Mercurial > repos > iuc > data_manager_mapseq

changeset 2:23511530b8fd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 960c1f69ec78943dfe72eff0a0992a2ce15d2555
author iuc
date Mon, 30 Sep 2024 10:08:03 +0000
parents 4cd97cc67061
children a0d77af1d226
files data_manager_fetch_mapseq_db.py macros.xml mapseq_db_fetcher.xml
diffstat 3 files changed, 57 insertions(+), 30 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager_fetch_mapseq_db.py	Sat Mar 23 07:20:14 2024 +0000
+++ b/data_manager_fetch_mapseq_db.py	Mon Sep 30 10:08:03 2024 +0000
@@ -10,18 +10,28 @@
 import wget
 
 DB_paths = {
-    "mgnify_lsu": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/silva_lsu-20200130.tar.gz",
-    "mgnify_ssu": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/silva_ssu-20200130.tar.gz",
-    "mgnify_its_unite": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/UNITE-20200214.tar.gz",
-    "mgnify_its_itsonedb": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/ITSoneDB-20200214.tar.gz",
+    "mgnify_v5_lsu": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/silva_lsu-20200130.tar.gz",
+    "mgnify_v5_ssu": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/silva_ssu-20200130.tar.gz",
+    "mgnify_v5_its_unite": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/UNITE-20200214.tar.gz",
+    "mgnify_v5_its_itsonedb": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/ITSoneDB-20200214.tar.gz",
+    "mgnify_v6_lsu": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipelines/tool-dbs/silva-lsu/silva-lsu_138.1.tar.gz",
+    "mgnify_v6_ssu": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipelines/tool-dbs/silva-ssu/silva-ssu_138.1.tar.gz",
+    "mgnify_v6_its_unite": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipelines/tool-dbs/unite/unite_9.0.tar.gz",
+    "mgnify_v6_its_itsonedb": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipelines/tool-dbs/itsonedb/itsonedb_1.141.tar.gz",
+    "mgnify_v6_pr2": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipelines/tool-dbs/pr2/pr2_5.0.0.tar.gz",
     "test_lsu": "https://zenodo.org/record/8205348/files/test_lsu.tar.gz",
 }
 
 DB_names = {
-    "mgnify_lsu": "MGnify LSU (v5.0.7) - silva_lsu-20200130",
-    "mgnify_ssu": "MGnify SSU (v5.0.7) - silva_ssu-20200130",
-    "mgnify_its_unite": "MGnify ITS UNITE (v5.0.7) - UNITE-20200214",
-    "mgnify_its_itsonedb": "MGnify ITS ITSonedb (v5.0.7) - ITSoneDB-20200214",
+    "mgnify_v5_lsu": "MGnify LSU (v5.0.7) - silva_lsu-20200130",
+    "mgnify_v5_ssu": "MGnify SSU (v5.0.7) - silva_ssu-20200130",
+    "mgnify_v5_its_unite": "MGnify ITS UNITE (v5.0.7) - UNITE-20200214",
+    "mgnify_v5_its_itsonedb": "MGnify ITS ITSonedb (v5.0.7) - ITSoneDB-20200214",
+    "mgnify_v6_lsu": "MGnify LSU (v6.0) - silva_lsu-20240702",
+    "mgnify_v6_ssu": "MGnify SSU (v6.0) - silva_ssu-20240701",
+    "mgnify_v6_its_unite": "MGnify ITS UNITE (v6.0) - UNITE-20240702",
+    "mgnify_v6_its_itsonedb": "MGnify ITS ITSonedb (v6.0) - ITSoneDB-20240702",
+    "mgnify_v6_pr2": "MGnify PR2 (v6.0) - PR2-20240702",
     "test_lsu": "Trimmed LSU Test DB",
 }
 
--- a/macros.xml	Sat Mar 23 07:20:14 2024 +0000
+++ b/macros.xml	Mon Sep 30 10:08:03 2024 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">1.1</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">22.05</token>
     <xml name="requirements">
         <requirements>
--- a/mapseq_db_fetcher.xml	Sat Mar 23 07:20:14 2024 +0000
+++ b/mapseq_db_fetcher.xml	Mon Sep 30 10:08:03 2024 +0000
@@ -1,4 +1,3 @@
-<?xml version="1.0"?>
 <tool id="mapseq_db_fetcher" name="Mapseq DB fetcher" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Fetches the DB required for mapseq</description>
     <macros>
@@ -12,36 +11,54 @@
         --out '${out_file}' 
         --version '${version}' 
         --database-type '${database_type}'
-        $test_data_manager
+        $test_data_manager_v5
+        $test_data_manager_v6
     ]]>
     </command>
     <inputs>
-    <!-- <param name="test_data_manager" type="hidden" /> -->
-    <param name="test_data_manager" type="boolean" truevalue="--test" falsevalue="" checked="False" label="Download minimal test DB and create mock data table entry." />
-
-    <param name="database_type" type="select" multiple="false" label="Database Type">
-        <option value="mgnify_lsu">MGnify LSU (v5.0.7)</option>
-        <option value="mgnify_ssu">MGnify SSU (v5.0.7)</option>
-        <option value="mgnify_its_itsonedb">MGnify ITS ITSonedb (v5.0.7)</option>
-        <option value="mgnify_its_unite">MGnify ITS UNITE (v5.0.7)</option>
-    </param>
-
-    <!-- <param name="test_data_manager" type="text" value=""/> -->
-    <param argument="--version" type="text" value="5.0.7" help="Check MGnify GitHub (https://github.com/EBI-Metagenomics/pipeline-v5/releases) for the version."/> 
+        <!-- <param name="test_data_manager" type="hidden" /> -->
+        <param name="test_data_manager_v5" type="boolean" truevalue="--test" falsevalue="" checked="False" label="Download minimal test DB and create mock data table entry." />
+        <param name="test_data_manager_v6" type="boolean" truevalue="--test" falsevalue="" checked="False" label="Download minimal test DB and create mock data table entry." />
+    
+        <param name="database_type" type="select" multiple="false" label="Database Type">
+            <option value="mgnify_v6_lsu">MGnify LSU (v6.0)</option>
+            <option value="mgnify_v6_ssu">MGnify SSU (v6.0)</option>
+            <option value="mgnify_v6_its_itsonedb">MGnify ITS ITSonedb (v6.0)</option>
+            <option value="mgnify_v6_its_unite">MGnify ITS UNITE (v6.0)</option>
+            <option value="mgnify_v6_pr2">MGnify PR2 (v6.0)</option>
+            <option value="mgnify_v5_lsu">MGnify LSU (v5.0.7)</option>
+            <option value="mgnify_v5_ssu">MGnify SSU (v5.0.7)</option>
+            <option value="mgnify_v5_its_itsonedb">MGnify ITS ITSonedb (v5.0.7)</option>
+            <option value="mgnify_v5_its_unite">MGnify ITS UNITE (v5.0.7)</option>
+        </param>
+    
+        <!-- <param name="test_data_manager" type="text" value=""/> -->
+        <param argument="--version" type="text" value="6.0" help="Check MGnify GitHub (https://github.com/EBI-Metagenomics/amplicon-pipeline) for the version."/>
     </inputs>
     <outputs>
         <data format="data_manager_json" name="out_file" />
     </outputs>
     <tests>
     <test expect_num_outputs="1">
-        <param name="test_data_manager" value="--test"/>
+        <param name="test_data_manager_v5" value="--test"/>
         <param name="version" value="5.0.7"/>
-        <param name="database_type" value="mgnify_lsu"/>
+        <param name="database_type" value="mgnify_v5_lsu"/>
         <output name="out_file">
-                <assert_contents>
-                    <has_text text="mgnify_lsu"/>
-                    <has_text text="5.0.7"/>
-                </assert_contents>
+            <assert_contents>
+                <has_text text="mgnify_v5_lsu"/>
+                <has_text text="5.0.7"/>
+            </assert_contents>
+        </output>
+    </test>
+    <test expect_num_outputs="1">
+        <param name="test_data_manager_v6" value="--test"/>
+        <param name="version" value="6.0"/>
+        <param name="database_type" value="mgnify_v6_pr2"/>
+        <output name="out_file">
+            <assert_contents>
+                <has_text text="mgnify_v6_pr2"/>
+                <has_text text="6.0"/>
+            </assert_contents>
         </output>
     </test>
     </tests>
@@ -51,4 +68,4 @@
     </help>
     <expand macro="citations" />
     <expand macro="creator" />
-</tool>
\ No newline at end of file
+</tool>