From b21f516390fcbbe3c098266ff0d72e64924aab00 Mon Sep 17 00:00:00 2001
From: Rand Zoabi <58028465+RZ9082@users.noreply.github.com>
Date: Fri, 12 Jul 2024 16:58:18 +0200
Subject: [PATCH] Add mg-toolkit original_metadata (#6142)
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* add mg-toolkit original_metadata

* add citation

* rename metadata.xml --> original_metadata.xml

* add license

* rename repo

* minor adjustments & input validator

* accession --> accessions

* Update tools/mg_toolkit/original_metadata.xml

* Apply suggestions from code review

* update command

* Update tools/mg_toolkit/original_metadata.xml

---------

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
---
 tools/mg_toolkit/.shed.yml             |  9 ++++
 tools/mg_toolkit/macros.xml            | 32 ++++++++++++
 tools/mg_toolkit/original_metadata.xml | 69 ++++++++++++++++++++++++++
 3 files changed, 110 insertions(+)
 create mode 100644 tools/mg_toolkit/.shed.yml
 create mode 100644 tools/mg_toolkit/macros.xml
 create mode 100644 tools/mg_toolkit/original_metadata.xml

diff --git a/tools/mg_toolkit/.shed.yml b/tools/mg_toolkit/.shed.yml
new file mode 100644
index 00000000000..0222385198b
--- /dev/null
+++ b/tools/mg_toolkit/.shed.yml
@@ -0,0 +1,9 @@
+name: mg_toolkit
+owner: iuc
+description: Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.
+homepage_url: https://github.com/EBI-Metagenomics/emg-toolkit
+long_description: |
+  Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file.
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg-toolkit
+categories:
+- Metagenomics
\ No newline at end of file
diff --git a/tools/mg_toolkit/macros.xml b/tools/mg_toolkit/macros.xml
new file mode 100644
index 00000000000..9c30689ecdd
--- /dev/null
+++ b/tools/mg_toolkit/macros.xml
@@ -0,0 +1,32 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.10.4</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">mg-toolkit</requirement>
+        </requirements>
+    </xml>
+    <xml name="biotools">
+        <xrefs>
+            <xref type="bio.tools">mg-toolkit</xref>
+        </xrefs>
+    </xml>
+    <xml name="creators">
+        <creator>
+            <person givenName="Rand" familyName="Zoabi" url="https://github.com/RZ9082" />
+        </creator>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @misc{emg_toolkit,
+                    author = {EBI Metagenomics},
+                    title = {EMG Toolkit},
+                    year = {2024},
+                    howpublished = {\url{https://github.com/EBI-metagenomics/emg-toolkit}},
+                    note = {Accessed: 2024-07-11}
+                }
+            </citation>
+        </citations>
+    </xml>
+</macros>
diff --git a/tools/mg_toolkit/original_metadata.xml b/tools/mg_toolkit/original_metadata.xml
new file mode 100644
index 00000000000..6e3294a5461
--- /dev/null
+++ b/tools/mg_toolkit/original_metadata.xml
@@ -0,0 +1,69 @@
+<tool id="mg_toolkit_original_metadata" name="Metagenomics toolkit Original Metadata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+    <description>Download original metadata for a study</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creators" />
+    <expand macro="biotools" />
+    <expand macro="requirements" />
+    <command><![CDATA[
+        mkdir output_metadata &&
+        mg-toolkit original_metadata -a ${accessions} &&
+        mv *.csv output_metadata
+    ]]></command>
+    
+    <inputs>
+        <param name="accessions" type="text" label="Accessions" help="Study/project accessions (e.g., ERP001736 SRP000319)" optional="false">
+            <validator type="regex" message="Accessions separated with white spaces">^([A-Za-z]{3,4}\d+)(\s[A-Za-z]{3,4}\d+)*$</validator>
+        </param>
+    </inputs>    
+    <outputs>
+        <collection name="output_collection" type="list" label="Original metadata">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+).csv" directory="output_metadata" format="csv"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="accessions" value="ERP001736 SRP000319" />
+            <output_collection name="output_collection" type="list">
+                <element name="ERP001736">
+                    <assert_contents>
+                        <has_n_lines n="250" />
+                        <has_size size="185577" />
+                    </assert_contents>
+                </element>
+                <element name="SRP000319">
+                    <assert_contents>
+                        <has_n_lines n="30" />
+                        <has_size size="2855" />
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+        <test>
+            <param name="accessions" value="ERP001736" />
+            <output_collection name="output_collection" type="list">
+                <element name="ERP001736">
+                    <assert_contents>
+                        <has_n_lines n="250" />                
+                        <has_size size="185577" />
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+    </tests>
+    <help>
+<![CDATA[ 
+The mg-toolkit original-metadata tool is part of the EMG Toolkit provided by EBI Metagenomics.
+This tool allows users to retrieve the original metadata associated with metagenomic studies and analyses.
+It facilitates the extraction of detailed contextual information submitted by researchers, 
+aiding in the interpretation and further analysis of metagenomic data.
+
+License
+-------
+* `Apache-2.0 license <https://raw.githubusercontent.com/EBI-Metagenomics/emg-toolkit/master/LICENSE>`_
+
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>