<tool id="pepquery2_index" name="PepQuery2 index" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
    <description>MS/MS data for faster search</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">pepquery</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
@CMD_IMPORTS@
@INDEX_SPECTRUM_FILES@
$index_spectrum_files($output.files_path, $inputs)
    ]]></command>
    <inputs>
        <param name="inputs" argument="-i" type="data" format="mfg,mzml,mzxml" multiple="true" label="MS Spectrum files">
        </param>
    </inputs>
    <outputs>
        <data name="output" format="txt" label="${tool.name} on ${on_string}: summary.txt" from_work_dir="index_dir/summary.txt"/> 
    </outputs>
    <tests>
        <test>
            <param name="inputs" ftype="mzml" value="small-index-filter.mzML"/>
            <output name="output">
                <assert_contents>
                    <has_text text="small-index-filter.mzML"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="inputs" value="small-index-filter.mzML,AgilentMassHunterTest.mzXML,immunopeptidomics.mgf"/>
            <output name="output">
                <assert_contents>
                    <has_text text="small-index-filter.mzML"/>
                    <has_text text="AgilentMassHunterTest.mzXML"/>
                    <has_text text="immunopeptidomics.mgf"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**PepQuery Index** 

Indexes MS/MS data for fast searching.  
This can significant speed up the search especially when the size of MS/MS data is very large.

The output can be used as input to **PepQuery2** Galaxy tool in the **MS/MS dataset to search** *Indexed MS/MS spectrums*.
    ]]></help>
    <expand macro="citations" />
</tool>