Mercurial > repos > devteam > data_manager_fetch_genome_dbkeys_all_fasta
view data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml @ 3:86fa71e9b427 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
author | devteam |
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date | Fri, 26 Aug 2016 12:46:47 -0400 |
parents | 776bb1b478a0 |
children | 60994ca04177 |
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<tool id="data_manager_fetch_genome_all_fasta_dbkey" name="Create DBKey and Reference Genome" version="0.0.2" tool_type="manage_data"> <description>fetching</description> <command><![CDATA[ python "$__tool_directory__"/data_manager_fetch_genome_all_fasta_dbkeys.py "${out_file}" #if str( $dbkey_source.dbkey_source_selector ) == 'existing': --dbkey_description ${ dbkey_source.dbkey.get_display_text() } #else --dbkey_description "${ dbkey_source.dbkey_name or $dbkey_source.dbkey }" #end if ]]></command> <inputs> <conditional name="dbkey_source"> <param name="dbkey_source_selector" type="select" label="Use existing dbkey or create a new one."> <option value="existing" selected="True">Existing</option> <option value="new">New</option> </param> <when value="existing"> <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" /> </when> <when value="new"> <param type="text" name="dbkey" value="" label="dbkey" optional="False" /> <param type="text" name="dbkey_name" value="" label="Display name for dbkey" /> </when> </conditional> <param type="text" name="sequence_name" value="" label="Name 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/accession" help="Identifiers (e.g 667699573) or accessions (e.g AC020606.7) may be used" 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 original data instead of copying" checked="False" /> </when> </conditional> <conditional name="sorting"> <param name="sort_selector" type="select" label="Sort by chromosome name"> <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> <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> </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.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>