Mercurial > repos > iuc > data_manager_bwa_mem2_index_builder
changeset 1:62d6a9024b3c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem2_index_builder commit 57d05675396f0b44265fb4dbc8f9f891c6073219
| author | iuc |
|---|---|
| date | Thu, 05 Dec 2024 06:49:08 +0000 |
| parents | 29e2285e3ae0 |
| children | a89d803c8b29 |
| files | data_manager/bwa_mem2_index_builder.xml data_manager_conf.xml test-data/all_fasta.loc test-data/bwa_mem2_data_manager.1.json test-data/bwa_mem2_data_manager.2.json |
| diffstat | 5 files changed, 8 insertions(+), 8 deletions(-) [+] |
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--- a/data_manager/bwa_mem2_index_builder.xml Mon Sep 30 10:12:41 2024 +0000 +++ b/data_manager/bwa_mem2_index_builder.xml Thu Dec 05 06:49:08 2024 +0000 @@ -1,8 +1,8 @@ -<tool id="bwa_mem2_index_builder_data_manager" name="Build BWA-MEM2 indexes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="22.05"> +<tool id="bwa_mem2_index_builder_data_manager" name="BWA-MEM2 index builder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="23.0"> <description></description> <macros> <token name="@TOOL_VERSION@">2.2.1</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">bwa-mem2</requirement> @@ -52,7 +52,7 @@ <test> <param name="all_fasta_source" value="phiX174"/> <param name="sequence_name" value="Galeocerdo cuvier"/> - <param name="sequence_id" value="fooBar1"/> + <param name="sequence_id" value="tigHai1"/> <output name="out_file" file="bwa_mem2_data_manager.2.json"/> </test> </tests>
--- a/data_manager_conf.xml Mon Sep 30 10:12:41 2024 +0000 +++ b/data_manager_conf.xml Thu Dec 05 06:49:08 2024 +0000 @@ -9,9 +9,9 @@ <column name="path" output_ref="out_file" > <move type="directory" relativize_symlinks="True"> <!-- <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}">${dbkey}/bwa_mem2_index/${value}</target> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">genomes/${dbkey}/bwa_mem_index/v2/${value}</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/bwa_mem2_index/${value}/${path}</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/genomes/${dbkey}/bwa_mem_index/v2/${value}/${path}</value_translation> <value_translation type="function">abspath</value_translation> </column> </output>
--- a/test-data/all_fasta.loc Mon Sep 30 10:12:41 2024 +0000 +++ b/test-data/all_fasta.loc Thu Dec 05 06:49:08 2024 +0000 @@ -16,4 +16,4 @@ #fasta file. So there will be multiple fasta files for each build, #such as with hg19 above. # -phiX174 phiX174 phiX174 ${__HERE__}/phiX174.fasta +phiX174 phiX174 phiX 174 ${__HERE__}/phiX174.fasta
--- a/test-data/bwa_mem2_data_manager.1.json Mon Sep 30 10:12:41 2024 +0000 +++ b/test-data/bwa_mem2_data_manager.1.json Thu Dec 05 06:49:08 2024 +0000 @@ -4,7 +4,7 @@ { "value": "phiX174", "dbkey": "phiX174", - "name": "phiX174", + "name": "phiX 174", "path": "phiX174.fasta" } ]
--- a/test-data/bwa_mem2_data_manager.2.json Mon Sep 30 10:12:41 2024 +0000 +++ b/test-data/bwa_mem2_data_manager.2.json Thu Dec 05 06:49:08 2024 +0000 @@ -2,7 +2,7 @@ "data_tables":{ "bwa_mem2_indexes":[ { - "value": "fooBar1", + "value": "tigHai1", "dbkey": "phiX174", "name": "Galeocerdo cuvier", "path": "phiX174.fasta"