comparison multiqc.xml @ 12:1c2db0054039 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 761a954744119f6317afe28eb50bd4f3fdea4984

11:f0ec41881020

<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.2">
    <description>aggregate results from bioinformatics analyses into a single report</description>
    <macros>
        <token name="@WRAPPER_VERSION@">1.5</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) == "plotFingerprintOutRawCounts"
                #set $pattern = "#plotFingerprint --outRawCounts"
                @LN_2_FILES@
            #end if
        #end for
    #elif str($repeat.software_cond.software) == "fastqc"
        #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
            @CREATE_REPEAT_DIR_1@
            #if str($repeat2.type) == "data"
                #for $k, $file in enumerate($repeat2.input)

                    <!--<option value="conpair">Conpair</option>-->
                    <!--<option value="dedup">DeDup</option>-->
                    <option value="deeptools">deepTools</option>
                    <!--<option value="disambiguate">Disambiguate</option>-->
                    <!--<option value="fastq_screen">FastQ Screen</option>-->
                    <option value="fastqc">FastQC</option>
                    <option value="featureCounts">featureCounts</option>
                    <option value="flexbar">Flexbar</option>
                    <option value="gatk">GATK</option>
                    <!--<option value="goleft_indexcov">goleft indexcov</option>-->

                            <option value="plotFingerprintOutQualityMetrics">plotFingerprintOutQualityMetrics</option>
                        </param>
                        <param name="input" type="data" format="txt" multiple="true" label="Bismark output"/>
                    </repeat>
                </when>
                <when value="fastqc">
                    <repeat name="output" title="FastQC output" min="1">
                        <param name="type" type="select" label="Type of FastQC output?">
                            <option value="data">Raw data</option>
                            <option value="theoretical_gc">Theorectical GC</option>

                    <param name="input" value="cutadapt.txt" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="fastqc" />
                    <repeat name="output">
                        <param name="type" value="data"/>
                        <param name="input" value="fastqc_1.txt,fastqc_2.txt"/>
                    </repeat>

            <output name="html_report">
                <assert_contents>
                    <has_text text="Title of the report" />
                    <has_text text="Commment for the report" />
                    <has_text text="cutadapt_plot" />
                    <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"/>
            <output_collection name="stats" type="list">
                <element name="cutadapt" file="cutadapt_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"/>

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) == "plotFingerprintOutRawCounts"
                #set $pattern = "#plotFingerprint --outRawCounts"
                @LN_2_FILES@
            #end if
        #end for
    #elif str($repeat.software_cond.software) == "fastp"
        #set $pattern = "report_title"
        #for $file in $repeat.software_cond.input
            @ESCAPE_IDENTIFIER@
            #set file_path = os.path.join($software_dir, str($identifier) + 'fastp.json')
            ln -s '$file' '$file_path' &&
            grep -q "$pattern" '$file_path' || die "'$pattern' or 'report_title' not found in the file" &&
        #end for
    #elif str($repeat.software_cond.software) == "fastqc"
        #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
            @CREATE_REPEAT_DIR_1@
            #if str($repeat2.type) == "data"
                #for $k, $file in enumerate($repeat2.input)

                    <!--<option value="conpair">Conpair</option>-->
                    <!--<option value="dedup">DeDup</option>-->
                    <option value="deeptools">deepTools</option>
                    <!--<option value="disambiguate">Disambiguate</option>-->
                    <!--<option value="fastq_screen">FastQ Screen</option>-->
                    <option value="fastp">fastp</option>
                    <option value="fastqc">FastQC</option>
                    <option value="featureCounts">featureCounts</option>
                    <option value="flexbar">Flexbar</option>
                    <option value="gatk">GATK</option>
                    <!--<option value="goleft_indexcov">goleft indexcov</option>-->

                            <option value="plotFingerprintOutQualityMetrics">plotFingerprintOutQualityMetrics</option>
                        </param>
                        <param name="input" type="data" format="txt" multiple="true" label="Bismark output"/>
                    </repeat>
                </when>
                <when value="fastp">
                    <param name="input" type="data" format="json" multiple="true" label="Output of fastp" help="It should be the json report from fastp containing 'report_title'"/>
                </when>
                <when value="fastqc">
                    <repeat name="output" title="FastQC output" min="1">
                        <param name="type" type="select" label="Type of FastQC output?">
                            <option value="data">Raw data</option>
                            <option value="theoretical_gc">Theorectical GC</option>

                    <param name="input" value="cutadapt.txt" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="fastp" />
                    <param name="input" value="fastp1.json.txt,fastp2.json.txt" />
                </conditional>
            </repeat>
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="fastqc" />
                    <repeat name="output">
                        <param name="type" value="data"/>
                        <param name="input" value="fastqc_1.txt,fastqc_2.txt"/>
                    </repeat>

            <output name="html_report">
                <assert_contents>
                    <has_text text="Title of the report" />
                    <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"/>
            <output_collection name="stats" type="list">
                <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"/>