From 03090c9f45e9be50ed4c5e4df6419d0e8525c52d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= <berenice.batut@gmail.com>
Date: Tue, 12 Mar 2024 12:33:14 +0100
Subject: [PATCH] mzToSQLite biotools (#752)
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* Add bio.tools for mz_to_sqlite

* Fix homepage_url

* Add citation

---------

Co-authored-by: Björn Grüning <bjoern.gruening@gmail.com>
---
 tools/mz_to_sqlite/.shed.yml        |  1 +
 tools/mz_to_sqlite/mz_to_sqlite.xml | 17 ++++++++++++++++-
 2 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/tools/mz_to_sqlite/.shed.yml b/tools/mz_to_sqlite/.shed.yml
index 64cf99c73..00b70a580 100644
--- a/tools/mz_to_sqlite/.shed.yml
+++ b/tools/mz_to_sqlite/.shed.yml
@@ -7,3 +7,4 @@ long_description: |
   Extract proteomics files: mzIdentML, mzML, MGF, fasta, uniprot_xml into a SQLite DB
 remote_repository_url: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite
 type: unrestricted
+homepage_url: https://github.com/galaxyproteomics/mzToSQLite
diff --git a/tools/mz_to_sqlite/mz_to_sqlite.xml b/tools/mz_to_sqlite/mz_to_sqlite.xml
index 1ea4a157e..e284aa77e 100644
--- a/tools/mz_to_sqlite/mz_to_sqlite.xml
+++ b/tools/mz_to_sqlite/mz_to_sqlite.xml
@@ -1,5 +1,8 @@
 <tool id="mz_to_sqlite" name="mz to sqlite" version="2.1.1+galaxy0">
     <description>Extract mzIdentML and associated proteomics datasets into a SQLite DB</description>
+    <xrefs>
+      <xref type="bio.tools">mztosqlite</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="2.1.1">mztosqlite</requirement>
     </requirements>
@@ -49,5 +52,17 @@ mz_to_sqlite
 
 ]]>
     </help>
-    <citations></citations>
+    <citations>
+        <citation type="bibtex">
+            @misc{
+                mzToSQLite, 
+                author = {GalaxyP}, 
+                year = {2021}, 
+                title = {mzToSQLite}, 
+                publisher = {GitHub}, 
+                journal = {GitHub repository}, 
+                url = {https://github.com/galaxyproteomics/mzToSQLite},
+            }
+        </citation>
+    </citations>
 </tool>