comparison snpfreqplot.xml @ 2:dc51db22310c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit d1c54d077cfc0eeb9699719760e668948cb9bbbc"

1:e362b3143cde

<tool id="snpfreqplot" name="Variant Frequency Plot" version="@VERSION@+galaxy@GALAXY_VERSION@" profile="20.09"
      license="GPL-3.0-or-later" >
    <description>Generates a heatmap of allele frequencies grouped by variant type for SnpEff-annotated SARS-CoV-2 data</description>
    <macros>
        <token name="@VERSION@">1.0</token>
        <token name="@GALAXY_VERSION@">1</token>
    </macros>
    <requirements>
        <requirement type="package" version="4.0">r-base</requirement>
        <requirement type="package" version="1.0.12">r-pheatmap</requirement>
        <requirement type="package" version="1.3.0">r-tidyverse</requirement>

            <!-- PDF, tabular inputs -->
            <param name="sinputs" ftype="tabular" value="input436.tabular,input437.tabular,input438.tabular,input439.tabular,input440.tabular,input441.tabular,input442.tabular,input443.tabular,input444.tabular" />
            <output name="outfile" ftype="pdf" value="heatmap.default.pdf" compare="sim_size" delta="250" />
        </test>
        <test expect_num_outputs="1">
            <!-- PNG, multiple inputs, non-numeric IDS -->
            <param name="sinputs" ftype="tabular" value="input436.tabular,input437.tabular,input443.tabular,input444.tabular" />
            <param name="varfreq" value="0.5" />
            <section name="advanced" >
                <param name="color" value="Spectral" />

                    <has_text text="viewBox=&quot;0 0 754 292&quot;" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <!-- SVG, Vcf test with problematic splice+syn at snpeff789.vcf for threshold = 0.0222 -->
            <param name="sinputs" ftype="vcf" value="snpeff.123.vcf,snpeff.456.vcf,snpeff.789.vcf" />
            <param name="varfreq" value="0.0222" />
            <section name="advanced" >
                <param name="output_type" value="svg" />
            </section>
            <output name="outfile" ftype="svg">
                <assert_contents>
                    <has_text text="viewBox=&quot;0 0 3101 879&quot;" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

2:dc51db22310c

<tool id="snpfreqplot" name="Variant Frequency Plot" version="@VERSION@+galaxy@GALAXY_VERSION@" profile="20.09"
      license="GPL-3.0-or-later" >
    <description>Generates a heatmap of allele frequencies grouped by variant type for SnpEff-annotated SARS-CoV-2 data</description>
    <macros>
        <token name="@VERSION@">1.0</token>
        <token name="@GALAXY_VERSION@">2</token>
    </macros>
    <requirements>
        <requirement type="package" version="4.0">r-base</requirement>
        <requirement type="package" version="1.0.12">r-pheatmap</requirement>
        <requirement type="package" version="1.3.0">r-tidyverse</requirement>

            <!-- PDF, tabular inputs -->
            <param name="sinputs" ftype="tabular" value="input436.tabular,input437.tabular,input438.tabular,input439.tabular,input440.tabular,input441.tabular,input442.tabular,input443.tabular,input444.tabular" />
            <output name="outfile" ftype="pdf" value="heatmap.default.pdf" compare="sim_size" delta="250" />
        </test>
        <test expect_num_outputs="1">
            <!-- PDF, tabular inputs, short color palette -->
            <param name="sinputs" ftype="tabular" value="input436.tabular,input437.tabular,input438.tabular,input439.tabular,input440.tabular,input441.tabular,input442.tabular,input443.tabular,input444.tabular" />
            <section name="advanced" >
                <param name="color" value="Set2" />
            </section>
            <output name="outfile" ftype="pdf" value="heatmap.default.pdf" compare="sim_size" delta="250" />
        </test>
        <test expect_num_outputs="1">
            <!-- PNG, multiple inputs, non-numeric IDS -->
            <param name="sinputs" ftype="tabular" value="input436.tabular,input437.tabular,input443.tabular,input444.tabular" />
            <param name="varfreq" value="0.5" />
            <section name="advanced" >
                <param name="color" value="Spectral" />

                    <has_text text="viewBox=&quot;0 0 754 292&quot;" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <!-- SVG, Vcf test with problematic splice+syn at snpeff789.vcf for threshold = 0.0222
            and an "empty" file (no variants) and a file with just one variant among its inputs -->
            <param name="sinputs" ftype="vcf" value="snpeff.123.vcf,snpeff.456.vcf,snpeff.789.vcf,no_variants.vcf,single_variant.vcf" />
            <param name="varfreq" value="0.0222" />
            <section name="advanced" >
                <param name="output_type" value="svg" />
            </section>
            <output name="outfile" ftype="svg">
                <assert_contents>
                    <has_text text="viewBox=&quot;0 0 1962 546&quot;" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[