diff mztabm_validate.xml @ 0:520706977927 draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/main/tools/mztabm commit 9e8dabb356b4d26714194c1a5506c6fedb07d8d8

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mztabm_validate.xml	Tue Jul 08 14:41:25 2025 +0000
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+<tool id="mztabm_validate" name="mztab-m validate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0" license="MIT">
+    <description>validate mztab-m files</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.0.6</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+
+    <xrefs>
+        <xref type="bio.tools">jmztab-m</xref>
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">jmztab-m</requirement>
+    </requirements>
+
+    <command detect_errors="exit_code"><![CDATA[
+        jmztab-m --level $level -c '$input_file' -o '$output_file' $checkSemantic
+    ]]></command>
+    <inputs>
+        <param name="input_file" type="data" format="mztab,txt,json" label="Input file" help="The mzTab-M or plain text file to be validated. mzTab-M is a standard format for reporting metabolomics results." />
+        <param name="level" type="select" label="Level" help="Select the validation level: Info (all messages), Warn (warnings and errors), or Error (only errors).">
+            <option value="Info" selected="true">Info</option>
+            <option value="Warn">Warn</option>
+            <option value="Error">Error</option>
+        </param>
+        <param argument="--checkSemantic" type="boolean" truevalue="--checkSemantic" falsevalue="" checked="false" label="Check semantic validation" help="If enabled, performs additional semantic validation checks on the input file." />
+    </inputs>
+    <outputs>
+        <data name="output_file" format="txt" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <!-- Hint: You can use [ctrl+alt+t] after defining the inputs/outputs to auto-scaffold some basic test cases. -->
+    <test expect_num_outputs="1">
+        <!--TODO: auto-generated test case. Please fill in the required values-->
+        <param name="input_file" value="MTBLS263.mztab" ftype="mztab"/>
+        <param name="checkSemantic" value="false"/>
+        <param name="level" value="Info"/>
+        <output name="output_file">
+            <assert_contents>
+                <has_text text="commit: '5fee003a3c97695b422bf556f4b5d9eb24080a3c'"/>
+                <has_line line="Validator set to level 'Info'"/>
+                <has_n_lines n="16"/>
+            </assert_contents>
+        </output>
+    </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+This tool validates mzTab-M files using the jmztab-m validator. mzTab-M is a standardized tabular format for reporting metabolomics results, including identification and quantification data. The validator checks the file for format compliance and, optionally, for semantic correctness.
+
+Usage
+.....
+
+1. **Input**
+    - Provide an mzTab-M or plain text file to be validated.
+    - Optionally enable semantic validation for deeper checks.
+    - Choose the desired validation level:
+        - **Info**: Show all messages (informational, warnings, errors).
+        - **Warn**: Show only warnings and errors.
+        - **Error**: Show only errors.
+
+2. **Output**
+    - A plain text report summarizing the validation results, including any detected issues.
+
+**Parameters**
+
+- **Input file**: The mzTab-M or text file to validate.
+- **Check semantic validation**: Enable to perform additional semantic checks.
+- **Level**: Controls the strictness of the validation output.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.5281/zenodo.3662402</citation>
+        <citation type="doi">10.1021/acs.analchem.8b04310</citation>
+        <citation type="doi">10.1021/acs.analchem.9b01987</citation>
+    </citations>
+</tool>
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