comparison bcftools_stats.xml @ 16:4d3ce9dc1525 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49

15:e8af591435d1

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1" profile="18.01">
    <description>Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats</description>
    <macros>
        <token name="@EXECUTABLE@">stats</token>
        <import>macros.xml</import>
    </macros>

                    <has_text_matching expression="ST\t0\tA>C\t16"/>
                </assert_contents>
            </output>
            <output name="output_pdf" file="summary.pdf" compare="sim_size" delta="25000" />
        </test>
    </tests>
    <help><![CDATA[
=====================================
 bcftools @EXECUTABLE@
=====================================

16:4d3ce9dc1525

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats</description>
    <macros>
        <token name="@EXECUTABLE@">stats</token>
        <import>macros.xml</import>
    </macros>

                    <has_text_matching expression="ST\t0\tA>C\t16"/>
                </assert_contents>
            </output>
            <output name="output_pdf" file="summary.pdf" compare="sim_size" delta="25000" />
        </test>
        <!-- Test region overlap option-->
        <test>
            <param name="input_file" ftype="vcf" value="stats.b.vcf" />
            <param name="inputB_file" ftype="vcf" value="stats.a.vcf" />
            <section name="sec_restrict">
                <param name="regions_overlap" value="1"/>
            </section>
            <output name="output_file">
                <assert_contents>
                    <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>
                    <has_text_matching expression="SN\t1\tnumber of samples:\t3"/>
                </assert_contents>
            </output>
            <assert_command>
                <has_text text="--regions-overlap" />
            </assert_command>
        </test>
        <!-- Test VCF.gz input file -> REQUIRES https://github.com/galaxyproject/galaxy/pull/14605
        <test>
            <param name="input_file"  value="mpileup.vcf.gz" />
            <output name="output_file">
                <assert_contents>
                    <has_text_matching expression="bcftools stats  input0.vcf.gz"/>
                    <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>
                    <has_text_matching expression="SN\t0\tnumber of records:\t4103"/>
                </assert_contents>
            </output>
        </test>
        -->
        <!-- Test modification in samples option -->
        <test>
            <param name="input_file" ftype="vcf" value="mpileup.vcf" />
            <section name="sec_restrict">
                <param name="samples" value="-" />
            </section>
            <output name="output_file">
                <assert_contents>
                    <has_text_matching expression="bcftools stats  --samples - "/>
                    <has_text_matching expression="PSC\t0\tHG00101\t0\t0\t0\t0\t0\t0\t4.8"/>
                    <has_text_matching expression="PSI\t0\tHG00102\t0"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
=====================================
 bcftools @EXECUTABLE@
=====================================