comparison bcftools_stats.xml @ 20:bf8325a07ce7 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bfc4ff4956b94885638ae07a2560bac5f84fcca8

19:a2f8dc22d7c0

        <param name="plot_title" type="text" value="" optional="true" label="Create a plots pdf with this title">
            <validator type="regex" message="">^\w.*\w$</validator>
        </param>
    </inputs>
    <outputs>
        <data name="output_file" format="txt"/>
        <data name="output_pdf" format="pdf" from_work_dir="plot_tmp/summary.pdf">
            <filter>plot_title</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="vcf" value="stats.b.vcf" />
            <param name="inputB_file" ftype="vcf" value="stats.a.vcf" />
            <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>
        </test>
        <test>
            <param name="input_file" ftype="vcf" value="mpileup.vcf" />
            <section name="sec_default">
                <expand macro="test_using_reference" select_from="cached" ref="mpileup" />
            </section>
            <output name="output_file">

                    <has_text_matching expression="SN\t0\tnumber of records:\t4103"/>
                    <has_text_matching expression="ST\t0\tA>C\t16"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_file" ftype="vcf" value="mpileup.vcf" />
            <param name="plot_title" value="Plot for mpileup.vcf" />
            <output name="output_file">
                <assert_contents>
                    <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>

                </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>

            <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"/>

                </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">

20:bf8325a07ce7

        <param name="plot_title" type="text" value="" optional="true" label="Create a plots pdf with this title">
            <validator type="regex" message="">^\w.*\w$</validator>
        </param>
    </inputs>
    <outputs>
        <data name="output_file" format="txt" label="${tool.name} on ${on_string}: txt" />
        <data name="output_pdf" format="pdf" label="${tool.name} on ${on_string}: PDF" from_work_dir="plot_tmp/summary.pdf">
            <filter>plot_title</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_file" ftype="vcf" value="stats.b.vcf" />
            <param name="inputB_file" ftype="vcf" value="stats.a.vcf" />
            <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>
        </test>
        <test expect_num_outputs="1">
            <param name="input_file" ftype="vcf" value="mpileup.vcf" />
            <section name="sec_default">
                <expand macro="test_using_reference" select_from="cached" ref="mpileup" />
            </section>
            <output name="output_file">

                    <has_text_matching expression="SN\t0\tnumber of records:\t4103"/>
                    <has_text_matching expression="ST\t0\tA>C\t16"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="2">
            <param name="input_file" ftype="vcf" value="mpileup.vcf" />
            <param name="plot_title" value="Plot for mpileup.vcf" />
            <output name="output_file">
                <assert_contents>
                    <has_text_matching expression="SN\t0\tnumber of samples:\t3"/>

                </assert_contents>
            </output>
            <output name="output_pdf" file="summary.pdf" compare="sim_size" delta="25000" />
        </test>
        <!-- Test region overlap option-->
        <test expect_num_outputs="1">
            <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>

            <assert_command>
                <has_text text="--regions-overlap" />
            </assert_command>
        </test>
        <!-- Test VCF.gz input file -> REQUIRES https://github.com/galaxyproject/galaxy/pull/14605
        <test expect_num_outputs="1">
            <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"/>

                </assert_contents>
            </output>
        </test>
        -->
        <!-- Test modification in samples option -->
        <test expect_num_outputs="1">
            <param name="input_file" ftype="vcf" value="mpileup.vcf" />
            <section name="sec_restrict">
                <param name="samples" value="-" />
            </section>
            <output name="output_file">