Mercurial > repos > galaxy-australia > alphafold2

diff macro_output.xml @ 24:31f648b7555a draft

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planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 44db277529c0e189149235cf60a627193a792fba
author galaxy-australia
date Sat, 05 Jul 2025 03:56:38 +0000
parents 2891385d6ace
children
line wrap: on
line diff
--- a/macro_output.xml	Wed Apr 16 05:46:58 2025 +0000
+++ b/macro_output.xml	Sat Jul 05 03:56:38 2025 +0000
@@ -2,23 +2,17 @@
     <xml name="output_pdb_models">
         <data name="model5" format="pdb" from_work_dir="output/alphafold/ranked_4.pdb" label="${tool.name} on ${on_string}: PDB ranked 4">
             <filter>advanced['limit_model_outputs'] > 4</filter>
-            <filter>not advanced['exit_after_msa']</filter>
         </data>
         <data name="model4" format="pdb" from_work_dir="output/alphafold/ranked_3.pdb" label="${tool.name} on ${on_string}: PDB ranked 3">
             <filter>advanced['limit_model_outputs'] > 3</filter>
-            <filter>not advanced['exit_after_msa']</filter>
         </data>
         <data name="model3" format="pdb" from_work_dir="output/alphafold/ranked_2.pdb" label="${tool.name} on ${on_string}: PDB ranked 2">
             <filter>advanced['limit_model_outputs'] > 2</filter>
-            <filter>not advanced['exit_after_msa']</filter>
         </data>
         <data name="model2" format="pdb" from_work_dir="output/alphafold/ranked_1.pdb" label="${tool.name} on ${on_string}: PDB ranked 1">
             <filter>advanced['limit_model_outputs'] > 1</filter>
-            <filter>not advanced['exit_after_msa']</filter>
         </data>
-        <data name="model1" format="pdb" from_work_dir="output/alphafold/ranked_0.pdb" label="${tool.name} on ${on_string}: PDB ranked 0">
-            <filter>not advanced['exit_after_msa']</filter>
-        </data>
+        <data name="model1" format="pdb" from_work_dir="output/alphafold/ranked_0.pdb" label="${tool.name} on ${on_string}: PDB ranked 0"/>
     </xml>
 
     <xml name="output_pae_csv">
@@ -31,7 +25,6 @@
             <filter>outputs['pae_csv']</filter>
             <filter>model_preset != "monomer"</filter>
             <filter>advanced['limit_model_outputs'] > 4</filter>
-            <filter>not advanced['exit_after_msa']</filter>
         </data>
         <data
             name="pae_ranked_3"
@@ -42,7 +35,6 @@
             <filter>outputs['pae_csv']</filter>
             <filter>model_preset != "monomer"</filter>
             <filter>advanced['limit_model_outputs'] > 3</filter>
-            <filter>not advanced['exit_after_msa']</filter>
         </data>
         <data
             name="pae_ranked_2"
@@ -53,7 +45,6 @@
             <filter>outputs['pae_csv']</filter>
             <filter>model_preset != "monomer"</filter>
             <filter>advanced['limit_model_outputs'] > 2</filter>
-            <filter>not advanced['exit_after_msa']</filter>
         </data>
         <data
             name="pae_ranked_1"
@@ -64,7 +55,6 @@
             <filter>outputs['pae_csv']</filter>
             <filter>model_preset != "monomer"</filter>
             <filter>advanced['limit_model_outputs'] > 1</filter>
-            <filter>not advanced['exit_after_msa']</filter>
         </data>
         <data
             name="pae_ranked_0"
@@ -74,7 +64,6 @@
         >
             <filter>outputs['pae_csv']</filter>
             <filter>model_preset != "monomer"</filter>
-            <filter>not advanced['exit_after_msa']</filter>
         </data>
     </xml>
 
@@ -87,7 +76,6 @@
         >
             <filter>outputs['model_pkls']</filter>
             <filter>advanced['limit_model_outputs'] > 4</filter>
-            <filter>not advanced['exit_after_msa']</filter>
         </data>
         <data
             name="output_ranked_3_pkl"
@@ -97,7 +85,6 @@
         >
             <filter>outputs['model_pkls']</filter>
             <filter>advanced['limit_model_outputs'] > 3</filter>
-            <filter>not advanced['exit_after_msa']</filter>
         </data>
         <data
             name="output_ranked_2_pkl"
@@ -107,7 +94,6 @@
         >
             <filter>outputs['model_pkls']</filter>
             <filter>advanced['limit_model_outputs'] > 2</filter>
-            <filter>not advanced['exit_after_msa']</filter>
         </data>
         <data
             name="output_ranked_1_pkl"
@@ -117,7 +103,6 @@
         >
             <filter>outputs['model_pkls']</filter>
             <filter>advanced['limit_model_outputs'] > 1</filter>
-            <filter>not advanced['exit_after_msa']</filter>
         </data>
         <data
             name="output_ranked_0_pkl"
@@ -126,7 +111,6 @@
             label="${tool.name} on ${on_string}: ranked_0.pkl"
         >
             <filter>outputs['model_pkls']</filter>
-            <filter>not advanced['exit_after_msa']</filter>
         </data>
     </xml>
 
@@ -139,7 +123,6 @@
         >
             <filter>outputs['plots']</filter>
             <filter>advanced['limit_model_outputs'] > 4</filter>
-            <filter>not advanced['exit_after_msa']</filter>
         </data>
         <data
             name="plot_ranked_3"
@@ -149,7 +132,6 @@
         >
             <filter>outputs['plots']</filter>
             <filter>advanced['limit_model_outputs'] > 3</filter>
-            <filter>not advanced['exit_after_msa']</filter>
         </data>
         <data
             name="plot_ranked_2"
@@ -159,7 +141,6 @@
         >
             <filter>outputs['plots']</filter>
             <filter>advanced['limit_model_outputs'] > 2</filter>
-            <filter>not advanced['exit_after_msa']</filter>
         </data>
         <data
             name="plot_ranked_1"
@@ -169,7 +150,6 @@
         >
             <filter>outputs['plots']</filter>
             <filter>advanced['limit_model_outputs'] > 1</filter>
-            <filter>not advanced['exit_after_msa']</filter>
         </data>
         <data
             name="plot_ranked_0"
@@ -178,7 +158,6 @@
             label="${tool.name} on ${on_string}: pLDDT/PAE plot ranked 0"
         >
             <filter>outputs['plots']</filter>
-            <filter>not advanced['exit_after_msa']</filter>
         </data>
     </xml>
 
@@ -190,7 +169,6 @@
             label="${tool.name} on ${on_string}: Model confidence scores"
         >
             <filter>outputs['confidence_scores']</filter>
-            <filter>not advanced['exit_after_msa']</filter>
         </data>
     </xml>
 
@@ -202,7 +180,6 @@
             label="${tool.name} on ${on_string}: MSA plot"
         >
             <filter>outputs['plot_msa']</filter>
-            <filter>not advanced['exit_after_msa']</filter>
         </data>
     </xml>
 
@@ -214,7 +191,6 @@
             label="${tool.name} on ${on_string}: Per-residue confidence scores (plddts)"
         >
             <filter>outputs['plddts']</filter>
-            <filter>not advanced['exit_after_msa']</filter>
         </data>
     </xml>
 
@@ -226,7 +202,6 @@
             label="${tool.name} on ${on_string}: relax_metrics_ranked.json"
         >
             <filter>outputs['relax_json']</filter>
-            <filter>not advanced['exit_after_msa']</filter>
         </data>
     </xml>
 
@@ -238,19 +213,6 @@
             label="${tool.name} on ${on_string}: timings.json"
         >
             <filter>outputs['timings_json']</filter>
-            <filter>not advanced['exit_after_msa']</filter>
         </data>
     </xml>
-
-    <xml name="output_msa">
-        <collection name="output_msa" type="list" label="${tool.name} on ${on_string}: MSAs">
-            <discover_datasets
-                pattern="__designation_and_ext__"
-                directory="output/alphafold/extra/msas"
-                format="zip"
-                visible="false"
-            />
-            <filter>outputs['msa'] or advanced['exit_after_msa']</filter>
-        </collection>
-    </xml>
 </macros>