comparison alphafold.xml @ 4:bc99b0a951ec draft

"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 2d7c3d151feaafc3be33ebb0081ec640680fbb4d-dirty"

3:58854e2e6654

<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@">1</token>
    </macros>
    <edam_topics>
      <edam_topic>topic_0082</edam_topic>
    </edam_topics>
    <edam_operations>

--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.">

4:bc99b0a951ec

<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@">2</token>
    </macros>
    <edam_topics>
      <edam_topic>topic_0082</edam_topic>
    </edam_topics>
    <edam_operations>

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

## This is a (hacky) fix for a bug that has appeared in multiple Pulsar servers.
## The working directory ends up two levels deep and the visualization html page
## fails to load the PDB files as static assets.
[ -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.">