diff omero_get_value.xml @ 0:1ae349b83c08 draft

planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/omero_get_value.xml	Tue Oct 22 11:52:46 2024 +0000
@@ -0,0 +1,82 @@
+<tool id="omero_get_value" name="OMERO get Object" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
+    <description> with ezomero </description>
+    <macros>
+        <import>macros.xml</import>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">omero</xref>
+    </xrefs>
+    <expand macro="ezomero_requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/omero_get_value.py'
+        --credential-file '$credentials'
+        @HOST_PORT@
+        --obj_type '$obj_type'
+        #if $ids_input.ids_format == "values"
+            --ids ${str($ids_input.ids).replace(',', ' ')}
+        #else
+            --ids_path '$ids_input.ids_path'
+        #end if
+        --tsv_file '$tsv'
+    ]]></command>
+    <configfiles>
+        <expand macro="credentials"/>
+    </configfiles>
+    <inputs>
+        <expand macro="host_port"/>
+        <param argument="obj_type" type="select" optional="false" label="Type of object to fetch:">
+            <option value="Annotation">Annotation</option>
+            <option value="Tag">Tag</option>
+            <option value="Table">Table</option>
+        </param>
+        <conditional name="ids_input">
+            <param name="ids_format" type="select" label="How do you provide the ID(s) of the OMERO object?">
+                <option value="values">Comma separated values</option>
+                <option value="file">From a dataset (one per line)</option>
+            </param>
+            <when value="values">
+                <param argument="--ids" type="text" value="" label="ID(s) of the object(s) to fetch on OMERO separated by comma">
+                    <validator type="regex" message="Enter a valid list of IDs (i.e. 2,45,56,67)">^(\d+)(,\d+)*$</validator>
+                </param>
+            </when>
+            <when value="file">
+                <param argument="--ids_path" type="data" format="txt,tabular" label="Dataset with ID(s) of the object(s) to fetch on OMERO (one per line)"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="tsv" format="tabular"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="omero_host" value="host.docker.internal"/>
+            <param name="omero_port" value="6064"/>
+            <param name="obj_type" value="Tag"/>
+            <conditional name="ids_input">
+                <param name="ids_format" value="values"/>
+                <param name="ids" value="1"/>
+            </conditional>
+            <param name="test_username" value="root"/>
+            <param name="test_password" value="omero"/>
+            <output name="tsv" ftype="tabular">
+                <assert_contents>
+                    <has_text text="test_tag"/>
+                    <has_n_lines n="2"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+Description
+-----------
+
+Tool to fetch Annotation, Tag and Tables from IDs.
+
+The IDs can be obtained with the tool OMERO get IDs with ezomero
+
+    </help>
+    <citations>
+        <citation type="doi">10.1038/nmeth.1896</citation>
+    </citations>
+</tool>
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