comparison snpfreqplot.xml @ 1:e362b3143cde draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snpfreqplot/ commit 1bde09fccd1a5412240ebd5c1f34a45ad73cebe2"

0:1062d6ad6503

<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@">0</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>
        <requirement type="package" version="1.36.0">bioconductor-variantannotation</requirement>
        <requirement type="package" version="">xorg-libxt</requirement>
    </requirements>
    <edam_topics>
        <edam_topic>topic_0797</edam_topic>
        <edam_topic>topic_0092</edam_topic>
    </edam_topics>

            <param name="varfreq" value="0.5" />
            <section name="advanced" >
                <param name="color" value="Spectral" />
                <param name="output_type" value="png" />
            </section>
            <output name="outfile" ftype="png" value="heatmap.imageopts.png" compare="sim_size" delta="86000" />
        </test>
        <test expect_num_outputs="1">
            <!-- SVG, clustering defaults -->
            <param name="sinputs" ftype="tabular" value="input438.tabular,input439.tabular,input440.tabular,input441.tabular,input442.tabular" />
            <conditional name="clustering">

                <param name="ratio" value="0.8" />
                <param name="output_type" value="svg" />
            </section>
            <output name="outfile" ftype="svg">
                <assert_contents>
                    <has_text text="viewBox=&quot;0 0 1156 335&quot;" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <!-- JPEG, clustering extras, mixed alphanumeric labels -->

            <section name="advanced" >
                <param name="color" value="Purples" />
                <param name="ratio" value="1.2" />
                <param name="output_type" value="jpeg" />
            </section>
            <output name="outfile" ftype="jpg" value="heatmap.clustering2.jpeg" compare="sim_size" delta="121000" />
        </test>
        <test expect_num_outputs="1">
            <!-- PDF, vcf test -->
            <param name="sinputs" ftype="vcf" value="snpeff.123.vcf,snpeff.456.vcf,snpeff.789.vcf" />
            <section name="advanced" >

            <section name="advanced" >
                <param name="output_type" value="svg" />
            </section>
            <output name="outfile" ftype="svg">
                <assert_contents>
                    <has_text text="viewBox=&quot;0 0 754 271&quot;" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <!-- SVG, Vcf test with problematic splice+syn at snpeff789.vcf for threshold = 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 697&quot;" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

   - ``EFF[*].GENE``
   - ``EFF[*].EFFECT``

   Such files can be produced with SnpSift Extract Fields and can be useful if
   preprocessing of the lists with standard text processing tools is required.

----

Example output:

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>
        <requirement type="package" version="1.36.0">bioconductor-variantannotation</requirement>
    </requirements>
    <edam_topics>
        <edam_topic>topic_0797</edam_topic>
        <edam_topic>topic_0092</edam_topic>
    </edam_topics>

            <param name="varfreq" value="0.5" />
            <section name="advanced" >
                <param name="color" value="Spectral" />
                <param name="output_type" value="png" />
            </section>
            <output name="outfile" ftype="png" value="heatmap.imageopts.png" compare="sim_size" delta="100000" />
        </test>
        <test expect_num_outputs="1">
            <!-- SVG, clustering defaults -->
            <param name="sinputs" ftype="tabular" value="input438.tabular,input439.tabular,input440.tabular,input441.tabular,input442.tabular" />
            <conditional name="clustering">

                <param name="ratio" value="0.8" />
                <param name="output_type" value="svg" />
            </section>
            <output name="outfile" ftype="svg">
                <assert_contents>
                    <has_text text="viewBox=&quot;0 0 1156 361&quot;" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <!-- JPEG, clustering extras, mixed alphanumeric labels -->

            <section name="advanced" >
                <param name="color" value="Purples" />
                <param name="ratio" value="1.2" />
                <param name="output_type" value="jpeg" />
            </section>
            <output name="outfile" ftype="jpg" value="heatmap.clustering2.jpeg" compare="sim_size" delta="130000" />
        </test>
        <test expect_num_outputs="1">
            <!-- PDF, vcf test -->
            <param name="sinputs" ftype="vcf" value="snpeff.123.vcf,snpeff.456.vcf,snpeff.789.vcf" />
            <section name="advanced" >

            <section name="advanced" >
                <param name="output_type" value="svg" />
            </section>
            <output name="outfile" ftype="svg">
                <assert_contents>
                    <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 -->

            <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[

   - ``EFF[*].GENE``
   - ``EFF[*].EFFECT``

   Such files can be produced with SnpSift Extract Fields and can be useful if
   preprocessing of the lists with standard text processing tools is required.

   .. class:: infomark

   To represent empty EFF fields in the tabular format you can choose between
   ``.`` and the empty string.

----

Example output: