Mercurial > repos > devteam > data_manager_fetch_genome_dbkeys_all_fasta
diff data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml @ 4:60994ca04177 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
| author | iuc |
|---|---|
| date | Tue, 04 Apr 2017 17:13:31 -0400 |
| parents | 86fa71e9b427 |
| children | a246b4f11133 |
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--- a/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml Fri Aug 26 12:46:47 2016 -0400 +++ b/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml Tue Apr 04 17:13:31 2017 -0400 @@ -1,11 +1,12 @@ <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}" + <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 ${ dbkey_source.dbkey.get_display_text() } + --dbkey_description '${ dbkey_source.dbkey.get_display_text() }' #else - --dbkey_description "${ dbkey_source.dbkey_name or $dbkey_source.dbkey }" + --dbkey_description '${ dbkey_source.dbkey_name or $dbkey_source.dbkey }' #end if ]]></command> <inputs> @@ -18,12 +19,12 @@ <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" /> + <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 type="text" name="sequence_name" value="" label="Name of sequence" /> - <param type="text" name="sequence_id" value="" label="ID for sequence" /> + <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> @@ -33,20 +34,20 @@ <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" /> + <param name="requested_dbkey" type="text" value="" optional="false" label="UCSC's DBKEY for source FASTA" /> </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" /> + <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 type="text" area="True" name="user_url" value="http://" label="URLs" optional="False" /> + <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" multiple="False" optional="False" /> + <param name="input_fasta" type="data" format="fasta" label="FASTA file" /> </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" /> + <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"> @@ -56,15 +57,12 @@ <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="as_is" /> + <when value="lexicographical" /> + <when value="gatk" /> <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" /> + <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> @@ -82,7 +80,6 @@ <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"/> @@ -97,11 +94,8 @@ ------ - - .. class:: infomark **Notice:** If you leave name, description, or id blank, it will be generated automatically. - </help> </tool>