Mercurial > repos > devteam > data_manager_bowtie2_index_builder
changeset 12:6754002631cd draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit e5971e34b23280f7c3d6291a03325b6dd47e3fdd
| author | iuc |
|---|---|
| date | Sat, 16 Aug 2025 14:35:19 +0000 |
| parents | 39865c64a4e1 |
| children | |
| files | data_manager/bowtie2_index_builder.xml data_manager_conf.xml test-data/bowtie2_data_manager.1.json test-data/bowtie2_data_manager.2.json |
| diffstat | 4 files changed, 9 insertions(+), 8 deletions(-) [+] |
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--- a/data_manager/bowtie2_index_builder.xml Thu Dec 05 06:48:52 2024 +0000 +++ b/data_manager/bowtie2_index_builder.xml Sat Aug 16 14:35:19 2025 +0000 @@ -2,7 +2,7 @@ <description>builder</description> <macros> <token name="@WRAPPER_VERSION@">2.5.4</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> </macros> <requirements> <requirement type="package" version="@WRAPPER_VERSION@">bowtie2</requirement> @@ -14,6 +14,7 @@ ln -s '${all_fasta_source.fields.path}' '${out_file.extra_files_path}/${fasta_file_name}' && cd '${out_file.extra_files_path}' && bowtie2-build --threads \${GALAXY_SLOTS:-1} '${out_file.extra_files_path}/${fasta_file_name}' '${value}' && + rm '${out_file.extra_files_path}/${fasta_file_name}' && cp '$dmjson' '$out_file' ]]></command> <configfiles> @@ -28,7 +29,7 @@ "value": "${value}", "dbkey": "${all_fasta_source.fields.dbkey}", "name": "${name}", - "path": "${fasta_file_name}" + "path": "${value}" } #if $tophat2: ], @@ -37,7 +38,7 @@ "value": "${value}", "dbkey": "${all_fasta_source.fields.dbkey}", "name": "${name}", - "path": "${fasta_file_name}" + "path": "${value}" } #end if ]
--- a/data_manager_conf.xml Thu Dec 05 06:48:52 2024 +0000 +++ b/data_manager_conf.xml Sat Aug 16 14:35:19 2025 +0000 @@ -11,7 +11,7 @@ <!-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base --> <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">genomes/${dbkey}/bowtie_index/v2/${value}</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/genomes/${dbkey}/bowtie_index/v2/${value}/${path}</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/genomes/${dbkey}/bowtie_index/v2/${value}/${value}</value_translation> <value_translation type="function">abspath</value_translation> </column> </output> @@ -24,7 +24,7 @@ <column name="name" /> <column name="path" output_ref="out_file" > <!-- no move, always happens as part of bowtie2 and uses that path --> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/genomes/${dbkey}/bowtie_index/v2/${value}/${path}</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/genomes/${dbkey}/bowtie_index/v2/${value}/${value}</value_translation> <value_translation type="function">abspath</value_translation> </column> </output>
--- a/test-data/bowtie2_data_manager.1.json Thu Dec 05 06:48:52 2024 +0000 +++ b/test-data/bowtie2_data_manager.1.json Sat Aug 16 14:35:19 2025 +0000 @@ -5,7 +5,7 @@ "value": "phiX174", "dbkey": "phiX174", "name": "phiX 174", - "path": "phiX174.fasta" + "path": "phiX174" } ], "tophat2_indexes":[ @@ -13,7 +13,7 @@ "value": "phiX174", "dbkey": "phiX174", "name": "phiX 174", - "path": "phiX174.fasta" + "path": "phiX174" } ] }