diff hal_halValidate.xml @ 0:13917eec61b1 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/haltools commit 6244b9d15a5ad97ae20191e2f8fbafe2050c3cac

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hal_halValidate.xml	Fri Feb 06 10:34:22 2026 +0000
@@ -0,0 +1,55 @@
+<tool id="hal_halvalidate" name="halValidate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>checks if a HAL file is valid</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/> 
+    <expand macro="stdio"/>
+    <command detect_errors="aggressive"><![CDATA[
+        halValidate
+            #if $genome:
+                --genome '$genome'
+            #end if
+            '$input_hal' > '$out_file'
+    ]]></command>
+    <inputs>
+        <expand macro="input_hal"/>
+        <param argument="--genome" type="text" value="" optional="true" label="Specific genome" help="Specific genome to validate instead of entire file">
+            <expand macro="sanitizer_default"/>
+            <expand macro="validator_trim"/>
+        </param>          
+    </inputs>
+    <outputs>
+        <data name="out_file" format="txt" label="${tool.name} on ${on_string}: Validation ${genome}"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_hal" value="halTest.hal"/>
+            <output name="out_file" ftype="txt">
+                <assert_contents>
+                    <has_line line="File valid"/>
+                    <has_n_lines n="2"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_hal" value="halTest.hal"/>
+            <param name="genome" value="Genome_0"/>
+            <output name="out_file" ftype="txt">
+                <assert_contents>
+                    <has_line line="File valid"/>
+                    <has_n_lines n="2"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+halValidate checks the structural and metadata integrity of a HAL file. 
+A HAL file is needed as input, and the tool reports a simple text message indicating whether the file is valid or not. 
+It can run a full file scan or limit the check to a single genome. 
+
+Use it to confirm that a HAL database is readable, consistent, and not corrupted before running downstream analyses.
+    ]]></help>
+    <expand macro="citation"/>
+    <expand macro="creator"/>
+</tool>
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