comparison ramclustr.xml @ 8:c043e1fd79d1 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4b8a43b863ff8a0ff1d5a08e516068853adf358d

7:09cabbc3d12d

<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy3" profile="21.09">
    <description>A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro='annotation'/>

        </conditional>
        <expand macro="main_parameters" />
    </inputs>

    <outputs>
        <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="csv" />
        <expand macro="output_msp"/>
    </outputs>

    <tests>
        <test expect_num_outputs="2"><!-- TEST 1 -->

            </section>
            <section name="extras">
                <param name="ExpDes" value="lc-ramclustr-define-experiment.csv" ftype="csv"/>
            </section>
            <output name="mass_spectra_merged" file="test1_fill_xcms_1.msp" ftype="msp"/>
            <output name="spec_abundance" file="test1_spec_abundance_xcms_1.csv" ftype="csv" compare="sim_size" delta="100"/>
        </test>
        <test expect_num_outputs="2"><!-- TEST 2 -->
            <section name="filetype">
                <param name="type_choice" value="xcms"/>
                <section name="xcms">

                <section name="normalisation_method">
                    <param name="batch_order_qc" value="test2_sample_metadata_xcms_2.csv" ftype="csv" />
                </section>
            </section>
            <output name="mass_spectra_merged" file="test2_fill_xcms_2.msp" ftype="msp" compare="sim_size" delta="100"/>
            <output name="spec_abundance" file="test2_spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/>
        </test>
        <test expect_num_outputs="2"><!-- TEST 3 -->
            <section name="filetype">
                <param name="type_choice" value="csv"/>
                <section name="ms_csv">

            <section name="performance">
                <param name="blocksize" value="1000"/>
                <param name="mult" value="1"/>
            </section>
            <output name="mass_spectra_merged" file="test3_spectra_csv_1.msp" ftype="msp"/>
            <output name="spec_abundance" file="test3_spec_abundance_csv_1.csv" ftype="csv"/>
        </test>
        <test expect_num_outputs="2"><!-- TEST 4 -->
            <section name="filetype">
                <param name="type_choice" value="csv"/>
                <section name="ms_csv">

8:c043e1fd79d1

<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy4" profile="21.09">
    <description>A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro='annotation'/>

        </conditional>
        <expand macro="main_parameters" />
    </inputs>

    <outputs>
        <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="tsv" />
        <expand macro="output_msp"/>
    </outputs>

    <tests>
        <test expect_num_outputs="2"><!-- TEST 1 -->

            </section>
            <section name="extras">
                <param name="ExpDes" value="lc-ramclustr-define-experiment.csv" ftype="csv"/>
            </section>
            <output name="mass_spectra_merged" file="test1_fill_xcms_1.msp" ftype="msp"/>
            <output name="spec_abundance" file="test1_spec_abundance_xcms_1.tsv" ftype="tsv" compare="sim_size" delta="100"/>
        </test>
        <test expect_num_outputs="2"><!-- TEST 2 -->
            <section name="filetype">
                <param name="type_choice" value="xcms"/>
                <section name="xcms">

                <section name="normalisation_method">
                    <param name="batch_order_qc" value="test2_sample_metadata_xcms_2.csv" ftype="csv" />
                </section>
            </section>
            <output name="mass_spectra_merged" file="test2_fill_xcms_2.msp" ftype="msp" compare="sim_size" delta="100"/>
            <output name="spec_abundance" file="test2_spec_abundance_xcms_2.tsv" ftype="tsv" compare="sim_size" delta="100"/>
        </test>
        <test expect_num_outputs="2"><!-- TEST 3 -->
            <section name="filetype">
                <param name="type_choice" value="csv"/>
                <section name="ms_csv">

            <section name="performance">
                <param name="blocksize" value="1000"/>
                <param name="mult" value="1"/>
            </section>
            <output name="mass_spectra_merged" file="test3_spectra_csv_1.msp" ftype="msp"/>
            <output name="spec_abundance" file="test3_spec_abundance_csv_1.tsv" ftype="tsv"/>
        </test>
        <test expect_num_outputs="2"><!-- TEST 4 -->
            <section name="filetype">
                <param name="type_choice" value="csv"/>
                <section name="ms_csv">