annotate thermo_converter.xml @ 2:edbeb2956484 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 9de08588cd6c525947f92bf475a144fcd6129fde

<tool id="thermo_raw_file_converter" name="Thermo" version="0.0.1">
    <description>RAW file converter (beta)</description>
    <requirements>
        <requirement type="package" version="0.0.2018.09.07">ThermoRawFileParser</requirement>
    </requirements>
    <command>
<![CDATA[

ln -s '$input' ./input.raw &&

ThermoRawFileParser.sh
    -i=input.raw
    -o=./
    -f=$output_format
    #if $metadata:
        --metadata=1
    #end if
    &&
    #if $output_format == '0':
        mv ./input.mgf '$output'
    #else:
        mv ./input.mzML '$output'
    #end if
]]>
    </command>
    <inputs>
        <param name="input" type="data" format="thermo.raw" label="Thermo RAW file" help="" />
        <param name="metadata" type="boolean" truevalue="" falsevalue="" checked="False"
            label="Output metadata" help="" />
        <param name="output_format" type="select" label="Choose an output format">
            <option value="0">mgf</option>
            <option value="1" selected="True">mzml</option>
        </param>
    </inputs>
    <outputs>
        <data format="mzml" name="output" from_work_dir="input.mzML" label="${tool.name} on ${on_string}">
            <change_format>
                <when input="output_format" value="0" format="mgf" />
            </change_format>
        </data>
        <data format="txt" name="output_metadata" from_work_dir="input-metadata.txt" label="${tool.name} on ${on_string}: Metadata">
            <filter>metadata</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" value="fake_input.txt"/>
            <assert_command>
                <has_text text="ThermoRawFileParser.sh"/>
            </assert_command>
        </test>
        <test>
            <param name="input" value="fake_input.txt"/>
            <param name="output_format" value="0"/>
            <assert_command>
                <has_text text="-f=0"/>
            </assert_command>
        </test>
    </tests>
    <help>
<![CDATA[

Thermo RAW file converter based on the great `ThermoRawFileParser <https://github.com/compomics/ThermoRawFileParser>`_ project.

]]>
    </help>
    <citations>
        <citation type="bibtex">@misc{Galaxy Proteomics Tools,
        author = {Niels Hulstaert, et al.},
        title = {Galaxy Proteomics Tools},
        publisher = {GitHub},
        journal = {GitHub repository},
        year = {2017}, url = {https://github.com/compomics/ThermoRawFileParser}}
        </citation>
    </citations>
</tool>