Mercurial > repos > devteam > data_manager_fetch_genome_dbkeys_all_fasta
diff 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 |
|---|---|
| date | Fri, 26 Aug 2016 12:46:47 -0400 |
| parents | 776bb1b478a0 |
| children | 60994ca04177 |
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--- a/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml Wed Oct 14 13:46:35 2015 -0400 +++ b/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml Fri Aug 26 12:46:47 2016 -0400 @@ -1,86 +1,77 @@ -<tool id="data_manager_fetch_genome_all_fasta_dbkey" name="Create DBKey and Reference Genome" version="0.0.1" tool_type="manage_data"> +<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 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 $dbkey_source.dbkey }" - #end if - - </command> + <command><![CDATA[ + python "$__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> + <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> + <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> - <conditional name="handle_not_listed"> + <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 value="discard"> - </when> - <when value="keep_append"> - </when> - <when value="keep_prepend"> - </when> - </conditional> - </when> + </when> </conditional> </inputs> <outputs> @@ -110,7 +101,7 @@ .. class:: infomark -**Notice:** If you leave name, description, or id blank, it will be generated automatically. +**Notice:** If you leave name, description, or id blank, it will be generated automatically. </help> </tool>