Mercurial > repos > ieguinoa > data_manager_fetch_gff
comparison data_manager/data_manager_fetch_gff.xml @ 2:c57bd7f3fb46 draft
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| author | ieguinoa |
|---|---|
| date | Tue, 10 Jul 2018 10:55:47 -0400 |
| parents | ac4fde07eaed |
| children | cb0fa3584aeb |
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| 1:955a8d483fa3 | 2:c57bd7f3fb46 |
|---|---|
| 1 <tool id="data_manager_fetch_gff" name="Create entries in gff data table" version="0.0.1" tool_type="manage_data"> | 1 <tool id="data_manager_fetch_gff" name="Create entries in gff data table" version="0.0.1" tool_type="manage_data"> |
| 2 <description>fetching</description> | 2 <description>fetching</description> |
| 3 <command><![CDATA[ | 3 <command><![CDATA[ |
| 4 python "$__tool_directory__"/data_manager_fetch_gff.py "${out_file}" | 4 python "$__tool_directory__"/data_manager_fetch_gff.py "${out_file}" |
| 5 --type $file_type | 5 --type $file_type |
| 6 #if str( $dbkey_source.dbkey_source_selector ) == 'existing': | 6 --dbkey_description ${ dbkey.get_display_text() } |
| 7 --dbkey_description ${ dbkey_source.dbkey.get_display_text() } | |
| 8 #else | |
| 9 --dbkey_description "${ dbkey_source.dbkey_name or $dbkey_source.dbkey }" | |
| 10 #end if | |
| 11 | 7 |
| 12 ]]></command> | 8 ]]></command> |
| 13 <inputs> | 9 <inputs> |
| 14 <param name="file_type" type="select" label="GFF file with only one representative transcript per gene (for htseq-count use) or full features file"> | 10 <param name="file_type" type="select" label="GFF file with only one representative transcript per gene (for htseq-count use) or full features file"> |
| 15 <option value="representative">Representative GFF</option> | 11 <option value="representative">Representative GFF</option> |
| 16 <option value="full">GFF with complete features</option> | 12 <option value="full">GFF with complete features</option> |
| 17 </param> | 13 </param> |
| 18 | 14 |
| 19 <conditional name="dbkey_source"> | 15 <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" /> |
| 20 <param name="dbkey_source_selector" type="select" label="Use existing dbkey or create a new one."> | |
| 21 <option value="existing" selected="True">Existing</option> | |
| 22 <option value="new">New</option> | |
| 23 </param> | |
| 24 <when value="existing"> | |
| 25 <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" /> | |
| 26 </when> | |
| 27 <when value="new"> | |
| 28 <param type="text" name="dbkey" value="" label="dbkey" optional="False" /> | |
| 29 <param type="text" name="dbkey_name" value="" label="Display name for dbkey" /> | |
| 30 </when> | |
| 31 </conditional> | |
| 32 <param type="text" name="sequence_name" value="" label="Name of sequence" /> | 16 <param type="text" name="sequence_name" value="" label="Name of sequence" /> |
| 33 <param type="text" name="sequence_id" value="" label="ID for sequence" /> | 17 <param type="text" name="sequence_id" value="" label="ID for sequence" /> |
| 34 <conditional name="reference_source"> | 18 <conditional name="reference_source"> |
| 35 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> | 19 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> |
| 36 <option value="url">URL</option> | 20 <option value="url">URL</option> |