Mercurial > repos > bgruening > data_manager_diamond_database_builder
diff data_manager/data_manager_diamond_database_builder.xml @ 0:ce62d0912b10 draft
Imported from capsule None
author | bgruening |
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date | Sun, 08 Feb 2015 10:05:20 -0500 |
parents | |
children | 5a0d0bee4f8d |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_diamond_database_builder.xml Sun Feb 08 10:05:20 2015 -0500 @@ -0,0 +1,46 @@ +<tool id="diamond_database_builder" name="Diamond" tool_type="manage_data" version="0.0.1"> + <description> Database builder</description> + <requirements> + <requirement type="package" version="0.6.13">diamond</requirement> + </requirements> + <command interpreter="python"> + data_manager_diamond_database_builder.py "${out_file}" + </command> + <inputs> + <param type="text" name="database_name" value="" label="Database name or description" + help="This will be shown to the user in the database selectbox."/> + <param type="text" name="database_id" value="" label="Database ID" help="This needs to be unique. No whitespaces allowed. Use underscores." /> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> + <option value="ncbi">NCBI</option> + <option value="url">URL</option> + <option value="history" selected="True" help="Recommended to archive the original FASTA file as well.">History</option> + <option value="directory">Directory on Server</option> + </param> + <when value="ncbi"> + <param type="text" name="requested_identifier" value="" label="NCBI identifier" help="e.g. nr" optional="False" /> + </when> + <when value="url"> + <param type="text" area="True" name="user_url" value="http://" label="URLs" optional="False" /> + </when> + <when value="history"> + <param name="input_fasta" type="data" format="fasta" label="FASTA File" multiple="False" optional="False" /> + </when> + <when value="directory"> + <param type="text" name="fasta_filename" value="" label="Full path to FASTA File on disk" optional="False" /> + <param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to orignal data instead of copying" checked="False" /> + </when> + </conditional> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json"/> + </outputs> + <help> + +.. class:: infomark + +NCBI databases can be downded from ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/ +For example the NR database can be downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz + + </help> +</tool>