Mercurial > repos > devteam > data_manager_fetch_genome_all_fasta
diff data_manager/data_manager_fetch_genome_all_fasta.xml @ 0:2ebc856bce29 draft
Uploaded data manager definition.
author | devteam |
---|---|
date | Fri, 28 Mar 2014 14:14:24 -0400 |
parents | |
children | fb744a070bee |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_fetch_genome_all_fasta.xml Fri Mar 28 14:14:24 2014 -0400 @@ -0,0 +1,97 @@ +<tool id="data_manager_fetch_genome_all_fasta" name="Reference Genome" version="0.0.1" tool_type="manage_data"> + <description>fetching</description> + <command interpreter="python">data_manager_fetch_genome_all_fasta.py "${out_file}" --dbkey_description ${ dbkey.get_display_text() }</command> + <inputs> + <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" /> + <param type="text" name="sequence_name" value="" label="Name of sequence" /> + <param type="text" name="sequence_desc" value="" label="Description of sequence" /> + <param type="text" name="sequence_id" value="" label="ID for sequence" /> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> + <option value="ucsc" selected="True">UCSC</option> + <option value="ncbi">NCBI</option> + <option value="url">URL</option> + <option value="history">History</option> + <option value="directory">Directory on Server</option> + </param> + <when value="ucsc"> + <param type="text" name="requested_dbkey" value="" label="UCSC's DBKEY for source FASTA" optional="False" /> + </when> + <when value="ncbi"> + <param type="text" name="requested_identifier" value="" label="NCBI identifier" 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> + <conditional name="sorting"> + <param name="sort_selector" type="select" label="Choose the source for the reference genome"> + <option value="as_is" selected="True">As is</option> + <option value="lexicographical">Lexicographical</option> + <option value="gatk">GATK</option> + <option value="custom">Custom</option> + </param> + <when value="as_is"> + </when> + <when value="lexicographical"> + </when> + <when value="gatk"> + </when> + <when value="custom"> + <repeat name="sequence_identifiers" title="Sequence Identifiers" min="1" default="1"> + <param type="text" name="identifier" value="" label="Sequence Identifier" optional="False" /> + </repeat> + <conditional name="handle_not_listed"> + <param name="handle_not_listed_selector" type="select" label="How to handle non-specified Identifiers"> + <option value="discard" selected="True">Discard</option> + <option value="keep_append">Keep and Append</option> + <option value="keep_prepend">Keep and Prepend</option> + </param> + <when value="discard"> + </when> + <when value="keep_append"> + </when> + <when value="keep_prepend"> + </when> + </conditional> + </when> + </conditional> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json"/> + </outputs> + <tests> + <!-- TODO: need some way to test that new entry was added to data table --> + <test> + <param name="dbkey" value="anoGam1"/> + <param name="sequence_name" value=""/> + <param name="sequence_desc" value=""/> + <param name="sequence_id" value=""/> + <param name="reference_source_selector" value="history"/> + <param name="input_fasta" value="phiX174.fasta"/> + <param name="sort_selector" value="as_is"/> + <output name="out_file" file="phiX174_as_anoGam1.data_manager_json"/> + </test> + </tests> + <help> +**What it does** + +Fetches a reference genome from various sources (UCSC, NCBI, URL, Galaxy History, or a server directory) and populates the "all_fasta" data table. + +------ + + + +.. class:: infomark + +**Notice:** If you leave name, description, or id blank, it will be generated automatically. + + </help> +</tool>