view circos/conf/galaxy_test_case.xml @ 9:e6440d0201f7 draft default tip

planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 7e335df423e3e06da3d33a5378a336a149e6cc6c

<!--
mkdir -p test-data/my-test-case/;
    cp /tmp/tmprZFxwp/files/000/dataset_5.dat test-data/my-test-case/input.fa;


cp /tmp/tmprZFxwp/files/000/dataset_8.dat test-data/my-test-case/0-0.wig;
cp /tmp/tmprZFxwp/files/000/dataset_7.dat test-data/my-test-case/1.gff3;
cp "/tmp/tmprZFxwp/files/000/dataset_40.dat" test-data/my-test-case/output.png;
cp "/tmp/tmprZFxwp/files/000/dataset_41.dat" test-data/my-test-case/output.svg;
-->
<test>
    <param name="reference_genome|reference_genome_source" value="history"/>
    <param name="reference_genome|genome_fasta" value="my-test-case/input.fa" />
    <!-- ideograms -->
    <param name="ideogram|spacing" value="0.005" />
    <param name="ideogram|radius" value="0.9" />
    <param name="ideogram|thickness" value="10.0" />
    <param name="ideogram|ideogram_labels|show_label" value="yes" />
    <param name="ideogram|ideogram_labels|parallel" value="yes" />
    <!-- Ticks -->
    <param name="ticks|show_ticks" value="yes" />
    <param name="ticks|radius" value="1.0" />
    <param name="ticks|color" value="#000000" />
    <param name="ticks|multiplier" value="0.001" />
    <param name="ticks|tick_group_0|tickspacing" value="5000.0" />
    <param name="ticks|tick_group_0|size" value="10.0" />
    <param name="ticks|tick_group_0|show_tick_labels" value="yes" />
    <param name="ticks|tick_group_0|label_size" value="20.0" />
    <param name="ticks|tick_group_0|label_offset" value="10.0" />
    <param name="ticks|tick_group_0|label_format" value="%d" />
    <param name="ticks|tick_group_1|tickspacing" value="1000.0" />
    <param name="ticks|tick_group_1|size" value="5.0" />
    <param name="ticks|tick_group_1|show_tick_labels" value="no" />
    <param name="ticks|tick_group_1|label_size" value="20.0" />
    <param name="ticks|tick_group_1|label_offset" value="10.0" />
    <param name="ticks|tick_group_1|label_format" value="%d" />
    <!-- Data -->
    <param name="sec_tdd|data_0|r0" value="0.95" />
    <param name="sec_tdd|data_0|r1" value="0.99" />
    <param name="sec_tdd|data_0|orientation" value="out" />
    <param name="sec_tdd|data_0|plot_format|plot_format_select" value="histogram" />
        <!-- Note, please double check your files -->
        <param name="sec_tdd|data_0|plot_format|data_source" value="my-test-case/0-0.wig" />
        <param name="sec_tdd|data_0|plot_format|format_specific|fill_color" value="brbg-15-div" />
        <param name="sec_tdd|data_0|plot_format|format_specific|extend_bins" value="yes" />

    <param name="sec_tdd|data_1|r0" value="0.8" />
    <param name="sec_tdd|data_1|r1" value="0.95" />
    <param name="sec_tdd|data_1|orientation" value="out" />
    <param name="sec_tdd|data_1|plot_format|plot_format_select" value="tile" />
        <!-- Note, please double check your files -->
        <param name="sec_tdd|data_1|plot_format|data_source" value="my-test-case/1.gff3" />
        <param name="sec_tdd|data_1|plot_format|format_specific|fill_color" value="oranges-13-seq" />
        <param name="sec_tdd|data_1|plot_format|format_specific|color" value="#000000" />
        <param name="sec_tdd|data_1|plot_format|format_specific|stroke_thickness" value="1" />
        <param name="sec_tdd|data_1|plot_format|format_specific|layers" value="20" />
        <param name="sec_tdd|data_1|plot_format|format_specific|thickness" value="8.0" />
        <param name="sec_tdd|data_1|plot_format|format_specific|padding" value="2.0" />
        <param name="sec_tdd|data_1|plot_format|format_specific|overflow|overflow_behavior" value="grow" />
        <param name="sec_tdd|data_1|plot_format|format_specific|overflow|layer_overflow_color" value="#000000" />



    <!-- Outputs -->
    <output name="output_png" file="my-test-case/output.png" />
    <output name="output_svg" file="my-test-case/output.svg" />
</test>