comparison macros.xml @ 30:4981b6c4f7fa draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc commit d4b9696c6c533ca1841c22b52bb3e73833e2e0d4

29:ef6bd40a30d2

<macros>
    <token name="@TOOL_VERSION@">1.27</token>
    <token name="@VERSION_SUFFIX@">4</token>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">multiqc</xref>
        </xrefs>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">multiqc</requirement>
        </requirements>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1101/gr.244293.118</citation>
        </citations>

                    <has_text text="bwa-mem-fastq1_fq"/>
                    <has_text text="25839_merged"/>
                    <has_text text="slamdunk-retained"/>
                    <has_text text="C2"/>
                    <has_n_lines n="11"/>
                    <has_n_columns n="22"/>
                </assert_contents>
            </output>
            <output_collection name="plots" type="list" count="29"/>
            <output_collection name="png_plot" type="list" count="38"/>
        </test>
        <!--Test 02-->
        <test expect_num_outputs="2">
            <repeat name="results">
                <conditional name="software_cond">

                    <has_text text="picard-gcbias"/>
                    <has_text text="prokka_plot"/>
                    <has_text text="qualimap"/>
                    <has_text text="samblaster_duplicates"/>
                    <has_text text="quast-stats"/>
                    <has_text text="samtools-flagstat-dp"/>
                    <has_text text="snpeff"/>
                </assert_contents>
            </output>
            <output name="stats">
                <assert_contents>

                    <has_text text="samtools_stats-error_rate"/>
                    <has_text text="samtools_stats_txt"/>
                    <has_text text="snpeff_csv"/>
                    <has_text text="bamtools-mapped_reads_pct"/>
                    <has_text text="bamtools-duplicates_pct"/>
                    <has_n_lines n="22"/>
                    <has_n_columns n="50"/>
                </assert_contents>
            </output>
        </test>
        <!--Test 04-->
        <test expect_num_outputs="2">

                    <param name="input" value="cc_ko15.bpc.tab,cc_wt15.bpc.tab"/>
                </conditional>
            </repeat>
            <output name="html_report" ftype="html">
                <assert_contents>
                    <has_size value="4766687" delta="500"/>
                </assert_contents>
            </output>
            <!--output name="stats" ftype="tabular">
                Not created anymore. Proper test needed.
                <assert_contents>

                    <assert_contents>
                        <has_size size="2877" delta="200"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output_collection name="png_plot" type="list" count="11"/>
            
        </test>
        <!--Test 06-->
        <test expect_num_outputs="2">
            <repeat name="results">

30:4981b6c4f7fa

<macros>
    <token name="@TOOL_VERSION@">1.33</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">multiqc</xref>
        </xrefs>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">multiqc</requirement>
        </requirements>
    </xml>
    <!--This stdio rule is temporary because of an issue with CheckM2 report columns, it needs to be removed when the issue is fixed -->
    <xml name="stdio">
        <stdio>
            <regex
                match="Module 'checkm2: .*not found in the file.*"
                source="both"
                level="fatal"
                description="Invalid CheckM2 TSV file: required header not found" />
        </stdio>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1101/gr.244293.118</citation>
        </citations>

                    <has_text text="bwa-mem-fastq1_fq"/>
                    <has_text text="25839_merged"/>
                    <has_text text="slamdunk-retained"/>
                    <has_text text="C2"/>
                    <has_n_lines n="11"/>
                    <has_n_columns n="24"/>
                </assert_contents>
            </output>
            <output_collection name="plots" type="list" count="29"/>
            <output_collection name="png_plot" type="list" count="36"/>
        </test>
        <!--Test 02-->
        <test expect_num_outputs="2">
            <repeat name="results">
                <conditional name="software_cond">

                    <has_text text="picard-gcbias"/>
                    <has_text text="prokka_plot"/>
                    <has_text text="qualimap"/>
                    <has_text text="samblaster_duplicates"/>
                    <has_text text="quast-stats"/>
                    <has_text text="samtools-flagstat-pct"/>
                    <has_text text="snpeff"/>
                </assert_contents>
            </output>
            <output name="stats">
                <assert_contents>

                    <has_text text="samtools_stats-error_rate"/>
                    <has_text text="samtools_stats_txt"/>
                    <has_text text="snpeff_csv"/>
                    <has_text text="bamtools-mapped_reads_pct"/>
                    <has_text text="bamtools-duplicates_pct"/>
                    <has_n_lines n="23"/>
                    <has_n_columns n="55"/>
                </assert_contents>
            </output>
        </test>
        <!--Test 04-->
        <test expect_num_outputs="2">

                    <param name="input" value="cc_ko15.bpc.tab,cc_wt15.bpc.tab"/>
                </conditional>
            </repeat>
            <output name="html_report" ftype="html">
                <assert_contents>
                    <has_size value="2142211" delta="500"/>
                </assert_contents>
            </output>
            <!--output name="stats" ftype="tabular">
                Not created anymore. Proper test needed.
                <assert_contents>

                    <assert_contents>
                        <has_size size="2877" delta="200"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output_collection name="png_plot" type="list" count="9"/>
            
        </test>
        <!--Test 06-->
        <test expect_num_outputs="2">
            <repeat name="results">