   <macros>
     <import>sc3-macros.xml</import>
   </macros>
-  <expand macro="requirements" />
   <expand macro="xrefs"/>
+  <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
 sc3-sc3-kmeans.R -i '${sc3_transformed}'
 #if $choose.method == "file":
diff --git a/tools/tertiary-analysis/sc3/sc3-prepare.xml b/tools/tertiary-analysis/sc3/sc3-prepare.xml
index 280f652a..c5564477 100644
--- a/tools/tertiary-analysis/sc3/sc3-prepare.xml
+++ b/tools/tertiary-analysis/sc3/sc3-prepare.xml
@@ -4,8 +4,8 @@
   <macros>
     <import>sc3-macros.xml</import>
   </macros>
-  <expand macro="requirements" />
   <expand macro="xrefs"/>
+  <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
 sc3-sc3-prepare.R -i '${scater_log}' -o '${sc3_prepared}' -t 1
 
diff --git a/tools/tertiary-analysis/scater/scater-calculate-cpm.xml b/tools/tertiary-analysis/scater/scater-calculate-cpm.xml
index a18eb3bc..6f56305a 100644
--- a/tools/tertiary-analysis/scater/scater-calculate-cpm.xml
+++ b/tools/tertiary-analysis/scater/scater-calculate-cpm.xml
@@ -3,8 +3,8 @@
   <macros>
     <import>scater_macros.xml</import>
   </macros>
-  <expand macro="requirements" />
   <expand macro="xrefs"/>
+  <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
 scater-calculate-cpm.R -i '${R_scater_serialized}'
     -s '$size_factors'
diff --git a/tools/tertiary-analysis/scater/scater-calculate-qc-metrics.xml b/tools/tertiary-analysis/scater/scater-calculate-qc-metrics.xml
index 81bbc6de..138939c9 100644
--- a/tools/tertiary-analysis/scater/scater-calculate-qc-metrics.xml
+++ b/tools/tertiary-analysis/scater/scater-calculate-qc-metrics.xml
@@ -3,8 +3,8 @@
   <macros>
     <import>scater_macros.xml</import>
   </macros>
-  <expand macro="requirements" />
   <expand macro="xrefs"/>
+  <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
 scater-calculate-qc-metrics.R -i '$R_scater_serialized'
 #if $exprs_values:
diff --git a/tools/tertiary-analysis/scater/scater-filter.xml b/tools/tertiary-analysis/scater/scater-filter.xml
index 663b597f..856fdae7 100644
--- a/tools/tertiary-analysis/scater/scater-filter.xml
+++ b/tools/tertiary-analysis/scater/scater-filter.xml
@@ -3,8 +3,8 @@
   <macros>
     <import>scater_macros.xml</import>
   </macros>
-  <expand macro="requirements" />
   <expand macro="xrefs"/>
+  <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
 scater-filter.R -i '${R_scater_qc}' -o '$R_scater_filtered'
 #if $cell_parameters
diff --git a/tools/tertiary-analysis/scater/scater-is-outlier.xml b/tools/tertiary-analysis/scater/scater-is-outlier.xml
index bd38804f..76e09813 100644
--- a/tools/tertiary-analysis/scater/scater-is-outlier.xml
+++ b/tools/tertiary-analysis/scater/scater-is-outlier.xml
@@ -3,8 +3,8 @@
   <macros>
     <import>scater_macros.xml</import>
   </macros>
-  <expand macro="requirements" />
   <expand macro="xrefs"/>
+  <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
 scater-extract-qc-metric.R -i '${R_scater_qc}' -m '$metrics' -o metrics.csv &&
 
diff --git a/tools/tertiary-analysis/scater/scater-normalize.xml b/tools/tertiary-analysis/scater/scater-normalize.xml
index c8d436ad..5fffde0f 100644
--- a/tools/tertiary-analysis/scater/scater-normalize.xml
+++ b/tools/tertiary-analysis/scater/scater-normalize.xml
@@ -3,8 +3,8 @@
   <macros>
     <import>scater_macros.xml</import>
   </macros>
-  <expand macro="requirements" />
   <expand macro="xrefs"/>
+  <expand macro="requirements" />
   <command detect_errors="exit_code"><![CDATA[
 scater-normalize.R -i '${R_scater_qc}'
 #if $exprs_value:
diff --git a/tools/tertiary-analysis/scater/scater-read-10x-results.xml b/tools/tertiary-analysis/scater/scater-read-10x-results.xml
index 310d2ca3..ee2b4e20 100644
--- a/tools/tertiary-analysis/scater/scater-read-10x-results.xml
+++ b/tools/tertiary-analysis/scater/scater-read-10x-results.xml
@@ -3,8 +3,8 @@
     <macros>
         <import>scater_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
     <expand macro="xrefs"/>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         ln -s '$matrix' matrix.mtx;
         ln -s '$genes' genes.tsv;
diff --git a/tools/tertiary-analysis/sccaf/run_sccaf.xml b/tools/tertiary-analysis/sccaf/run_sccaf.xml
index 9c0bcb73..f01bc343 100644
--- a/tools/tertiary-analysis/sccaf/run_sccaf.xml
+++ b/tools/tertiary-analysis/sccaf/run_sccaf.xml
@@ -4,6 +4,7 @@
   <macros>
     <import>sccaf_macros.xml</import>
   </macros>
+  <expand macro="xrefs"/>
   <expand macro="requirements"/>
   <command detect_errors="exit_code"><![CDATA[
 ln -s ${input_obj_file} input.h5 &&
diff --git a/tools/tertiary-analysis/sccaf/sccaf_asses.xml b/tools/tertiary-analysis/sccaf/sccaf_asses.xml
index eb3ee8ae..b90a0445 100644
--- a/tools/tertiary-analysis/sccaf/sccaf_asses.xml
+++ b/tools/tertiary-analysis/sccaf/sccaf_asses.xml
@@ -4,6 +4,7 @@
   <macros>
     <import>sccaf_macros.xml</import>
   </macros>
+  <expand macro="xrefs"/>
   <expand macro="requirements"/>
   <command detect_errors="exit_code"><![CDATA[
 ln -s ${input_obj_file} input.h5 &&
diff --git a/tools/tertiary-analysis/sccaf/sccaf_asses_merger.xml b/tools/tertiary-analysis/sccaf/sccaf_asses_merger.xml
index 15d57b6d..abdc70d2 100644
--- a/tools/tertiary-analysis/sccaf/sccaf_asses_merger.xml
+++ b/tools/tertiary-analysis/sccaf/sccaf_asses_merger.xml
@@ -4,6 +4,7 @@
   <macros>
     <import>sccaf_macros.xml</import>
   </macros>
+  <expand macro="xrefs"/>
   <expand macro="requirements"/>
   <command detect_errors="exit_code"><![CDATA[
 
@@ -49,7 +50,7 @@ provided by the optimisation process.
 
 To produce the required Round files collection, RUN SCCAF needs to be run in
 optimisation mode and enable the `Produce parameter walk for asessment distribution`
-option. 
+option.
 ]]></help>
   <!-- <expand macro="citations"/> -->
 </tool>
diff --git a/tools/tertiary-analysis/sccaf/sccaf_macros.xml b/tools/tertiary-analysis/sccaf/sccaf_macros.xml
index 10dbaab3..1ea29f1d 100644
--- a/tools/tertiary-analysis/sccaf/sccaf_macros.xml
+++ b/tools/tertiary-analysis/sccaf/sccaf_macros.xml
@@ -1,4 +1,9 @@
 <macros>
+  <xml name="xrefs">
+    <xrefs>
+      <xref type="bio.tools">sccaf</xref>
+    </xrefs>
+  </xml>
   <xml name="requirements">
     <requirements>
       <requirement type="package" version="@TOOL_VERSION@">sccaf</requirement>
diff --git a/tools/tertiary-analysis/sccaf/sccaf_regress_out.xml b/tools/tertiary-analysis/sccaf/sccaf_regress_out.xml
index 7a35dad3..1f9a156a 100644
--- a/tools/tertiary-analysis/sccaf/sccaf_regress_out.xml
+++ b/tools/tertiary-analysis/sccaf/sccaf_regress_out.xml
@@ -4,6 +4,7 @@
   <macros>
     <import>sccaf_macros.xml</import>
   </macros>
+  <expand macro="xrefs"/>
   <expand macro="requirements"/>
   <command detect_errors="exit_code"><![CDATA[
   ln -s '${input_obj_file}' input.h5 &&
diff --git a/tools/tertiary-analysis/sceasy/sceasy_convert.xml b/tools/tertiary-analysis/sceasy/sceasy_convert.xml
index 709651a4..8c0f26ca 100644
--- a/tools/tertiary-analysis/sceasy/sceasy_convert.xml
+++ b/tools/tertiary-analysis/sceasy/sceasy_convert.xml
@@ -4,8 +4,8 @@
   <macros>
     <import>sceasy_macros.xml</import>
   </macros>
-  <expand macro="requirements"/>
   <expand macro="xrefs"/>
+  <expand macro="requirements"/>
   <command detect_errors="exit_code"><![CDATA[
 #if str($conversion['direction']).startswith("loom")
     ln -s ${conversion.input_object_file} input.loom &&
diff --git a/tools/tertiary-analysis/scmap/scmap_get_std_output.xml b/tools/tertiary-analysis/scmap/scmap_get_std_output.xml
index c74ff7b7..20cfce68 100644
--- a/tools/tertiary-analysis/scmap/scmap_get_std_output.xml
+++ b/tools/tertiary-analysis/scmap/scmap_get_std_output.xml
@@ -3,8 +3,8 @@
     <macros>
          <import>scmap_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
     <expand macro="xrefs"/>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         scmap_get_std_output.R
         --predictions-file "${input_predictions_file}"
@@ -14,7 +14,7 @@
         --sim-col-name "${sim_col_name}"
         #if $index
           --index "${index}"
-        #end if   
+        #end if
     ]]></command>
     <inputs>
         <param type="data" name="input_predictions_file" label="Scmap predictions file in text format" format="txt" help="Path to the predictions file in text format" />
@@ -43,16 +43,14 @@
         </test>
     </tests>
     <help><![CDATA[
-    Generate output tables in tab-separated format compatible with input specified in cell-types-analysis package: https://github.com/ebi-gene-expression-group/cell-types-analysis. 
-    See the example snippet below: 
+    Generate output tables in tab-separated format compatible with input specified in cell-types-analysis package: https://github.com/ebi-gene-expression-group/cell-types-analysis.
+    See the example snippet below:
     ________________________________________
     |  cell_id   | predicted_label | score |
     | ERR2632411 | memory B cell   |  0.8  |
     ...
-    
+
     @VERSION_HISTORY@
     ]]></help>
     <expand macro="citations" />
 </tool>
-
-
diff --git a/tools/tertiary-analysis/scmap/scmap_index_cell.xml b/tools/tertiary-analysis/scmap/scmap_index_cell.xml
index 42b3b601..0d4b8ee3 100644
--- a/tools/tertiary-analysis/scmap/scmap_index_cell.xml
+++ b/tools/tertiary-analysis/scmap/scmap_index_cell.xml
@@ -3,19 +3,19 @@
     <macros>
         <import>scmap_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
     <expand macro="xrefs"/>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object sce_object_preprocessed.rds &&
         scmap-index-cell.R --input-object-file sce_object_preprocessed.rds --output-object-file '$output_single_cell_experiment' --random-seed '$random_seed' --remove-mat '${remove_mat}'
         #if $train_id
-        --train-id '${train_id}' 
+        --train-id '${train_id}'
         #end if
         #if $n_chunks
         --number-chunks '$n_chunks'
         #end if
         #if $n_clusters
-        --number-clusters '$n_clusters' 
+        --number-clusters '$n_clusters'
         #end if
 
     ]]></command>
@@ -39,7 +39,7 @@
     </tests>
     <help><![CDATA[
     @HELP@
-    
+
     @VERSION_HISTORY@
     ]]></help>
     <expand macro="citations" />
diff --git a/tools/tertiary-analysis/scmap/scmap_index_cluster.xml b/tools/tertiary-analysis/scmap/scmap_index_cluster.xml
index aab281a5..aa53e228 100644
--- a/tools/tertiary-analysis/scmap/scmap_index_cluster.xml
+++ b/tools/tertiary-analysis/scmap/scmap_index_cluster.xml
@@ -3,13 +3,13 @@
     <macros>
         <import>scmap_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
     <expand macro="xrefs"/>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object sce_object_preprocessed.rds && scmap-index-cluster.R --input-object-file sce_object_preprocessed.rds --cluster-col '$cluster_col' --output-object-file '$output_single_cell_experiment' --output-plot-file '$plot'
         --remove-mat '${remove_mat}'
         #if $train_id
-        --train-id '${train_id}' 
+        --train-id '${train_id}'
         #end if
     ]]></command>
     <inputs>
@@ -32,7 +32,7 @@
     </tests>
     <help><![CDATA[
     @HELP@
-    
+
     @VERSION_HISTORY@
     ]]></help>
     <expand macro="citations" />
diff --git a/tools/tertiary-analysis/scmap/scmap_preprocess_sce.xml b/tools/tertiary-analysis/scmap/scmap_preprocess_sce.xml
index 5d8733bf..128b2e44 100644
--- a/tools/tertiary-analysis/scmap/scmap_preprocess_sce.xml
+++ b/tools/tertiary-analysis/scmap/scmap_preprocess_sce.xml
@@ -3,8 +3,8 @@
     <macros>
         <import>scmap_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
     <expand macro="xrefs"/>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         scmap-preprocess-sce.R --input-object "${input_single_cell_experiment}" --output-sce-object "${output_single_cell_experiment}"
         ]]></command>
@@ -16,7 +16,7 @@
     </outputs>
     <help><![CDATA[
     @HELP@
-    
+
     @VERSION_HISTORY@
     ]]></help>
     <expand macro="citations" />
diff --git a/tools/tertiary-analysis/scmap/scmap_scmap_cell.xml b/tools/tertiary-analysis/scmap/scmap_scmap_cell.xml
index 24cf9347..70ee96d7 100644
--- a/tools/tertiary-analysis/scmap/scmap_scmap_cell.xml
+++ b/tools/tertiary-analysis/scmap/scmap_scmap_cell.xml
@@ -3,8 +3,8 @@
     <macros>
         <import>scmap_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
     <expand macro="xrefs"/>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         scmap-scmap-cell.R
             -i '$index_single_cell_experiment'
diff --git a/tools/tertiary-analysis/scmap/scmap_scmap_cluster.xml b/tools/tertiary-analysis/scmap/scmap_scmap_cluster.xml
index ee345354..a0ecc2a8 100644
--- a/tools/tertiary-analysis/scmap/scmap_scmap_cluster.xml
+++ b/tools/tertiary-analysis/scmap/scmap_scmap_cluster.xml
@@ -3,8 +3,8 @@
     <macros>
         <import>scmap_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
     <expand macro="xrefs"/>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         scmap-scmap-cluster.R --index-object-file '$index_single_cell_experiment' --projection-object-file '$project_single_cell_experiment' --threshold '$threshold' --output-object-file '$output_single_cell_experiment' --output-text-file '$output_txt'
     ]]></command>
@@ -36,7 +36,7 @@
     </tests>
     <help><![CDATA[
     @HELP@
-    
+
     @VERSION_HISTORY@
     ]]></help>
     <expand macro="citations" />
diff --git a/tools/tertiary-analysis/scmap/scmap_select_features.xml b/tools/tertiary-analysis/scmap/scmap_select_features.xml
index 4ad9bdca..64d3c710 100644
--- a/tools/tertiary-analysis/scmap/scmap_select_features.xml
+++ b/tools/tertiary-analysis/scmap/scmap_select_features.xml
@@ -3,13 +3,13 @@
     <macros>
         <import>scmap_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
     <expand macro="xrefs"/>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        scmap-preprocess-sce.R 
+        scmap-preprocess-sce.R
          --input-object "${input_single_cell_experiment}"
-         --output-sce-object "result.preprocessed" && 
-        scmap-select-features.R 
+         --output-sce-object "result.preprocessed" &&
+        scmap-select-features.R
          --input-object-file "result.preprocessed"
          --n-features '$n_features'
          --output-object-file '$output_single_cell_experiment'
@@ -32,7 +32,7 @@
     </tests>
     <help><![CDATA[
     @HELP@
-    
+
     @VERSION_HISTORY@
     ]]></help>
     <expand macro="citations" />
diff --git a/tools/tertiary-analysis/scpred/scpred_get_feature_space.xml b/tools/tertiary-analysis/scpred/scpred_get_feature_space.xml
index 5c253b07..d9cf363d 100644
--- a/tools/tertiary-analysis/scpred/scpred_get_feature_space.xml
+++ b/tools/tertiary-analysis/scpred/scpred_get_feature_space.xml
@@ -3,20 +3,20 @@
     <macros>
          <import>scpred_macros.xml</import>
     </macros>
-    <expand macro='requirements' />
     <expand macro="xrefs"/>
+    <expand macro='requirements' />
     <command detect_errors='exit_code'><![CDATA[
-        scpred_get_feature_space.R  --input-object '${input_object}'  --prediction-column '${prediction_column}'   --output-path '${output_obj_path}' 
-     
+        scpred_get_feature_space.R  --input-object '${input_object}'  --prediction-column '${prediction_column}'   --output-path '${output_obj_path}'
+
         #if $correction_method
-        --correction-method '${correction_method}' 
+        --correction-method '${correction_method}'
         #end if
         #if $significance_threshold
         --significance-threshold '${significance_threshold}'
-        #end if 
+        #end if
         #if $reduction_parameter
         --reduction-parameter '${reduction_parameter}'
-        #end if 
+        #end if
 
 
         ]]></command>
@@ -26,7 +26,7 @@
         <param type='text' name='correction_method' label='Correction Method' optional='true' value="fdr" help='Method for mulpiple testing correction' />
         <param type='float' name='significance_threshold' label='Significance Threshold' optional='true' value="1.0" help='Significance threshold for principal components explaining class identity' />
         <param type='text' name='reduction_parameter' label='Reduction Parameter' optional='true' value="pca" help='Name of reduction in Seurat objet to be used to determine the feature space. Default: "pca"' />
-        
+
     </inputs>
     <outputs>
         <data name='output_obj_path' format='rdata' />
@@ -39,7 +39,7 @@
     </tests>
     <help><![CDATA[
     @HELP@
-    
+
     @VERSION_HISTORY@
     ]]></help>
     <expand macro='citations' />
diff --git a/tools/tertiary-analysis/scpred/scpred_get_std_output.xml b/tools/tertiary-analysis/scpred/scpred_get_std_output.xml
index 422b31f4..ce8549c9 100644
--- a/tools/tertiary-analysis/scpred/scpred_get_std_output.xml
+++ b/tools/tertiary-analysis/scpred/scpred_get_std_output.xml
@@ -3,10 +3,10 @@
     <macros>
         <import>scpred_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
     <expand macro="xrefs"/>
-    <command detect_errors="exit_code"><![CDATA[ 
-        scpred_get_std_output.R --predictions-object "${predictions_object}" --get-scores "${get_scores}" --classifier '${classifier}' --output-table "${output_table}" 
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        scpred_get_std_output.R --predictions-object "${predictions_object}" --get-scores "${get_scores}" --classifier '${classifier}' --output-table "${output_table}"
         ]]></command>
     <inputs>
         <param type="data" name="predictions_object" label="Predictions Object" format="rdata" help="Path to the predictions file in text format" />
@@ -26,7 +26,7 @@
     </tests>
     <help><![CDATA[
     @HELP@
-    
+
     @VERSION_HISTORY@
     ]]></help>
     <expand macro="citations" />
diff --git a/tools/tertiary-analysis/scpred/scpred_predict.xml b/tools/tertiary-analysis/scpred/scpred_predict.xml
index 2fe31738..898c2d05 100644
--- a/tools/tertiary-analysis/scpred/scpred_predict.xml
+++ b/tools/tertiary-analysis/scpred/scpred_predict.xml
@@ -3,10 +3,10 @@
      <macros>
         <import>scpred_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
     <expand macro="xrefs"/>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        scpred_predict.R --input-object "${input_object}" --pred-data "${pred_data}" --normalise-data "${normalise_data}"       --recompute-alignment "${recompute_alignment}" --reference-scaling "${reference_scaling}" --output-path "${output_path}"  
+        scpred_predict.R --input-object "${input_object}" --pred-data "${pred_data}" --normalise-data "${normalise_data}"       --recompute-alignment "${recompute_alignment}" --reference-scaling "${reference_scaling}" --output-path "${output_path}"
 
         #if $normalisation_method
         --normalisation-method "${normalisation_method}"
@@ -48,8 +48,8 @@
     </tests>
      <help><![CDATA[
     @HELP@
-    
+
     @VERSION_HISTORY@
     ]]></help>
     <expand macro="citations" />
-</tool> 
+</tool>
diff --git a/tools/tertiary-analysis/scpred/scpred_train_model.xml b/tools/tertiary-analysis/scpred/scpred_train_model.xml
index 9e086738..32a9e1a4 100644
--- a/tools/tertiary-analysis/scpred/scpred_train_model.xml
+++ b/tools/tertiary-analysis/scpred/scpred_train_model.xml
@@ -3,21 +3,21 @@
     <macros>
         <import>scpred_macros.xml</import>
     </macros>
-    <expand macro="requirements" />
     <expand macro="xrefs"/>
+    <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        scpred_train_model.R --input-object "${input_object}" --model "${model}" --output-path "${output_obj_path}" --iter-num "${iter_num}" --num-cores \${GALAXY_SLOTS:-1} --tune-length "${tune_length}" --metric "${metric}" --preprocess "${preprocess}" --return-data "${return_data}" --save-predictions "${save_predictions}" 
-        
+        scpred_train_model.R --input-object "${input_object}" --model "${model}" --output-path "${output_obj_path}" --iter-num "${iter_num}" --num-cores \${GALAXY_SLOTS:-1} --tune-length "${tune_length}" --metric "${metric}" --preprocess "${preprocess}" --return-data "${return_data}" --save-predictions "${save_predictions}"
+
         #if $train_id
-        --train-id '${train_id}' 
+        --train-id '${train_id}'
         #end if
         #if $resample_method
-        --resample-method '${resample_method}' 
+        --resample-method '${resample_method}'
         #end if
         #if $reclassify
-        --reclassify "${reclassify}" 
+        --reclassify "${reclassify}"
         #end if
-        
+
         ]]></command>
     <inputs>
 
@@ -46,8 +46,8 @@
     </tests>
      <help><![CDATA[
     @HELP@
-    
+
     @VERSION_HISTORY@
     ]]></help>
     <expand macro="citations" />
-</tool> 
+</tool>
diff --git a/tools/tertiary-analysis/ucsc-cell-browser/cell-browser.xml b/tools/tertiary-analysis/ucsc-cell-browser/cell-browser.xml
index 6711f6ed..4c4d071a 100644
--- a/tools/tertiary-analysis/ucsc-cell-browser/cell-browser.xml
+++ b/tools/tertiary-analysis/ucsc-cell-browser/cell-browser.xml
@@ -1,5 +1,8 @@
 <tool id="ucsc_cell_browser" name="UCSC Cell Browser" version="1.0.0+galaxy1" profile="18.01">
   <description>displays single-cell clusterized data in an interactive web application.</description>
+  <xrefs>
+      <xref type="bio.tools">ucsc_cell_browser</xref>
+  </xrefs>
   <requirements>
     <requirement type="package" version="1.0.0">ucsc-cell-browser</requirement>
   </requirements>