From d18d4019032921c6b6b632b37ccf8d4ccc112ce5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= <berenice.batut@gmail.com>
Date: Fri, 17 May 2024 15:16:08 +0200
Subject: [PATCH] Add xrefs with bio.tools to XMLs

---
 q2galaxy/core/templaters/action.py            | 3 ++-
 q2galaxy/core/templaters/common.py            | 7 +++++++
 q2galaxy/core/templaters/export_data.py       | 3 ++-
 q2galaxy/core/templaters/import_data.py       | 4 +++-
 q2galaxy/core/templaters/import_fastq_data.py | 4 +++-
 q2galaxy/core/util.py                         | 2 +-
 6 files changed, 18 insertions(+), 5 deletions(-)

diff --git a/q2galaxy/core/templaters/action.py b/q2galaxy/core/templaters/action.py
index ec110fc..b79c01e 100644
--- a/q2galaxy/core/templaters/action.py
+++ b/q2galaxy/core/templaters/action.py
@@ -14,7 +14,7 @@
 from q2galaxy.core.util import XMLNode, galaxy_ui_var, rst_header
 from q2galaxy.core.templaters.common import (
     make_tool_id, make_tool_name, make_config, make_citations,
-    make_requirements)
+    make_requirements, make_xrefs)
 from q2galaxy.core.templaters.helpers import signature_to_galaxy
 
 
@@ -76,6 +76,7 @@ def make_tool(conda_meta, plugin, action, test_dir):
     tool.append(make_help(plugin, action, test_dir))
     tool.append(make_citations(plugin, action))
     tool.append(make_requirements(conda_meta, plugin.project_name))
+    tool.append(make_xrefs())
     return tool
 
 
diff --git a/q2galaxy/core/templaters/common.py b/q2galaxy/core/templaters/common.py
index e54b84c..c03750f 100644
--- a/q2galaxy/core/templaters/common.py
+++ b/q2galaxy/core/templaters/common.py
@@ -115,3 +115,10 @@ def make_formats_help(formats):
             help_ += f' - {format_.__name__}\n'
 
     return help_
+
+
+def make_xrefs():
+    xefs = XMLNode('xefs')
+    xefs.append(
+        XMLNode('xref', 'qiime2', type='bio.tools'))
+    return xefs
\ No newline at end of file
diff --git a/q2galaxy/core/templaters/export_data.py b/q2galaxy/core/templaters/export_data.py
index 781d25e..18f2fca 100644
--- a/q2galaxy/core/templaters/export_data.py
+++ b/q2galaxy/core/templaters/export_data.py
@@ -12,7 +12,7 @@
 from q2galaxy.core.util import XMLNode, galaxy_esc, pretty_fmt_name, rst_header
 from q2galaxy.core.templaters.common import (
     make_builtin_version, make_requirements, make_tool_name_from_id,
-    make_config, make_citations, make_formats_help)
+    make_config, make_citations, make_formats_help, make_xrefs)
 
 
 def make_builtin_export(meta, tool_id):
@@ -170,6 +170,7 @@ def make_builtin_export(meta, tool_id):
     tool.append(make_citations())
     tool.append(make_requirements(meta, *[p.project_name for p in plugins]))
     tool.append(_make_help(known_formats))
+    tool.append(make_xrefs())
 
     return tool
 
diff --git a/q2galaxy/core/templaters/import_data.py b/q2galaxy/core/templaters/import_data.py
index fd06adb..67cc243 100644
--- a/q2galaxy/core/templaters/import_data.py
+++ b/q2galaxy/core/templaters/import_data.py
@@ -17,7 +17,8 @@
                                              make_tool_name_from_id,
                                              make_requirements,
                                              make_citations,
-                                             make_formats_help)
+                                             make_formats_help,
+                                             make_xrefs)
 
 
 def make_builtin_import(meta, tool_id):
@@ -110,6 +111,7 @@ def make_builtin_import(meta, tool_id):
     tool.append(make_citations())
     tool.append(make_requirements(meta, *[p.project_name for p in plugins]))
     tool.append(_make_help(known_formats))
+    tool.append(make_xrefs())
     return tool
 
 
diff --git a/q2galaxy/core/templaters/import_fastq_data.py b/q2galaxy/core/templaters/import_fastq_data.py
index c01ab55..da74f1b 100644
--- a/q2galaxy/core/templaters/import_fastq_data.py
+++ b/q2galaxy/core/templaters/import_fastq_data.py
@@ -11,7 +11,8 @@
 from q2galaxy.core.templaters.common import (make_builtin_version,
                                              make_tool_name_from_id,
                                              make_requirements,
-                                             make_citations)
+                                             make_citations,
+                                             make_xrefs)
 
 
 def make_builtin_import_fastq(meta, tool_id):
@@ -33,6 +34,7 @@ def make_builtin_import_fastq(meta, tool_id):
     tool.append(_make_config())
     tool.append(make_citations())
     tool.append(make_requirements(meta, *[p.project_name for p in plugins]))
+    tool.append(make_xrefs())
     return tool
 
 
diff --git a/q2galaxy/core/util.py b/q2galaxy/core/util.py
index 3a74bd1..bd0b369 100644
--- a/q2galaxy/core/util.py
+++ b/q2galaxy/core/util.py
@@ -18,7 +18,7 @@
 
 class OrderedTool(collections.OrderedDict):
     order = ["description", "macros", "edam_topics", "edam_operations",
-             "parallelism", "requirements", "code", "stdio", "version_command",
+             "parallelism", "xrefs", "requirements", "code", "stdio", "version_command",
              "command", "environment_variables", "configfiles", "inputs",
              "request_param_translation", "outputs", "tests", "help",
              "citations"]