Mercurial > repos > devteam > data_manager_fetch_genome_all_fasta
view data_manager/data_manager_fetch_genome_all_fasta.xml @ 0:2ebc856bce29 draft
Uploaded data manager definition.
author | devteam |
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date | Fri, 28 Mar 2014 14:14:24 -0400 |
parents | |
children | fb744a070bee |
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<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>