diff alphafold.xml @ 8:ca90d17ff51b draft

"planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 03537aada92b5fff565ff48dd47c81462c5df47e"

--- a/alphafold.xml	Tue Apr 19 00:39:29 2022 +0000
+++ b/alphafold.xml	Fri Aug 19 00:29:16 2022 +0000
@@ -2,7 +2,7 @@
     <description> - AI-guided 3D structural prediction of proteins</description>
     <macros>
       <token name="@TOOL_VERSION@">2.1.2</token>
-      <token name="@VERSION_SUFFIX@">0</token>
+      <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <edam_topics>
       <edam_topic>topic_0082</edam_topic>
@@ -30,8 +30,8 @@
 #end if
 
 python3 '$__tool_directory__/validate_fasta.py' input.fasta
---min_length \${ALPHAFOLD_AA_LENGTH_MIN:-30}
---max_length \${ALPHAFOLD_AA_LENGTH_MAX:-2000}
+--min_length \${ALPHAFOLD_AA_LENGTH_MIN:-0}
+--max_length \${ALPHAFOLD_AA_LENGTH_MAX:-0}
 > alphafold.fasta &&
 
 ## env vars -------------------------------
@@ -53,12 +53,9 @@
 --bfd_database_path \${ALPHAFOLD_DB:-/data}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
 --uniclust30_database_path \${ALPHAFOLD_DB:-/data}/uniclust30/uniclust30_2018_08/uniclust30_2018_08
 ## Param introduced in AlphaFold v2.1.2:
---use_gpu_relax=True
+--use_gpu_relax=\${ALPHAFOLD_USE_GPU:-True}
 &&
 
-## Uncomment for "dummy" output - read output from test-data
-## cp -r '$__tool_directory__/output' . &&
-
 ## Generate additional outputs ------------
 python3 '$__tool_directory__/gen_extra_outputs.py' output/alphafold $output_plddts &&
 
@@ -75,7 +72,7 @@
     ]]></command>
     <inputs>
         <conditional name="fasta_or_text">
-            <param name="input_mode" type="select" label="Fasta Input" help="Single protein sequence to fold. Input can be fasta file from history, or text. Provide only 1 sequence per job.">
+            <param name="input_mode" type="select" label="Fasta Input" help="Single protein sequence to fold. Input can be fasta file from history, or text. Sequence must be valid IUPAC amino acid characters. Provide only 1 sequence per job.">
                 <option value="history">Use fasta from history</option>
                 <option value="textbox">Paste sequence into textbox</option>
             </param>