changeset 8:ca90d17ff51b draft

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

--- a/README.rst	Tue Apr 19 00:39:29 2022 +0000
+++ b/README.rst	Fri Aug 19 00:29:16 2022 +0000
@@ -9,7 +9,9 @@
 
 This document is designed to provide details on the compute environment
 required for Alphafold operation, and the Galaxy job destination
-settings to run the wrapper.
+settings to run the wrapper. We strongly suggest reading this entire document
+to ensure that your setup is compatible with the hardware that you are
+deploying to.
 
 For full details on Alphafold requirements, see
 https://github.com/deepmind/alphafold.
@@ -163,11 +165,9 @@
 A few parameters can be customized with the use of environment variables set in the job destination:
 
 - ``ALPHAFOLD_DB``: path to the reference database root (default ``/data``)
-- ``ALPHAFOLD_AA_LENGTH_MIN``: minimum accepted sequence length (default ``30``)
-- ``ALPHAFOLD_AA_LENGTH_MAX``: maximum accepted sequence length (default ``2000``)
-
-For the last two, these could be set to ``0`` and ``50000`` respectively to remove the valiation entirely.
-
+- ``ALPHAFOLD_USE_GPU [True/False]``: set to ``False`` to disable GPU dependency (defaults to ``True``)
+- ``ALPHAFOLD_AA_LENGTH_MIN``: minimum accepted sequence length (default ``0``)
+- ``ALPHAFOLD_AA_LENGTH_MAX``: maximum accepted sequence length (default ``0`` - no validation)
 
 Closing
 ~~~~~~~

--- 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>

--- a/validate_fasta.py	Tue Apr 19 00:39:29 2022 +0000
+++ b/validate_fasta.py	Fri Aug 19 00:29:16 2022 +0000
@@ -3,7 +3,7 @@
 import re
 import sys
 import argparse
-from typing import List, TextIO
+from typing import List
 
 
 class Fasta:
@@ -98,10 +98,10 @@
     def validate_num_seqs(self) -> None:
         """Assert that only one sequence has been provided."""
         if len(self.fasta_list) > 1:
-            raise ValueError(
-                'Error encountered validating FASTA:\n'
-                f' More than 1 sequence detected ({len(self.fasta_list)}).'
-                ' Please use single FASTA sequence as input.')
+            sys.stderr.write(
+                'WARNING: More than 1 sequence detected.'
+                ' Using first FASTA sequence as input.\n')
+            self.fasta_list = self.fasta_list[:1]
         elif len(self.fasta_list) == 0:
             raise ValueError(
                 'Error encountered validating FASTA:\n'
@@ -159,7 +159,7 @@
         formatted_seq = ''
         for i in range(0, len(aa_seq), self.line_wrap):
             formatted_seq += aa_seq[i: i + self.line_wrap] + '\n'
-        return formatted_seq
+        return formatted_seq.upper()
 
 
 def main():