--- a/alphafold.xml	Wed May 08 06:26:55 2024 +0000
+++ b/alphafold.xml	Sun Jul 28 20:09:55 2024 +0000
@@ -1,9 +1,9 @@
-<tool id="alphafold" name="Alphafold 2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
+<tool id="alphafold" name="Alphafold 2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
     <description> - AI-guided 3D structural prediction of proteins</description>
     <macros>
-      <token name="@TOOL_VERSION@">2.3.1</token>
+      <token name="@TOOL_VERSION@">2.3.2</token>
       <token name="@TOOL_MINOR_VERSION@">2.3</token>
-      <token name="@VERSION_SUFFIX@">5</token>
+      <token name="@VERSION_SUFFIX@">0</token>
       <import>macro_output.xml</import>
       <import>macro_test_output.xml</import>
     </macros>
@@ -17,12 +17,12 @@
       <xref type="bio.tools">alphafold_2</xref>
     </xrefs>
     <requirements>
-        <container type="docker">neoformit/alphafold:v2.3.1_2</container>
+        <container type="docker">neoformit/alphafold:v2.3.2_0</container>
     </requirements>
     <required_files>
         <include path="scripts/outputs.py" />
         <include path="scripts/validate_fasta.py" />
-        <include path="alphafold.html" />
+        <include path="scripts/alphafold.html" />
     </required_files>
     <command detect_errors="exit_code"><![CDATA[
 
@@ -46,7 +46,7 @@
 && python3 '$__tool_directory__/scripts/validate_fasta.py' input.fasta
 --min_length \${ALPHAFOLD_AA_LENGTH_MIN:-0}
 --max_length \${ALPHAFOLD_AA_LENGTH_MAX:-0}
-#if $model_preset == 'multimer':
+#if $model_preset.selection == 'multimer':
 --multimer
 --max-sequences \${ALPHAFOLD_MAX_SEQUENCES:-10}
 #end if
@@ -60,7 +60,7 @@
 ## Run AlphaFold  -------------------------------------------------------------
 #if os.environ.get('PLANEMO_TESTING'):
     ## Run in testing mode (mocks a successful AlphaFold run by copying outputs)
-    && echo "Creating dummy outputs for model_preset=$model_preset..."
+    && echo "Creating dummy outputs for model_preset=$model_preset.selection..."
     && bash '$__tool_directory__/scripts/mock_alphafold.sh' $model_preset
 #else:
     ## Run AlphaFold
@@ -68,7 +68,7 @@
         --fasta_paths alphafold.fasta
         --output_dir output
         --data_dir \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/
-        --model_preset=$model_preset
+        --model_preset=$model_preset.selection
 
         ## Set reference database paths
         --uniref90_database_path   \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/uniref90/uniref90.fasta
@@ -83,21 +83,33 @@
         --small_bfd_database_path  \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/small_bfd/bfd-first_non_consensus_sequences.fasta
         #end if
 
-        #if $max_template_date:
-        --max_template_date=$max_template_date
+        #if $advanced.max_template_date:
+        --max_template_date=$advanced.max_template_date
         #else
         --max_template_date=\$TODAY
         #end if
 
-        --use_gpu_relax=\${ALPHAFOLD_USE_GPU:-True}  ## introduced in v2.1.2
+        --use_gpu_relax=\${ALPHAFOLD_USE_GPU:-True}
 
-        #if $model_preset == 'multimer':
+        #if $model_preset.selection == 'multimer':
         --pdb_seqres_database_path=\${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/pdb_seqres/pdb_seqres.txt
         --uniprot_database_path=\${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/uniprot/uniprot.fasta
-        --num_multimer_predictions_per_model=1  ## introduced in v2.2.0
+        --num_multimer_predictions_per_model=$model_preset.num_multimer_predictions_per_model
         #else
         --pdb70_database_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/pdb70/pdb70
         #end if
+
+        ## Galaxy-specific options --------------------------------------------
+        ## See https://github.com/neoformit/alphafold/tree/release_2.3.2_galaxy
+        #if $advanced.disable_amber_relax:
+        --disable_amber_relax
+        #end if
+
+        #if $advanced.limit_model_outputs:
+        --output_models=$limit_model_outputs
+        #end if
+        ## End Galaxy-specific options ----------------------------------------
+
 #end if
 
 ## Generate additional outputs ------------------------------------------------
@@ -106,13 +118,13 @@
 $outputs.model_pkls
 $outputs.pae_csv
 $outputs.plots
-#if $model_preset == 'multimer':
+#if $model_preset.selection == 'multimer':
 --multimer
 #end if
 
 ## HTML output
 && mkdir -p '${ html.files_path }'
-&& cp '$__tool_directory__/alphafold.html' '${html}'
+&& cp output/alphafold/extra/alphafold.html '${html}'
 && cp output/alphafold/ranked_*.pdb '${html.files_path}'
 
 ## This is a (hacky) fix for a bug that has appeared in multiple Pulsar servers.
@@ -136,21 +148,6 @@
         </conditional>
 
         <param
-            name="max_template_date"
-            type="text"
-            label="Max template date (yyyy-mm-dd) (optional)"
-            help="The model will reference PDB structures deposited before this date only. Defaults to today's date."
-            optional="true"
-        >
-            <sanitizer>
-                <valid initial="string.digits">
-                    <add value="-" />
-                </valid>
-            </sanitizer>
-            <validator type="regex">[0-9]{4}-[0-9]{2}-[0-9]{2}</validator>
-        </param>
-
-        <param
           name="dbs"
           type="select"
           display="radio"
@@ -162,8 +159,9 @@
           <option value="full">Full database</option>
         </param>
 
+        <conditional name="model_preset">
         <param
-            name="model_preset"
+                name="selection"
             type="select"
             label="Model preset"
             help="Select which prediction model to run. The monomer model is the most accurate for single protein prediction. The multimer model allows prediction of protein complexes."
@@ -176,6 +174,56 @@
                 multimer - model a protein complex (requires multi-sequence FASTA input)
             </option>
         </param>
+            <when value="monomer"></when>
+            <when value="monomer_ptm"></when>
+            <when value="multimer">
+                <param
+                    name="num_multimer_predictions_per_model"
+                    type="integer"
+                    value="5"
+                    label="Multimer predictions per model"
+                    help="How many predictions (each with a different random seed) will be generated per model. E.g. if this is 2 and there are 5 models then there will be 10 predictions per input. For a small drop in accuracy you may wish to run a single seed per model (default 5, max 10)."
+                    min="1"
+                    max="10"
+                />
+            </when>
+        </conditional>
+
+        <section name="advanced" title="Advanced options" expanded="false">
+            <param
+                name="max_template_date"
+                type="text"
+                label="Max template date (yyyy-mm-dd) (optional)"
+                help="The model will reference PDB structures deposited before this date only. Defaults to today's date."
+                optional="true"
+            >
+                <sanitizer>
+                    <valid initial="string.digits">
+                        <add value="-" />
+                    </valid>
+                </sanitizer>
+                <validator type="regex">[0-9]{4}-[0-9]{2}-[0-9]{2}</validator>
+            </param>
+
+            <param
+                name="disable_amber_relax"
+                type="boolean"
+                label="Disable Amber relaxation"
+                value="false"
+                optional="true"
+                help="Amber relaxation can be disabled to speed up processing time. Amber relaxation is used to refine predicted structures by removing stereochemical violations, resulting in more accurate prediction of side-chain geometry. Disabling this option with large proteins may lead to artefacts in the predicted structure. Disabling amber relax will result in the unrelaxed models being collected as PDB outputs."
+            />
+
+            <param
+                name="limit_model_outputs"
+                type="integer"
+                label="Limit model outputs"
+                value="5"
+                help="Limit the number of models to output. The top N models will be output, where N is the value entered here (default 5). Please note that the top-ranking model is not always the correct one, and it is usually recommended to inspect multiple models. Reducing the number of models will result in a slight reduction in run time."
+                min="1"
+                max="5"
+            />
+        </section>
 
         <section name="outputs" title="Optional outputs" expanded="false">
             <param
@@ -228,6 +276,13 @@
                 label="relax_metrics.json"
                 help="A JSON-formatted text file containing relax metrics (mostly remaining violations)."
             />
+            <param
+                name="timings_json"
+                type="boolean"
+                checked="false"
+                label="timings.json"
+                help="A JSON file with timings reported for each phase of the AlphaFold run."
+            />
         </section>
     </inputs>
 
@@ -241,6 +296,7 @@
         <expand macro="output_pae_csv" />
         <expand macro="output_plots" />
         <expand macro="output_relax_json" />
+        <expand macro="output_timings_json" />
     </outputs>
 
     <tests>
@@ -250,7 +306,7 @@
                 <param name="input_mode" value="history"/>
                 <param name="fasta_file" value="test1.fasta"/>
             </conditional>
-            <param name="model_preset" value="monomer"/>
+            <param name="model_preset|selection" value="monomer"/>
             <expand macro="test_output_pdb_models" />
         </test>
 
@@ -260,7 +316,7 @@
                 <param name="input_mode" value="history"/>
                 <param name="fasta_file" value="test1.fasta"/>
             </conditional>
-            <param name="model_preset" value="monomer"/>
+            <param name="model_preset|selection" value="monomer"/>
             <param name="outputs|plots" value="true"/>
             <param name="outputs|confidence_scores" value="true"/>
             <param name="outputs|plddts" value="true"/>
@@ -281,7 +337,7 @@
                 <param name="input_mode" value="history"/>
                 <param name="fasta_file" value="test1.fasta"/>
             </conditional>
-            <param name="model_preset" value="monomer_ptm"/>
+            <param name="model_preset|selection" value="monomer_ptm"/>
             <param name="outputs|plots" value="true"/>
             <param name="outputs|confidence_scores" value="true"/>
             <param name="outputs|plddts" value="true"/>
@@ -303,19 +359,21 @@
                 <param name="input_mode" value="history"/>
                 <param name="fasta_file" value="multimer.fasta"/>
             </conditional>
-            <param name="model_preset" value="multimer"/>
+            <param name="model_preset|selection" value="multimer"/>
             <param name="outputs|plots" value="true"/>
             <param name="outputs|confidence_scores" value="true"/>
             <param name="outputs|plddts" value="true"/>
             <param name="outputs|pae_csv" value="true"/>
             <param name="outputs|model_pkls" value="true"/>
             <param name="outputs|relax_json" value="true"/>
+            <param name="outputs|timings_json" value="true"/>
             <expand macro="test_output_plots_3" />
             <expand macro="test_output_confidence_scores" />
             <expand macro="test_output_plddts" />
             <expand macro="test_output_pdb_models" />
             <expand macro="test_output_pickles" />
             <expand macro="test_output_relax_json" />
+            <expand macro="test_output_timings_json" />
             <expand macro="test_output_pae_csv" />
         </test>
     </tests>
@@ -325,7 +383,7 @@
 
     | AlphaFold v2: AI-guided 3D structural prediction of proteins
     |
-    | **NOTE: this tool packages AlphaFold v2.3.1.**
+    | **NOTE: this tool packages** `a modified branch of AlphaFold v2.3.2. <https://github.com/neoformit/alphafold/tree/release_2.3.2_galaxy>`_
     |
     | This means that the neural network has been trained on PDBs with a release
     | date before 2021-09-30 (the training cutoff was 2018-04-30 until ``v2.3.0``).
@@ -333,12 +391,9 @@
     | Find out more in the technical and release notes:
     |
 
-    - `Release notes for v2.3.1 <https://github.com/deepmind/alphafold/releases/tag/v2.3.1>`_
+    - `Release notes for v2.3.2 <https://github.com/deepmind/alphafold/releases/tag/v2.3.2>`_
     - `Technical notes for v2.3 <https://github.com/deepmind/alphafold/blob/main/docs/technical_note_v2.3.0.md>`_
 
-    | If you want to use AlphaFold trained against an older cutoff date, switch to Galaxy version ``2.1.2`` (which was trained to data up to 2018-04-30).
-    |
-
     **What it does**
 
     *What is AlphaFold?*
@@ -362,6 +417,7 @@
     | You can choose to input either a file from your Galaxy history or paste a sequence into a text box.
     | If you choose the ``multimer`` option, you can supply a FASTA file containing **multiple sequences** to be folded concurrently into a multimer.
     |
+    | For pairwise screening of target-candidate with multimer, you can submit a list of paired protein sequences in batch mode (i.e. two protein sequences in each FASTA file).
     |
 
     **Outputs**
@@ -380,7 +436,7 @@
 
     *PDB files*
 
-    | Five PDB (Protein Data Bank) files are be created, ordered by rank, as predicted by AlphaFold.
+    | PDB (Protein Data Bank) files (5 by default) are be created, ordered by rank, as predicted by AlphaFold. The tool produces 5 models by default, but this can be reduced with the "Limit model outputs" for a reduced run time.
     | These files describe the molecular structures and can be used for downstream analysis. e.g. *in silico* molecular docking.
     | **PLEASE NOTE** that all outputs have been renamed to their respective rank order, including model and model.pkl files.
     |
@@ -421,6 +477,12 @@
     |
     |
 
+    *timings.json (optional)*
+
+    | A JSON-formatted text file containing the timings for each phase of the prediction.
+    |
+    |
+
     **AlphaFold configuration**
 
     | We have configured AlphaFold to run with the parameters suggested by default on `AlphaFold's GitHub <https://github.com/deepmind/alphafold>`_.