Mercurial > repos > devteam > data_manager_fetch_genome_dbkeys_all_fasta
diff data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml @ 0:c669787306ae draft
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author | devteam |
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date | Tue, 03 Feb 2015 10:08:46 -0500 |
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children | 776bb1b478a0 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml Tue Feb 03 10:08:46 2015 -0500 @@ -0,0 +1,116 @@ +<tool id="data_manager_fetch_genome_all_fasta_dbkey" name="Create DBKey and Reference Genome" version="0.0.1" tool_type="manage_data"> + <description>fetching</description> + <command interpreter="python">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" 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="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.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>