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view data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml @ 9:4d3eff1bc421 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit d95d06f8cad152876ce15713c65099db116f8ace"
author | iuc |
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date | Thu, 05 Dec 2019 17:10:39 -0500 |
parents | 14eb0fc65c62 |
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<tool id="data_manager_fetch_genome_all_fasta_dbkey" name="Create DBKey and Reference Genome" version="0.0.4" tool_type="manage_data" profile="19.01"> <description>fetching</description> <requirements> <requirement type="package" version="3.7">python</requirement> </requirements> <command detect_errors="exit_code"><![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}' #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 name="dbkey" type="text" value="" optional="false" label="dbkey" /> <param name="dbkey_name" type="text" value="" label="Display name for dbkey" /> </when> </conditional> <param name="sequence_name" type="text" value="" label="Name of sequence" /> <param name="sequence_id" type="text" 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 name="requested_dbkey" type="text" value="" optional="false" label="UCSC's DBKEY for source FASTA" /> </when> <when value="ncbi"> <param name="requested_identifier" type="text" value="" optional="false" label="NCBI identifier/accession" help="Identifiers (e.g 667699573) or accessions (e.g AC020606.7) may be used" /> </when> <when value="url"> <param name="user_url" type="text" area="True" value="http://" optional="false" label="URLs" /> </when> <when value="history"> <param name="input_fasta" type="data" format="fasta" label="FASTA file" /> </when> <when value="directory"> <param name="fasta_filename" type="text" value="" optional="false" label="Full path to FASTA file on disk" /> <param name="create_symlink" type="boolean" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to original data instead of copying" /> </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 value="lexicographical" /> <when value="gatk" /> <when value="custom"> <repeat name="sequence_identifiers" title="Sequence Identifiers" min="1" default="1"> <param name="identifier" type="text" value="" optional="false" label="Sequence Identifier" /> </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="phiX174"/> <param name="dbkey_source|dbkey_source_selector" value="new"/> <param name="sequence_name" value="phiX174 sequence name"/> <param name="sequence_id" value="phix174"/> <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>