comparison alphafold.xml @ 8:ca90d17ff51b draft

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

7:eb085b3dbaf8

<tool id="alphafold" name="Alphafold 2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
    <description> - AI-guided 3D structural prediction of proteins</description>
    <macros>
      <token name="@TOOL_VERSION@">2.1.2</token>
      <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <edam_topics>
      <edam_topic>topic_0082</edam_topic>
    </edam_topics>
    <edam_operations>

#elif $fasta_or_text.input_mode == 'textbox':
    echo '$fasta_or_text.fasta_text' > input.fasta &&
#end if

python3 '$__tool_directory__/validate_fasta.py' input.fasta
--min_length \${ALPHAFOLD_AA_LENGTH_MIN:-30}
--max_length \${ALPHAFOLD_AA_LENGTH_MAX:-2000}
> alphafold.fasta &&

## env vars -------------------------------
export TF_FORCE_UNIFIED_MEMORY=1 &&
export XLA_PYTHON_CLIENT_MEM_FRACTION=4.0 &&

--obsolete_pdbs_path \${ALPHAFOLD_DB:-/data}/pdb_mmcif/obsolete.dat
--max_template_date=\$DATE
--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
&&

## 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 &&

## HTML output

[ -d working ] && cp -r working/* .

    ]]></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.">
                <option value="history">Use fasta from history</option>
                <option value="textbox">Paste sequence into textbox</option>
            </param>
            <when value="history">
                <param name="fasta_file" type="data" format="fasta" label="Fasta file from history" help="Select single fasta protein sequence from your history. If you wish to fold multiple proteins, submit an individual job for each protein." />

8:ca90d17ff51b

<tool id="alphafold" name="Alphafold 2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
    <description> - AI-guided 3D structural prediction of proteins</description>
    <macros>
      <token name="@TOOL_VERSION@">2.1.2</token>
      <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <edam_topics>
      <edam_topic>topic_0082</edam_topic>
    </edam_topics>
    <edam_operations>

#elif $fasta_or_text.input_mode == 'textbox':
    echo '$fasta_or_text.fasta_text' > input.fasta &&
#end if

python3 '$__tool_directory__/validate_fasta.py' input.fasta
--min_length \${ALPHAFOLD_AA_LENGTH_MIN:-0}
--max_length \${ALPHAFOLD_AA_LENGTH_MAX:-0}
> alphafold.fasta &&

## env vars -------------------------------
export TF_FORCE_UNIFIED_MEMORY=1 &&
export XLA_PYTHON_CLIENT_MEM_FRACTION=4.0 &&

--obsolete_pdbs_path \${ALPHAFOLD_DB:-/data}/pdb_mmcif/obsolete.dat
--max_template_date=\$DATE
--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=\${ALPHAFOLD_USE_GPU:-True}
&&

## Generate additional outputs ------------
python3 '$__tool_directory__/gen_extra_outputs.py' output/alphafold $output_plddts &&

## HTML output

[ -d working ] && cp -r working/* .

    ]]></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. 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>
            <when value="history">
                <param name="fasta_file" type="data" format="fasta" label="Fasta file from history" help="Select single fasta protein sequence from your history. If you wish to fold multiple proteins, submit an individual job for each protein." />