view encyclopedia_library_to_blib.xml @ 4:97df51029d0e draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 0bb79ebbaf73fe6e902f6ef20cc9c9741063bf34

<tool id="encyclopedia_library_to_blib" name="ConvertLibraryToBlib" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
    <description>Convert EncyclopeDIA Library to BLIB for Skyline</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        EncyclopeDIA -convert -libtoblib
            -Djava.awt.headless=true -Duser.language=en-US -Duser.region=US
            -Xmx\$[ \${GALAXY_MEMORY_MB:-20480} / 1024 ]g
            -numberOfThreadsUsed "\${GALAXY_SLOTS:-4}"
        -i '$i'
        -o '$output'
        #if $istest == 'yes'
        && sqlite3 -readonly '$output' 'SELECT distinct peptideSeq FROM RefSpectra;' > '$test_output'
        #end if
    ]]></command>
    <inputs>
        <param argument="-i" type="data" format="elib,dlib" label="Library: Chromatagram .ELIB or Spectrum .DLIB"/>
        <param name="istest" type="hidden" value="no"/>
    </inputs>
    <outputs>
        <data name="output" format="blib" label="${i.name} blib"/>
        <data name="test_output" format="txt" >
            <filter>istest == 'yes'</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="i" ftype="dlib" value="PrositLib.dlib"/>
            <param name="istest" value="yes"/>
            <output name="test_output" ftype="txt">
                <assert_contents>
                    <has_text text="AGGVLHDDENLWSFGK"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        Convert EncyclopeDIA Library to BLIB for Skyline.
    ]]></help>
    <expand macro="citations" />
</tool>