comparison multiqc.xml @ 13:161f4383df15 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8ebda44b3ef25ef8ba030460134560547082289b

12:1c2db0054039

<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@">
    <description>aggregate results from bioinformatics analyses into a single report</description>
    <macros>
        <token name="@WRAPPER_VERSION@">1.6</token>
        <token name="@ESCAPE_IDENTIFIER@">
<![CDATA[
#set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
        ]]></token>
        <token name="@CHECK_LN_FILE@">

            #elif str($repeat2.type.type) == "rmdup"
                #set $pattern = "[bam_rmdup"
                @LN_3_FILES@
            #end if
        #end for
    #elif str($repeat.software_cond.software) == "snpeff"
        #set $pattern = "SnpEff_version"
        @LN_FILES@
    #elif str($repeat.software_cond.software) == "sortmerna"
        #set $pattern = "Minimal SW score based on E-value"

                    <!--<option value="salmon">Salmon</option>-->
                    <option value="samblaster">Samblaster</option>
                    <option value="samtools">Samtools</option>
                    <!--<option value="sargasso">Sargasso</option>-->
                    <!--<option value="skewer">Skewer</option>-->
                    <!--<option value="slamdunk">Slamdunk</option>-->
                    <option value="snpeff">SnpEff</option>
                    <option value="sortmerna">SortMeRNA</option>
                    <option value="star">STAR</option>
                    <!--<option value="supernova">Supernova</option>-->
                    <!--<option value="theta2">THeTA2</option>-->

                                <param name="input" type="data" format="txt" multiple="true" label="Samtools rmdup output" help="It should contain '[bam_rmdup'"/>
                            </when>
                        </conditional>
                    </repeat>
                </when>
                <when value="sortmerna">
                    <param name="input" type="data" format="txt" multiple="true" label="Log file of SortMeRNA" help="It should contain 'Minimal SW score based on E-value'"/>
                </when>
                <when value="snpeff">
                    <param name="input" type="data" format="csv" multiple="true" label="Output of SnpEff"/>
                </when>
                <when value="star">
                    <repeat name="output" title="STAR output" min="1">
                        <conditional name="type">
                            <param name="type" type="select" label="Type of STAR output?">

                    <param name="input" value="flexbar.txt" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="sortmerna" />
                    <param name="input" value="sortmerna.txt" />
                </conditional>
            </repeat>
            <repeat name="results">

                    <has_text text="Commment for the report" />
                    <has_text text="cutadapt_plot" />
                    <has_text text="An ultra-fast all-in-one FASTQ preprocessor" />
                    <has_text text="fastqc_seq_heatmap_key_t" />
                    <has_text text="flexbar_plot" />
                    <has_text text="sortmerna-detailed-plot" />
                    <has_text text="trimmomatic_plot" />
                </assert_contents>
            </output>
            <output name="log" file="pre_alignment_soft_log.txt" compare="sim_size"/>

                <element name="cutadapt" file="cutadapt_stats.tabular" compare="sim_size" delta="10"/>
                <element name="fastp" file="fastp_stats.tabular" compare="sim_size" delta="10"/>
                <element name="fastqc" file="fastqc_stats.tabular" compare="sim_size" delta="10"/>
                <element name="flexbar" file="flexbar_stats.tabular" compare="sim_size" delta="10"/>
                <element name="general_stats" file="pre_alignment_soft_stats.tabular" compare="sim_size" delta="30"/>
                <element name="sortmerna" file="sortmerna_stats.tabular" compare="sim_size" delta="30"/>
                <element name="trimmomatic" file="trimmomatic_stats.tabular" compare="sim_size" delta="0"/>
            </output_collection>
        </test>
        <test>

13:161f4383df15

<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@">
    <description>aggregate results from bioinformatics analyses into a single report</description>
    <macros>
        <token name="@WRAPPER_VERSION@">1.7</token>
        <token name="@ESCAPE_IDENTIFIER@">
<![CDATA[
#set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
        ]]></token>
        <token name="@CHECK_LN_FILE@">

            #elif str($repeat2.type.type) == "rmdup"
                #set $pattern = "[bam_rmdup"
                @LN_3_FILES@
            #end if
        #end for
    #elif str($repeat.software_cond.software) == "slamdunk"
        #set $pattern = "# slamdunk"
        @LN_FILES@
    #elif str($repeat.software_cond.software) == "snpeff"
        #set $pattern = "SnpEff_version"
        @LN_FILES@
    #elif str($repeat.software_cond.software) == "sortmerna"
        #set $pattern = "Minimal SW score based on E-value"

                    <!--<option value="salmon">Salmon</option>-->
                    <option value="samblaster">Samblaster</option>
                    <option value="samtools">Samtools</option>
                    <!--<option value="sargasso">Sargasso</option>-->
                    <!--<option value="skewer">Skewer</option>-->
                    <option value="slamdunk">Slamdunk</option>
                    <option value="snpeff">SnpEff</option>
                    <option value="sortmerna">SortMeRNA</option>
                    <option value="star">STAR</option>
                    <!--<option value="supernova">Supernova</option>-->
                    <!--<option value="theta2">THeTA2</option>-->

                                <param name="input" type="data" format="txt" multiple="true" label="Samtools rmdup output" help="It should contain '[bam_rmdup'"/>
                            </when>
                        </conditional>
                    </repeat>
                </when>
                <when value="slamdunk">
                    <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of Slamdunk Alleyoop" help="It should contain '# slamdunk'"/>
                </when>
                <when value="snpeff">
                    <param name="input" type="data" format="csv" multiple="true" label="Output of SnpEff"/>
                </when>
                <when value="sortmerna">
                    <param name="input" type="data" format="txt" multiple="true" label="Log file of SortMeRNA" help="It should contain 'Minimal SW score based on E-value'"/>
                </when>
                <when value="star">
                    <repeat name="output" title="STAR output" min="1">
                        <conditional name="type">
                            <param name="type" type="select" label="Type of STAR output?">

                    <param name="input" value="flexbar.txt" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="slamdunk" />
                    <param name="input" value="slamdunk_summary.txt,slamdunk_reads1_overallrates.csv,slamdunk_reads2_overallrates.csv" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="sortmerna" />
                    <param name="input" value="sortmerna.txt" />
                </conditional>
            </repeat>
            <repeat name="results">

                    <has_text text="Commment for the report" />
                    <has_text text="cutadapt_plot" />
                    <has_text text="An ultra-fast all-in-one FASTQ preprocessor" />
                    <has_text text="fastqc_seq_heatmap_key_t" />
                    <has_text text="flexbar_plot" />
                    <has_text text="a tool to analyze SLAMSeq data" />
                    <has_text text="sortmerna-detailed-plot" />
                    <has_text text="trimmomatic_plot" />
                </assert_contents>
            </output>
            <output name="log" file="pre_alignment_soft_log.txt" compare="sim_size"/>

                <element name="cutadapt" file="cutadapt_stats.tabular" compare="sim_size" delta="10"/>
                <element name="fastp" file="fastp_stats.tabular" compare="sim_size" delta="10"/>
                <element name="fastqc" file="fastqc_stats.tabular" compare="sim_size" delta="10"/>
                <element name="flexbar" file="flexbar_stats.tabular" compare="sim_size" delta="10"/>
                <element name="general_stats" file="pre_alignment_soft_stats.tabular" compare="sim_size" delta="30"/>
                <element name="slamdunk_readrates_plus" file="slamdunk_readrates_plus.tabular" compare="sim_size" delta="10"/>
                <element name="sortmerna" file="sortmerna_stats.tabular" compare="sim_size" delta="30"/>
                <element name="trimmomatic" file="trimmomatic_stats.tabular" compare="sim_size" delta="0"/>
            </output_collection>
        </test>
        <test>