annotate mzspeclib_describe.xml @ 0:4484e5822a6b draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/main/tools/mzspeclib commit 6707579ea4c2d22b625b85c30e5b9705ae142b20

<tool id="mzspeclib_describe" name="mzspeclib describe" version="@TOOL_VERSION@+galaxy0" profile="23.0">
    <description>Summarize and describe mzspeclib files using mzspeclib.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <xrefs>
        <xref type="bio.tools">mzspeclib</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">mzspeclib</requirement>
    </requirements>

    <command detect_errors="exit_code"><![CDATA[
    mzspeclib describe -i mzspeclib.${input.ext} ${input} > ${output}
    ]]></command>

    <inputs>
        <param name="input" type="data" format="txt,json" label="Input mzspeclib file" help="Input mzspeclib file (text or JSON) to be summarized."/>
    </inputs>

    <outputs>
        <data name="output" format="txt"/>
    </outputs>

    <tests>
        <test>
            <param name="input" value="sample.txt" ftype="txt"/>
            <output name="output" file="sample_describe_report.txt" compare="diff" lines_diff="2">
                <!-- <assert_contents>
                    <has_line line="Format: text"/>
                    <has_line line="Spectrum Count: 6"/>
                    <has_line line="MS:1003186|library format version=1.0"/>
                </assert_contents> -->
            </output>
        </test>
    </tests>

    <help><![CDATA[
.. _mzspeclib_describe:

==========================
mzspeclib Describe Tool
==========================

**Tool Description**

This tool summarizes and describes mzspeclib files using the mzspeclib library. It provides an overview of the content, such as the number of spectra, library type, and other metadata.

Inputs
------

- **Input mzspeclib file**  
  The mzspeclib file to be summarized. Supported formats: text (txt), JSON.

Outputs
-------

- **mzspeclib description**  
  A text file containing a summary and description of the mzspeclib file.

Example
-------

Suppose you have a file `sample.txt` in mzspeclib text format. Upload this file as input and run the tool. The output will be a summary report describing the contents of the file.

Notes
-----

- Ensure your input file is in mzspeclib text or JSON format.
- Use this tool to quickly inspect the contents and structure of your mzspeclib files.
    ]]></help>
    <expand macro="citations"/>
</tool>