Mercurial > repos > iuc > data_manager_build_kraken2_database

changeset 11:1e34d2e3d285 draft

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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 09:21:32 +0000
parents 13851aefa67a
children 90b4d4f0a3a4
files data_manager/kraken2_build_database.xml
diffstat 1 files changed, 38 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/kraken2_build_database.xml	Thu Jun 13 12:18:58 2024 +0000
+++ b/data_manager/kraken2_build_database.xml	Mon Jul 15 09:21:32 2024 +0000
@@ -3,7 +3,7 @@
     <description>database builder</description>
     <macros>
         <token name="@TOOL_VERSION@">2.1.3</token>
-        <token name="@VERSION_SUFFIX@">1</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" />
@@ -13,7 +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>
@@ -103,6 +103,7 @@
             <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>
@@ -111,6 +112,21 @@
                         <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"/>
@@ -287,6 +303,26 @@
                 </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>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 Build Kraken2 databases or download `prebuilt Kraken2 RefSeq indexes <https://benlangmead.github.io/aws-indexes/k2>`__