Mercurial > repos > iuc > data_manager_build_kraken2_database

changeset 9:539b008cfe1c 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 3c6cc780d2d8ea156d167289cc2576fc3e43d2fd
author iuc
date Thu, 06 Jun 2024 09:03:14 +0000
parents e4b4837f06f5
children 13851aefa67a
files data_manager/kraken2_build_database.xml
diffstat 1 files changed, 38 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/kraken2_build_database.xml	Mon Dec 18 09:36:03 2023 +0000
+++ b/data_manager/kraken2_build_database.xml	Thu Jun 06 09:03:14 2024 +0000
@@ -2,9 +2,9 @@
 <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@">1</token>
-        <token name="@PROFILE@">21.01</token>
+        <token name="@TOOL_VERSION@">2.1.3</token>
+        <token name="@VERSION_SUFFIX@">0</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" />
@@ -103,12 +103,44 @@
             <when value="standard_prebuilt">
                 <conditional name="prebuild">
                     <param name="prebuilt_date" type="select" label="Select index build date">
+                        <option value="2024-12-01">December 1, 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="2024-12-01">
+                        <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"/>
@@ -221,15 +253,15 @@
                 <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>