comparison alphafold.xml @ 1:6c92e000d684 draft

"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"

0:7ae9d78b06f5

<tool id="alphafold" name="alphafold" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
    <description>Alphafold v2.0: AI-guided 3D structure prediction of proteins</description>
    <macros>
        <token name="@TOOL_VERSION@">2.0.0</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <edam_topics>
        <edam_topic>topic_0082</edam_topic>
    </edam_topics>
    <edam_operations>
        <edam_operation>operation_0474</edam_operation>
    </edam_operations>
    <requirements>
        <container type="docker">neoformit/alphafold-galaxy@sha256:6adf7f07062b307d08c11130c39a28abc7c290b23f6c347b09c2c649c054c338</container>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        ## fasta setup ----------------------------
        #if $fasta_or_text.input_mode == 'history':
            cp '$fasta_or_text.fasta_file' input.fasta &&

        #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 &&

        ## env vars -------------------------------
        export TF_FORCE_UNIFIED_MEMORY=1 &&
        export XLA_PYTHON_CLIENT_MEM_FRACTION=4.0 &&
        export DATE=`date +"%Y-%m-%d"` &&

        ## run alphafold  -------------------------
        ln -s /app/alphafold/alphafold alphafold &&
  	    python /app/alphafold/run_alphafold.py
  	    --fasta_paths alphafold.fasta
        --output_dir output
        --data_dir /data                   ## location of the alphafold databases on pulsar node --> could this maybe a env var? $ALPHAFOLD_DB --> \${ALPHAFOLD_DB:-/data}
        --uniref90_database_path /data/uniref90/uniref90.fasta
        --mgnify_database_path /data/mgnify/mgy_clusters_2018_12.fa
        --pdb70_database_path /data/pdb70/pdb70
        --template_mmcif_dir /data/pdb_mmcif/mmcif_files
        --obsolete_pdbs_path /data/pdb_mmcif/obsolete.dat
        --max_template_date=\$DATE
        --bfd_database_path /data/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
        --uniclust30_database_path /data/uniclust30/uniclust30_2018_08/uniclust30_2018_08
        &&

        ## for dry run testing
        ## cp -r '$__tool_directory__/output' . &&

        ## generate extra outputs -----------------
        ## plddts
        python3 '$__tool_directory__/gen_extra_outputs.py' output/alphafold $output_plddts &&

        ## html
        mkdir -p '${ html.files_path }' &&
        cp '$__tool_directory__/alphafold.html' ${html} &&
        cp output/alphafold/ranked_*.pdb '${html.files_path}' &&

        ## For some reason the working directory ends up being one level too deep!
        mv 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>

1:6c92e000d684

<tool id="alphafold" name="alphafold" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
    <description>Alphafold v2.0: AI-guided 3D structure prediction of proteins</description>
    <macros>
      <token name="@TOOL_VERSION@">2.0.0</token>
      <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <edam_topics>
      <edam_topic>topic_0082</edam_topic>
    </edam_topics>
    <edam_operations>
      <edam_operation>operation_0474</edam_operation>
    </edam_operations>
    <xrefs>
      <xref type="bio.tools">alphafold_2.0</xref>
    </xrefs>
    <requirements>
        <container type="docker">neoformit/alphafold:latest</container>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

## $ALPHAFOLD_DB variable should point to the location of the AlphaFold
## databases - defaults to /data

## fasta setup ----------------------------
#if $fasta_or_text.input_mode == 'history':
    cp '$fasta_or_text.fasta_file' input.fasta &&

#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 &&

## env vars -------------------------------
export TF_FORCE_UNIFIED_MEMORY=1 &&
export XLA_PYTHON_CLIENT_MEM_FRACTION=4.0 &&
export DATE=`date +"%Y-%m-%d"` &&

## run alphafold  -------------------------
python /app/alphafold/run_alphafold.py
--fasta_paths alphafold.fasta
--output_dir output
--data_dir \${ALPHAFOLD_DB:-/data}
--uniref90_database_path \${ALPHAFOLD_DB:-/data}/uniref90/uniref90.fasta
--mgnify_database_path \${ALPHAFOLD_DB:-/data}/mgnify/mgy_clusters_2018_12.fa
--pdb70_database_path \${ALPHAFOLD_DB:-/data}/pdb70/pdb70
--template_mmcif_dir \${ALPHAFOLD_DB:-/data}/pdb_mmcif/mmcif_files
--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
--use_gpu_relax=True
&&

## Uncomment for "dummy run" - skip alphafold run and 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
mkdir -p '${ html.files_path }' &&
cp '$__tool_directory__/alphafold.html' '${html}' &&
cp output/alphafold/ranked_*.pdb '${html.files_path}'

    ]]></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>