view encyclopedia_prosit_csv_to_library.xml @ 4:1c26fb6b5a31 draft default tip

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

<tool id="encyclopedia_prosit_csv_to_library" name="ConvertPrositCSVToLibrary" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
    <description>Convert Prosit/Spectronaut CSV to EncyclopeDIA DLIB library</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        EncyclopeDIA -convert -prositcsvtolibrary
        -numberOfThreadsUsed "\${GALAXY_SLOTS:-4}"
        -i '$i'
        -f '$f'
        -o '$output'
        #if $istest == 'yes'
        && sqlite3 -readonly '$output' 'select distinct ProteinAccession from peptidetoprotein;' > '$test_output'
        #end if
    ]]></command>
    <inputs>
        <param argument="-i" type="data" format="csv" label="Prosit output csv file"/>
        <param argument="-f" type="data" format="fasta" label="Protein Fasta database"/>
        <param name="istest" type="hidden" value="no"/>
    </inputs>
    <outputs>
        <data name="output" format="dlib" label="${i.name} DLIB"/>
        <data name="test_output" format="txt" >
            <filter>istest == 'yes'</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="i" ftype="csv" value="PrositLib.csv"/>
            <param name="f" ftype="fasta" value="YeastProteinFasta5.fasta"/>
            <param name="istest" value="yes"/>
            <output name="test_output" ftype="txt">
                <assert_contents>
                    <has_text text="PCL1_YEAST"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        Convert Prosit/Spectronaut CSV to library DLIB
    ]]></help>
    <expand macro="citations" />
</tool>