Mercurial > repos > iuc > data_manager_build_kraken2_database
changeset 8:1108eae823a8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
| author | iuc |
|---|---|
| date | Mon, 15 Jul 2024 09:21:25 +0000 |
| parents | ce75e9475f0f |
| children | ba981d05e216 |
| files | data_manager/kraken2_build_database.xml |
| diffstat | 1 files changed, 97 insertions(+), 9 deletions(-) [+] |
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--- a/data_manager/kraken2_build_database.xml Sun Apr 16 08:26:45 2023 +0000 +++ b/data_manager/kraken2_build_database.xml Mon Jul 15 09:21:25 2024 +0000 @@ -1,9 +1,10 @@ <?xml version="1.0"?> <tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>database builder</description> <macros> - <token name="@TOOL_VERSION@">2.1.2</token> - <token name="@VERSION_SUFFIX@">0</token> - <token name="@PROFILE@">21.01</token> + <token name="@TOOL_VERSION@">2.1.3</token> + <token name="@VERSION_SUFFIX@">2</token> + <token name="@PROFILE@">22.01</token> <xml name="common_params"> <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" /> <param name="minimizer_len" type="integer" value="31" label="Minimizer length" /> @@ -12,7 +13,7 @@ <param name="clean" type="boolean" truevalue="--clean" falsevalue="" checked="true" label="Clean up extra files" /> </xml> <xml name="viral"> - <option value="viral">Viral (viral; ~50 GB)</option> + <option value="viral">Viral (viral; ~0.5 GB)</option> </xml> <xml name="minusb"> <option value="minusb">MinusB (archaea, viral, plasmid, human, UniVec_Core; ~8 GB)</option> @@ -45,7 +46,6 @@ <option value="pluspfp_16gb">PlusPFP-16 (PlusPFP with DB capped at 16 GB; ~15 GB)</option> </xml> </macros> - <description>database builder</description> <requirements> <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement> <requirement type="package" version="3.7">python</requirement> @@ -103,12 +103,60 @@ <when value="standard_prebuilt"> <conditional name="prebuild"> <param name="prebuilt_date" type="select" label="Select index build date"> + <option value="2024-06-05">June 5, 2024</option> + <option value="2024-01-12">January 12, 2024</option> + <option value="2023-06-05">June 5, 2023</option> <option value="2022-06-07">June 7, 2022</option> <option value="2021-05-17">May 17, 2021</option> <option value="2021-01-27">January 27, 2021</option> <option value="2020-12-02">December 2, 2020</option> <option value="2020-09-19">September 19, 2020</option> </param> + <when value="2024-06-05"> + <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download"> + <expand macro="viral"/> + <expand macro="minusb"/> + <expand macro="standard"/> + <expand macro="standard_08gb"/> + <expand macro="standard_16gb"/> + <expand macro="pluspf"/> + <expand macro="pluspf_08gb"/> + <expand macro="pluspf_16gb"/> + <expand macro="pluspfp"/> + <expand macro="pluspfp_08gb"/> + <expand macro="pluspfp_16gb"/> + </param> + </when> + <when value="2024-01-12"> + <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download"> + <expand macro="viral"/> + <expand macro="minusb"/> + <expand macro="standard"/> + <expand macro="standard_08gb"/> + <expand macro="standard_16gb"/> + <expand macro="pluspf"/> + <expand macro="pluspf_08gb"/> + <expand macro="pluspf_16gb"/> + <expand macro="pluspfp"/> + <expand macro="pluspfp_08gb"/> + <expand macro="pluspfp_16gb"/> + </param> + </when> + <when value="2023-06-05"> + <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download"> + <expand macro="viral"/> + <expand macro="minusb"/> + <expand macro="standard"/> + <expand macro="standard_08gb"/> + <expand macro="standard_16gb"/> + <expand macro="pluspf"/> + <expand macro="pluspf_08gb"/> + <expand macro="pluspf_16gb"/> + <expand macro="pluspfp"/> + <expand macro="pluspfp_08gb"/> + <expand macro="pluspfp_16gb"/> + </param> + </when> <when value="2022-06-07"> <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download"> <expand macro="viral"/> @@ -206,7 +254,7 @@ <param name="kmer_len" value="35" /> <param name="minimizer_spaces" value="6"/> <param name="load_factor" value="0.7" /> - <param name="clean" truevalue="--clean"/> + <param name="clean" value="true"/> </conditional> <output name="out_file"> <assert_contents> @@ -221,15 +269,55 @@ <param name="database_type" value="standard_prebuilt" /> <conditional name="prebuild"> <param name="prebuilt_date" value="2022-06-07"/> - <param name="prebuilt_db" value="standard_08gb"/> + <param name="prebuilt_db" value="viral"/> </conditional> </conditional> <output name="out_file"> <assert_contents> <has_text text="kraken2_databases"/> <has_text text="path"/> - <has_text text="Standard-8"/> - <has_text text="_standard_prebuilt_standard_08gb_2022-06-07"/> + <has_text text="Viral"/> + <has_text text="_standard_prebuilt_viral_2022-06-07"/> + <has_text text="Version"/> + <has_text text="Downloaded"/> + </assert_contents> + </output> + </test> + <!-- test with latest version --> + <test> + <conditional name="database_type"> + <param name="database_type" value="standard_prebuilt" /> + <conditional name="prebuild"> + <param name="prebuilt_date" value="2024-01-12"/> + <param name="prebuilt_db" value="viral"/> + </conditional> + </conditional> + <output name="out_file"> + <assert_contents> + <has_text text="kraken2_databases"/> + <has_text text="path"/> + <has_text text="Viral"/> + <has_text text="_standard_prebuilt_viral_2024-01-12"/> + <has_text text="Version"/> + <has_text text="Downloaded"/> + </assert_contents> + </output> + </test> + <!-- test with first 2024 version --> + <test> + <conditional name="database_type"> + <param name="database_type" value="standard_prebuilt" /> + <conditional name="prebuild"> + <param name="prebuilt_date" value="2024-06-05"/> + <param name="prebuilt_db" value="viral"/> + </conditional> + </conditional> + <output name="out_file"> + <assert_contents> + <has_text text="kraken2_databases"/> + <has_text text="path"/> + <has_text text="Viral"/> + <has_text text="_standard_prebuilt_viral_2024-06-05"/> <has_text text="Version"/> <has_text text="Downloaded"/> </assert_contents>