Mercurial > repos > iuc > multiqc
changeset 24:f7e2f1eb3a16 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
| author | iuc |
|---|---|
| date | Mon, 02 Sep 2024 14:22:54 +0000 |
| parents | abfd8a6544d7 |
| children | |
| files | bamtools_plugin.xml bcftools_plugin.xml bismark_plugin.xml bowtie2_plugin.xml busco_plugin.xml cutadapt_plugin.xml deeptools_plugin.xml fastp_plugin.xml fastqc_plugin.xml featurecounts_plugin.xml flexbar_plugin.xml gatk_plugin.xml macros.xml multiqc.xml picard_plugin.xml pycoqc_plugin.xml qualimap_plugin.xml rseqc_plugin.xml salmon_plugin.xml samtools_plugin.xml star_plugin.xml template_plugin.xml test-data/mqc_fastqc_per_base_sequence_quality_plot_1.txt trimmomatic_plugin.xml vcftools_plugin.xml |
| diffstat | 25 files changed, 2054 insertions(+), 1114 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamtools_plugin.xml Mon Sep 02 14:22:54 2024 +0000 @@ -0,0 +1,39 @@ +<macros> + <token name="@BAMTOOLS_COMMAND@"><![CDATA[ + #set $pattern = "Stats for BAM file(s)" + @LN_FILES@ + ]]></token> + <xml name="bamtools_form"> + <param name="input" type="data" format="txt" multiple="true" label="Output of BAMtools" help="It should contain 'This file was produced by bcftools stats'"/> + </xml> + <xml name="bamtools_test"> + <test expect_num_outputs="3"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="bamtools"/> + <param name="input" value="bamtools.txt"/> + </conditional> + </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> + <param name="flat" value="true"/> + <param name="export" value="true"/> + <output name="html_report"> + <assert_contents> + <has_text text="Title of the report"/> + <has_text text="Commment for the report"/> + <has_text text="bamtools-stats"/> + </assert_contents> + </output> + <output name="stats"> + <assert_contents> + <has_text text="bamtools_txt"/> + <has_text text="Bamtools"/> + <has_n_lines n="2"/> + <has_n_columns n="3"/> + </assert_contents> + </output> + <output_collection name="plots" type="list" count="1"/> + </test> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bcftools_plugin.xml Mon Sep 02 14:22:54 2024 +0000 @@ -0,0 +1,42 @@ +<macros> + <token name="@BCFTOOLS_COMMAND@"><![CDATA[ + #set $pattern = "This file was produced by bcftools stats" + @LN_FILES@ + ]]></token> + <xml name="bcftools_form"> + <param name="input" type="data" format="txt" multiple="true" label="Output of BCFtools" help="It should contain 'This file was produced by bcftools stats'"/> + </xml> + <!-- add here your test files and tests, the more stringent the better --> + <xml name="bcftools_test"> + <test expect_num_outputs="3"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="bcftools"/> + <param name="input" value="bcftools.txt"/> + </conditional> + </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> + <param name="flat" value="true"/> + <param name="export" value="true"/> + <output name="html_report"> + <assert_contents> + <has_text text="Title of the report"/> + <has_text text="Commment for the report"/> + <has_text text="bcftools_stats_indel-lengths"/> + </assert_contents> + </output> + <output name="stats"> + <assert_contents> + <has_text text="Stats_mqc_generalstats_bcftools_stats_number_of_records"/> + <has_text text="Stats_mqc_generalstats_bcftools_stats_number_of_SNPs"/> + <has_text text="Test1"/> + <has_text text="72330"/> + <has_n_lines n="2"/> + <has_n_columns n="8"/> + </assert_contents> + </output> + <output_collection name="plots" type="list" count="0"/> + </test> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bismark_plugin.xml Mon Sep 02 14:22:54 2024 +0000 @@ -0,0 +1,83 @@ +<macros> + <token name="@BISMARK_COMMAND@"><![CDATA[ + #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) + @CREATE_REPEAT_DIR_1@ + #if str($repeat2.type) == "align" + #for $file in $repeat2.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '_SE_report.txt') + ln -s '$file' '$file_path' && + #end for + #elif str($repeat2.type) == "dedup" + #for $file in $repeat2.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '_deduplication_report.txt') + ln -s '$file' '$file_path' && + #end for + #elif str($repeat2.type) == "meth_extract" + #for $file in $repeat2.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '_splitting_report.txt') + ln -s '$file' '$file_path' && + #end for + #elif str($repeat2.type) == "m_bias" + #for $file in $repeat2.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '_M-bias.txt') + ln -s '$file' '$file_path' && + #end for + #elif str($repeat2.type) == "bam2nuc" + #for $file in $repeat2.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '.nucleotide_stats.txt') + ln -s '$file' '$file_path' && + #end for + #end if + #end for + ]]></token> + <xml name="bismark_form"> + <repeat name="output" title="Bismark output" min="1"> + <param name="type" type="select" label="Type of Bismark output?"> + <option value="align">Alignment file</option> + <option value="dedup">Deduplication file</option> + <option value="meth_extract">Methylation file</option> + <option value="m_bias">m_bias file</option> + <option value="bam2nuc">bam2nuc file</option> + </param> + <param name="input" type="data" format="txt" multiple="true" label="Bismark output"/> + </repeat> + </xml> + <!-- add here your test files and tests, the more stringent the better --> + <xml name="bismark_test"> + <test expect_num_outputs="3"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="bismark"/> + <repeat name="output"> + <param name="type" value="align"/> + <param name="input" value="bismark.txt"/> + </repeat> + </conditional> + </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> + <param name="flat" value="true"/> + <param name="export" value="true"/> + <output name="html_report"> + <assert_contents> + <has_text text="Title of the report"/> + <has_text text="Commment for the report"/> + <has_text text="bismark-alignment"/> + </assert_contents> + </output> + <output name="stats"> + <assert_contents> + <has_text text="bismark_txt_SE_report"/> + <has_n_lines n="2"/> + <has_n_columns n="3"/> + </assert_contents> + </output> + <output_collection name="plots" type="list" count="0"/> + </test> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bowtie2_plugin.xml Mon Sep 02 14:22:54 2024 +0000 @@ -0,0 +1,40 @@ +<macros> + <token name="@BOWTIE2_COMMAND@"><![CDATA[ + #set $pattern = "% overall alignment rate" + @LN_FILES@ + ]]></token> + <xml name="bowtie2_form"> + <param name="input" type="data" format="txt" multiple="true" label="Output of Bowtie 2" help="It should contain 'reads; of these:'"/> + </xml> + <!-- add here your test files and tests, the more stringent the better --> + <xml name="bowtie2_test"> + <test expect_num_outputs="3"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="bowtie2"/> + <param name="input" value="bowtie2_1.txt,bowtie2_2.txt"/> + </conditional> + </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> + <param name="flat" value="true"/> + <param name="export" value="true"/> + <output name="html_report"> + <assert_contents> + <has_text text="Title of the report"/> + <has_text text="Commment for the report"/> + <has_text text="bowtie2_se_plot"/> + <has_text text="mqc-module-section-bowtie2"/> + </assert_contents> + </output> + <output name="stats"> + <assert_contents> + <has_text text="bowtie2_1_txt"/> + <has_n_lines n="3"/> + <has_n_columns n="2"/> + </assert_contents> + </output> + <output_collection name="plots" type="list" count="1"/> + </test> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/busco_plugin.xml Mon Sep 02 14:22:54 2024 +0000 @@ -0,0 +1,48 @@ +<macros> + <token name="@BUSCO_COMMAND@"><![CDATA[ + ## Searches for files "short_summary_[samplename].txt" + #for $file in $repeat.software_cond.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($software_dir, 'short_summary_' + str($identifier)) + ln -s '$file' '$file_path' && + #end for + ]]></token> + <xml name="busco_form"> + <param name="input" type="data" format="txt" multiple="true" label="Output of BUSCO"/> + </xml> + <!-- add here your test files and tests, the more stringent the better --> + <xml name="busco_test"> + <test expect_num_outputs="3"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="busco"/> + <param name="input" value="busco.txt"/> + </conditional> + </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> + <param name="flat" value="true"/> + <param name="export" value="true"/> + <output name="html_report"> + <assert_contents> + <has_text text="Title of the report"/> + <has_text text="Commment for the report"/> + <has_text text="busco-lineage-fungi_odb9"/> + </assert_contents> + </output> + <!-- Not sure why this is empty + <output name="stats"> + <assert_contents> + <has_text text="R1_fq"/> + <has_text text="result_right"/> + <has_text text="25839_merged"/> + <has_text text="C2"/> + <has_n_lines n="11"/> + <has_n_columns n="22"/> + </assert_contents> + </output> + --> + <output_collection name="plots" type="list" count="1"/> + </test> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cutadapt_plugin.xml Mon Sep 02 14:22:54 2024 +0000 @@ -0,0 +1,48 @@ +<macros> + <token name="@CUTADAPT_COMMAND@"><![CDATA[ + #set $pattern = "This is cutadapt" + #for $file in $repeat.software_cond.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($software_dir, str($identifier) + '.txt') + ln -s '$file' '$file_path' && + ## replace header for old cutadapt release + sed -i.old 's/You are running/This is/' '$file_path' && + grep -q "$pattern" '$file_path' || die "'$pattern' or 'You are running cutadapt' not found in the file" && + #end for + ]]></token> + <xml name="cutadapt_form"> + <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Cutadapt" help="It should contain 'This is cutadapt' or 'You are running cutadapt'"/> + </xml> + <xml name="cutadapt_test"> + <test expect_num_outputs="3"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="cutadapt"/> + <param name="input" value="cutadapt.txt"/> + </conditional> + </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> + <param name="flat" value="true"/> + <param name="export" value="true"/> + <output name="html_report"> + <assert_contents> + <has_text text="Title of the report"/> + <has_text text="Commment for the report"/> + <has_text text="cutadapt_trimmed_sequences_plot"/> + </assert_contents> + </output> + <output name="stats"> + <assert_contents> + <has_text text="Cutadapt"/> + <has_text text="Cutadapt_mqc_generalstats_cutadapt_percent_trimmed"/> + <has_text text="10"/> + <has_text text="Cutadapt_mqc_generalstats_cutadapt_percent_trimmed"/> + <has_n_lines n="2"/> + <has_n_columns n="2"/> + </assert_contents> + </output> + <output_collection name="plots" type="list" count="2"/> + </test> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/deeptools_plugin.xml Mon Sep 02 14:22:54 2024 +0000 @@ -0,0 +1,39 @@ +<macros> + <token name="@DEEPTOOLS_COMMAND@"><![CDATA[ + #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) + #if str($repeat2.type) == "bamPEFragmentSize" + #set $pattern = "Frag." + @LN_2_FILES@ + #elif str($repeat2.type) == "estimateReadFiltering" + #set $pattern = "Internally-determined Duplicate" + @LN_2_FILES@ + #elif str($repeat2.type) == "plotCoverageStdout" + #set $pattern = "sample" + @LN_2_FILES@ + #elif str($repeat2.type) == "plotCoverageOutRawCounts" + #set $pattern = "#plotCoverage --outRawCounts" + @LN_2_FILES@ + #elif str($repeat2.type) == "plotEnrichment" + #set $pattern = "featureReadCount" + @LN_2_FILES@ + #elif str($repeat2.type) == "plotFingerprintOutRawCounts" + #set $pattern = "#plotFingerprint --outRawCounts" + @LN_2_FILES@ + #end if + #end for + ]]></token> + <xml name="deeptools_form"> + <repeat name="output" title="deepTools output" min="1"> + <param name="type" type="select" label="deepTool used to generate the output?"> + <option value="bamPEFragmentSize">bamPEFragmentSize</option> + <option value="estimateReadFiltering">estimateReadFiltering</option> + <option value="plotCoverageStdout">plotCoverageStdout</option> + <option value="plotCoverageOutRawCounts">plotCoverageOutRawCounts</option> + <option value="plotEnrichment">plotEnrichment</option> + <option value="plotFingerprintOutRawCounts">plotFingerprintOutRawCounts</option> + <option value="plotFingerprintOutQualityMetrics">plotFingerprintOutQualityMetrics</option> + </param> + <param name="input" type="data" format="txt" label="Bismark output" multiple="true"/> + </repeat> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastp_plugin.xml Mon Sep 02 14:22:54 2024 +0000 @@ -0,0 +1,47 @@ +<macros> + <token name="@FASTP_COMMAND@"><![CDATA[ + #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 + ]]></token> + <xml name="fastp_form"> + <param name="input" type="data" format="json" label="Output of fastp" help="It should be the json report from fastp containing 'report_title" multiple="true"/> + </xml> + <!-- add here your test files and tests, the more stringent the better --> + <xml name="fastp_test"> + <test expect_num_outputs="3"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="fastp"/> + <param name="input" value="fastp1.json.txt,fastp2.json.txt"/> + </conditional> + </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> + <param name="flat" value="true"/> + <param name="export" value="true"/> + <output name="html_report"> + <assert_contents> + <has_text text="Title of the report"/> + <has_text text="Commment for the report"/> + <has_text text="All-in-one FASTQ preprocessor"/> + </assert_contents> + </output> + <output name="stats"> + <assert_contents> + <has_text text="fastp_mqc_generalstats_fastp_pct_duplication"/> + <has_text text="R1_fq"/> + <has_text text="fastp_mqc_generalstats_fastp_after_filtering_q30_rate"/> + <has_text text="bwa-mem-fastq1_fq"/> + <has_n_lines n="3"/> + <has_n_columns n="8"/> + </assert_contents> + </output> + <output_collection name="plots" type="list" count="15"/> + </test> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastqc_plugin.xml Mon Sep 02 14:22:54 2024 +0000 @@ -0,0 +1,71 @@ +<macros> +<token name="@FASTQC_COMMAND@"><![CDATA[ + #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) + #set file_dir = os.path.join($repeat_dir, 'file_' + str($k)) + #set file_path = os.path.join($file_dir, 'fastqc_data.txt') + mkdir '$file_dir' && + ln -s '$file' '$file_path' && + #end for + #elif str($repeat2.type) == "theoretical_gc" + #for $file in $repeat2.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '_fastqc_theoretical_gc') + ln -s '$file' '$file_path' && + #end for + #end if + #end for +]]></token> + +<xml name="fastqc_form"> + <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> + <param name="input" type="data" format="txt" multiple="true" label="FastQC output"> + <validator type="expression" message="MultiQC does not accept the HTML report generated by FastQC, only the Raw Data">value is not None and value.extension != "html"</validator> + </param> + </repeat> +</xml> + +<!-- add here your test files and tests, the more stringent the better --> +<xml name="fastqc_test"> + <test expect_num_outputs="3"> + <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> + </conditional> + </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> + <param name="flat" value="true"/> + <param name="export" value="true"/> + <output name="html_report"> + <assert_contents> + <has_text text="Title of the report" /> + <has_text text="Commment for the report" /> + <has_text text="fastqc_seq_heatmap_key_t" /> + </assert_contents> + </output> + <output name="stats"> + <assert_contents> + <has_text text="poulet5_1"/> + <has_text text="poulet5_2"/> + <has_text text="FastQC_mqc_generalstats_fastqc_median_sequence_length"/> + <has_n_lines n="3"/> + <has_n_columns n="7"/> + </assert_contents> + </output> + <output_collection name="plots" type="list" count="7"/> + </test> +</xml> + + +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/featurecounts_plugin.xml Mon Sep 02 14:22:54 2024 +0000 @@ -0,0 +1,50 @@ +<macros> + <token name="@FEATURECOUNTS_COMMAND@"><![CDATA[ + #for $file in $repeat.software_cond.input + @ESCAPE_IDENTIFIER@ + #set file_prefix = os.path.join($software_dir, str($identifier)) + if grep -qw Status '$file'; then + ln -s '$file' '${file_prefix}.summary'; + else + echo -e 'Status\t${identifier}' > '${file_prefix}.summary'; + cat '$file' >> '${file_prefix}.summary'; + fi && + #end for + ]]></token> + <xml name="featurecounts_form"> + <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of FeatureCounts"/> + </xml> + <!-- add here your test files and tests, the more stringent the better --> + <xml name="featurecounts_test"> + <test expect_num_outputs="3"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="featureCounts"/> + <param name="input" value="featureCounts.txt"/> + </conditional> + </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> + <param name="flat" value="true"/> + <param name="export" value="true"/> + <output name="html_report"> + <assert_contents> + <has_text text="Title of the report"/> + <has_text text="Commment for the report"/> + <has_text text="featureCounts_assignment_plot"/> + </assert_contents> + </output> + <output name="stats"> + <assert_contents> + <has_text text="featureCounts_mqc_generalstats_featurecounts_Assigned"/> + <has_text text="accepted_hits"/> + <has_text text="TopHat"/> + <has_text text="featureCounts_mqc_generalstats_featurecounts_percent_assigned"/> + <has_n_lines n="7"/> + <has_n_columns n="3"/> + </assert_contents> + </output> + <output_collection name="plots" type="list" count="1"/> + </test> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flexbar_plugin.xml Mon Sep 02 14:22:54 2024 +0000 @@ -0,0 +1,40 @@ +<macros> + <token name="@FLEXBAR_COMMAND@"><![CDATA[ + #set $pattern = "flexible barcode and adapter removal" + @LN_FILES@ + ]]></token> + <xml name="flexbar_form"> + <param name="input" type="data" format="txt,tabular,tsv,csv" label="Output of Flexbar" help="It should contain 'Flexbar - flexible barcode and adapter removal" multiple="true"/> + </xml> + <!-- add here your test files and tests, the more stringent the better --> + <xml name="flexbar_test"> + <test expect_num_outputs="3"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="flexbar"/> + <param name="input" value="flexbar.txt"/> + </conditional> + </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> + <param name="flat" value="true"/> + <param name="export" value="true"/> + <output name="html_report"> + <assert_contents> + <has_text text="Title of the report"/> + <has_text text="Commment for the report"/> + <has_text text="flexbar_plot"/> + </assert_contents> + </output> + <output name="stats"> + <assert_contents> + <has_text text="Flexbar_mqc_generalstats_flexbar_removed_bases_pct"/> + <has_text text="result_right"/> + <has_n_lines n="2"/> + <has_n_columns n="2"/> + </assert_contents> + </output> + <output_collection name="plots" type="list" count="1"/> + </test> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gatk_plugin.xml Mon Sep 02 14:22:54 2024 +0000 @@ -0,0 +1,59 @@ +<macros> + <token name="@GATK_COMMAND@"><![CDATA[ + #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) + #if str($repeat2.type) == "varianteval" + #set $pattern = "#:GATKTable:TiTvVariantEvaluator" + @LN_2_FILES@ + #elif str($repeat2.type) == "base_recalibrator" + #set $pattern = "#:GATKTable:Arguments:Recalibration" + @LN_2_FILES@ + #end if + #end for + ]]></token> + <xml name="gatk_form"> + <repeat name="output" title="GATK output" min="1"> + <param name="type" type="select" label="Type of GATK output?"> + <option value="varianteval">Variant eval file</option> + <option value="base_recalibrator">Base recalibrator file</option> + </param> + <param name="input" type="data" format="txt" multiple="true" label="GATK output"/> + </repeat> + </xml> + <!-- add here your test files and tests, the more stringent the better --> + <xml name="gatk_test"> + <test expect_num_outputs="3"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="gatk"/> + <repeat name="output"> + <param name="type" value="base_recalibrator"/> + <param name="input" value="gatk_BaseRecalibrator.txt"/> + </repeat> + <repeat name="output"> + <param name="type" value="varianteval"/> + <param name="input" value="gatk_varianteval.txt"/> + </repeat> + </conditional> + </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> + <param name="flat" value="true"/> + <param name="export" value="true"/> + <output name="html_report"> + <assert_contents> + <has_text text="Title of the report"/> + <has_text text="Commment for the report"/> + <has_text text="gatk_varianteval_variant_plot"/> + </assert_contents> + </output> + <output name="stats"> + <assert_contents> + <has_text text="gatk_varianteval_txt"/> + <has_n_lines n="2"/> + <has_n_columns n="3"/> + </assert_contents> + </output> + <output_collection name="plots" type="list" count="4"/> + </test> + </xml> +</macros>
--- a/macros.xml Sat Dec 10 11:22:18 2022 +0000 +++ b/macros.xml Mon Sep 02 14:22:54 2024 +0000 @@ -1,6 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">1.11</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">1.24.1</token> + <token name="@VERSION_SUFFIX@">0</token> <xml name="bio_tools"> <xrefs> <xref type="bio.tools">multiqc</xref> @@ -9,14 +9,46 @@ <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">multiqc</requirement> - </requirements> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1101/gr.244293.118</citation> + </citations> </xml> - + <xml name="configfile"> + <configfiles> + <configfile name="multiqc_config"> +<![CDATA[ +custom_data: +#for $i, $repeat in enumerate( $results ) + #if str($repeat.software_cond.software) == "custom_content" + section_$i: + file_format: 'tsv' + section_name: '$repeat.software_cond.section_name' + title: '$repeat.software_cond.title' + description: '$repeat.software_cond.description' + plot_type: '$repeat.software_cond.plot_type' + pconfig: + id: 'section_${i}_${repeat.software_cond.plot_type}' + ylab: '$repeat.software_cond.ylab' + xlab: '$repeat.software_cond.xlab' + #end if +#end for +sp: +#for $i, $repeat in enumerate( $results ) + #if str($repeat.software_cond.software) == "custom_content" + section_$i: + fn: 'file_${i}_*' + #end if +#end for + ]]></configfile> + </configfiles> + </xml> <token name="@ESCAPE_IDENTIFIER@"> <![CDATA[ #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier)) ]]></token> - <token name="@CHECK_LN_FILE@"> <![CDATA[ #if $file_path in $file_paths @@ -26,33 +58,25 @@ grep -q '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" && ln -s '$file' '$file_path' && ]]></token> - <token name="@CREATE_REPEAT_DIR_1@"> <![CDATA[ #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j)) mkdir '$repeat_dir' && ]]></token> - - <token name="@CREATE_REPEAT_DIR_1@"> - <![CDATA[ - #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j)) - mkdir '$repeat_dir' && - ]]></token> - <token name="@CREATE_REPEAT_DIR_2@"> + <token name="@CREATE_REPEAT_DIR_2@"> <![CDATA[ #set repeat_dir = os.path.join($software_dir, str($repeat2.type.type) + '_' + str($j)) mkdir '$repeat_dir' && - ]]></token> - <token name="@LN_FILES@"> + ]]></token> + <token name="@LN_FILES@"> <![CDATA[ #set file_paths = [] - #for $file in $repeat.software_cond.input + #for $file in $repeat.software_cond.input: @ESCAPE_IDENTIFIER@ #set file_path = os.path.join($software_dir, str($identifier)) @CHECK_LN_FILE@ #end for ]]></token> - <token name="@LN_2_FILES@"> <![CDATA[ #set file_paths = [] @@ -63,7 +87,6 @@ @CHECK_LN_FILE@ #end for ]]></token> - <token name="@LN_3_FILES@"> <![CDATA[ #set file_paths = [] @@ -73,293 +96,7 @@ @CHECK_LN_FILE@ #end for ]]></token> - - <token name="@BISMARK_INPUT@"><![CDATA[ - #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) - @CREATE_REPEAT_DIR_1@ - #if str($repeat2.type) == "align" - #for $file in $repeat2.input - @ESCAPE_IDENTIFIER@ - #set file_path = os.path.join($repeat_dir, str($identifier) + '_SE_report.txt') - ln -s '$file' '$file_path' && - #end for - #elif str($repeat2.type) == "dedup" - #for $file in $repeat2.input - @ESCAPE_IDENTIFIER@ - #set file_path = os.path.join($repeat_dir, str($identifier) + '_deduplication_report.txt') - ln -s '$file' '$file_path' && - #end for - #elif str($repeat2.type) == "meth_extract" - #for $file in $repeat2.input - @ESCAPE_IDENTIFIER@ - #set file_path = os.path.join($repeat_dir, str($identifier) + '_splitting_report.txt') - ln -s '$file' '$file_path' && - #end for - #elif str($repeat2.type) == "m_bias" - #for $file in $repeat2.input - @ESCAPE_IDENTIFIER@ - #set file_path = os.path.join($repeat_dir, str($identifier) + '_M-bias.txt') - ln -s '$file' '$file_path' && - #end for - #elif str($repeat2.type) == "bam2nuc" - #for $file in $repeat2.input - @ESCAPE_IDENTIFIER@ - #set file_path = os.path.join($repeat_dir, str($identifier) + '.nucleotide_stats.txt') - ln -s '$file' '$file_path' && - #end for - #end if - #end for - ]]></token> - - <token name="@DEEPTOOLS_INPUT@"><![CDATA[ - #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) - #if str($repeat2.type) == "bamPEFragmentSize" - #set $pattern = "Frag." - @LN_2_FILES@ - #elif str($repeat2.type) == "estimateReadFiltering" - #set $pattern = "Internally-determined Duplicate" - @LN_2_FILES@ - #elif str($repeat2.type) == "plotCoverageStdout" - #set $pattern = "sample" - @LN_2_FILES@ - #elif str($repeat2.type) == "plotCoverageOutRawCounts" - #set $pattern = "#plotCoverage --outRawCounts" - @LN_2_FILES@ - #elif str($repeat2.type) == "plotEnrichment" - #set $pattern = "featureReadCount" - @LN_2_FILES@ - #elif str($repeat2.type) == "plotFingerprintOutRawCounts" - #set $pattern = "#plotFingerprint --outRawCounts" - @LN_2_FILES@ - #end if - #end for - ]]></token> - - <token name="@PICCARD_INPUT@"><![CDATA[ - #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) - #if str($repeat2.type) == "alignment_metrics" - #set $pattern = "picard.analysis.AlignmentSummaryMetrics" - @LN_2_FILES@ - #elif str($repeat2.type) == "basedistributionbycycle" - #set $pattern = "picard.analysis.BaseDistributionByCycleMetrics" - @LN_2_FILES@ - #elif str($repeat2.type) == "gcbias" - #set $pattern = "picard.analysis.GcBias" - @LN_2_FILES@ - #elif str($repeat2.type) == "hsmetrics" - #set $pattern = "picard.analysis.directed.HsMetrics" - @ @ - #elif str($repeat2.type) == "insertsize" - #set $pattern = "picard.analysis.InsertSizeMetrics" - @LN_2_FILES@ - #elif str($repeat2.type) == "markdups" - #set $pattern = "MarkDuplicates" - @LN_2_FILES@ - #elif str($repeat2.type) == "oxogmetrics" - #set $pattern = "picard.analysis.CollectOxoGMetrics" - @LN_2_FILES@ - #elif str($repeat2.type) == "pcr_metrics" - #set $pattern = "picard.analysis.directed.TargetedPcrMetrics" - @LN_2_FILES@ - #elif str($repeat2.type) == "rnaseqmetrics" - #set $pattern = "Collect" - @LN_2_FILES@ - #elif str($repeat2.type) == "rrbs_metrics" - #set $pattern = "picard.analysis.RrbsSummaryMetrics" - @LN_2_FILES@ - #elif str($repeat2.type) == "wgs_metrics" - #set $pattern = "picard.analysis.CollectWgsMetrics$WgsMetrics" - @LN_2_FILES@ - #end if - #end for - ]]></token> - - <token name="@FASTQC_INPUT@"><![CDATA[ - #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) - #set file_dir = os.path.join($repeat_dir, 'file_' + str($k)) - #set file_path = os.path.join($file_dir, 'fastqc_data.txt') - mkdir '$file_dir' && - ln -s '$file' '$file_path' && - #end for - #elif str($repeat2.type) == "theoretical_gc" - #for $file in $repeat2.input - @ESCAPE_IDENTIFIER@ - #set file_path = os.path.join($repeat_dir, str($identifier) + '_fastqc_theoretical_gc') - ln -s '$file' '$file_path' && - #end for - #end if - #end for - ]]></token> - - <token name="@RSEQ_INPUT@"><![CDATA[ - #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) - @CREATE_REPEAT_DIR_2@ - #if str($repeat2.type.type) == "bam_stat" - #set $pattern = "Proper-paired reads map to different chrom:" - @LN_3_FILES@ - #elif str($repeat2.type.type) == "gene_body_coverage" - #for $k, $file in enumerate($repeat2.type.input) - #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.geneBodyCoverage.txt') - ln -s '$file' '$file_path' && - #end for - #elif str($repeat2.type.type) == "inner_distance" - #for $k, $file in enumerate($repeat2.type.input) - #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.inner_distance_freq.txt') - ln -s '${file}' '$file_path' && - #end for - #elif str($repeat2.type.type) == "junction_annotation" - #set $pattern = "Partial Novel Splicing Junctions:" - @LN_3_FILES@ - #elif str($repeat2.type.type) == "read_gc" - #for $k, $file in enumerate($repeat2.type.input) - #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.GC.xls') - ln -s '$file' '$file_path' && - #end for - #elif str($repeat2.type.type) == "junction_saturation" - #for $k, $file in enumerate($repeat2.type.input) - #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.junctionSaturation_plot.r') - ln -s '${file}' '$file_path' && - #end for - #elif str($repeat2.type.type) == "read_distribution" - #set $pattern = "Group Total_bases Tag_count Tags/Kb" - @LN_3_FILES@ - #elif str($repeat2.type.type) == "read_duplication_pos" - #for $k, $file in enumerate($repeat2.type.input) - #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.pos.DupRate.xls') - ln -s '$file' '$file_path' && - #end for - #elif str($repeat2.type.type) == "infer_experiment" - #set $pattern = "Fraction of reads explained by" - #for $file in $repeat2.type.input - @ESCAPE_IDENTIFIER@ - #set file_path = os.path.join($repeat_dir, str($identifier)) - grep -q "$pattern" $file || die "'$pattern' not found in the file" && - ln -s '$file' '$file_path' && - #end for - #end if - #end for - ]]></token> - - <token name="@VCFTOOLS_INPUT@"><![CDATA[ - #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) - @CREATE_REPEAT_DIR_2@ - #if str($repeat2.type.type) == "relatedness2" - #for $file in $repeat2.type.input - @ESCAPE_IDENTIFIER@ - #set file_path = os.path.join($repeat_dir, str($identifier) + '.relatedness2') - ln -s '$file' '$file_path' && - #end for - #elif str($repeat2.type) == "tstv_by_count" - #for $file in $repeat2.type.input - @ESCAPE_IDENTIFIER@ - #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.count') - ln -s '$file' '$file_path' && - #end for - #elif str($repeat2.type) == "tstv_by_qual" - #for $file in $repeat2.type.input - @ESCAPE_IDENTIFIER@ - #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.qual') - ln -s '$file' '$file_path' && - #end for - #elif str($repeat2.type) == "tstv_summary" - #for $file in $repeat2.type.input - @ESCAPE_IDENTIFIER@ - #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.summary') - ln -s '$file' '$file_path' && - #end for - #end if - #end for - ]]></token> - - <token name="@QUALIMAP_INPUT@"><![CDATA[ - #for $file in $repeat.software_cond.input - #if re.search("genome_results", str($file.element_identifier)) - sample="\$(grep 'bam file = ' $file | sed 's/bam file = //g' | sed 's: ::g')" && - dir_name="$software_dir/\${sample}" && - mkdir -p \${dir_name} && - filepath_1="\${dir_name}/genome_results.txt" && - ln -sf '$file' \${filepath_1} && - #elif re.search("coverage_histogram", str($file.element_identifier)) - nested_dir_name="\${dir_name}/raw_data_qualimapReport/" && - mkdir -p \${nested_dir_name} && - filepath_2="\${nested_dir_name}/coverage_histogram.txt" && - ln -sf '$file' \${filepath_2} && - #elif re.search("gc-content_distribution", str($file.element_identifier)) - nested_dir_name="\${dir_name}/raw_data_qualimapReport/" && - mkdir -p \${nested_dir_name} && - filepath_3="\${nested_dir_name}/mapped_reads_gc-content_distribution.txt" && - ln -sf '$file' \${filepath_3} && - #else - #pass - #end if - #end for - ]]></token> - - <token name="@SALMON_INPUT@"><![CDATA[ - #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) - @CREATE_REPEAT_DIR_2@ - #if str($repeat2.type.type) == "meta" - #for $k, $file in enumerate($repeat2.type.input) - #set file_dir = os.path.join($repeat_dir, 'file_' + str($k)) - #set file_path = os.path.join($file_dir, 'meta_info.json') - mkdir '$file_dir' && - ln -s '$file' '$file_path' && - #end for - #elif str($repeat2.type.type) == "fld" - #for $k, $file in enumerate($repeat2.type.input) - #set file_dir = os.path.join($repeat_dir, 'file_' + str($k)) - #set file_path = os.path.join($file_dir,'flenDist.txt') - mkdir '$file_dir' && - ln -s '$file' '$file_path' && - #end for - #end if - #end for - ]]></token> - - <token name="@SAMTOOLS_INPUT@"><![CDATA[ - #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) - @CREATE_REPEAT_DIR_2@ - #if str($repeat2.type.type) == "stats" - #set $pattern = "This file was produced by samtools stats" - @LN_3_FILES@ - #elif str($repeat2.type.type) == "flagstat" - #set $pattern = "in total (QC-passed reads + QC-failed reads)" - @LN_3_FILES@ - #elif str($repeat2.type.type) == "idxstats" - #for $file in $repeat2.type.input - @ESCAPE_IDENTIFIER@ - #set file_path = os.path.join($repeat_dir, str($identifier) + '_idxstat') - ln -s '$file' '$file_path' && - #end for - #elif str($repeat2.type.type) == "rmdup" - #set $pattern = "[bam_rmdup" - @LN_3_FILES@ - #end if - #end for - ]]></token> - - <token name="@STAR_INPUT@"><![CDATA[ - #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) - @CREATE_REPEAT_DIR_2@ - #if str($repeat2.type.type) == "log" - #for $file in $repeat2.type.input - @ESCAPE_IDENTIFIER@ - #set file_path = os.path.join($repeat_dir, str($identifier) + '_Log.final.out') - ln -s '$file' '$file_path' && - #end for - #elif str($repeat2.type.type) == "genecounts" - #for $file in $repeat2.type.input - @ESCAPE_IDENTIFIER@ - #set file_path = os.path.join($repeat_dir, str($identifier) + '_ReadsPerGene.out.tab') - ln -s '$file' '$file_path' && - #end for - #end if - #end for - ]]></token> - + <!-- is currently not used --> <xml name="element_assert" token_name="" token_lines="" token_columns="" token_text=""> <element name="@NAME@"> <assert_contents> @@ -370,10 +107,499 @@ </assert_contents> </element> </xml> - - <xml name="citations"> - <citations> - <citation type="doi">10.1101/gr.244293.118</citation> - </citations> + <xml name="general_tests"> + <!--Test 01--> + <test expect_num_outputs="3"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="cutadapt"/> + <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> + </conditional> + </repeat> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="flexbar"/> + <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"> + <conditional name="software_cond"> + <param name="software" value="trimmomatic"/> + <param name="input" value="trimmomatic.txt"/> + </conditional> + </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> + <param name="flat" value="true"/> + <param name="export" value="true"/> + <output name="html_report"> + <assert_contents> + <has_text text="Title of the report"/> + <has_text text="Commment for the report"/> + <has_text text="cutadapt_trimmed_sequences_plot"/> + <has_text text="All-in-one FASTQ preprocessor"/> + <has_text text="fastqc_seq_heatmap_key_t"/> + <has_text text="flexbar_plot"/> + <has_text text="Slamdunk"/> + <has_text text="sortmerna-detailed-plot"/> + <has_text text="trimmomatic_plot"/> + </assert_contents> + </output> + <output name="stats"> + <assert_contents> + <has_text text="dataset_33"/> + <has_text text="R1_fq"/> + <has_text text="poulet5_1"/> + <has_text text="result_right"/> + <has_text text="bwa-mem-fastq1_fq"/> + <has_text text="25839_merged"/> + <has_text text="Slamdunk_mqc_generalstats_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"/> + </test> + <!--Test 02--> + <test expect_num_outputs="2"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="bismark"/> + <repeat name="output"> + <param name="type" value="align"/> + <param name="input" value="bismark.txt"/> + </repeat> + </conditional> + </repeat> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="bowtie2"/> + <param name="input" value="bowtie2_1.txt,bowtie2_2.txt"/> + </conditional> + </repeat> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="hisat2"/> + <param name="input" value="hisat2_1.txt,hisat2_2.txt"/> + </conditional> + </repeat> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="hicexplorer"/> + <param name="input" value="hicexplorer1.log,hicexplorer1.log,hicexplorer2.log"/> + </conditional> + </repeat> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="kallisto"/> + <param name="input" value="kallisto_1.txt,kallisto_2.txt"/> + </conditional> + </repeat> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="macs2"/> + <param name="input" value="macs_1.txt,macs_2.txt"/> + </conditional> + </repeat> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="star"/> + <repeat name="output"> + <conditional name="type"> + <param name="type" value="log"/> + <param name="input" value="star_log.txt"/> + </conditional> + </repeat> + <repeat name="output"> + <conditional name="type"> + <param name="type" value="genecounts"/> + <param name="input" value="star_counts.txt"/> + </conditional> + </repeat> + </conditional> + </repeat> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="tophat"/> + <param name="input" value="tophat.txt"/> + </conditional> + </repeat> + <output name="html_report"> + <assert_contents> + <has_text text="bismark-alignment"/> + <has_text text="bowtie2_se_plot"/> + <has_text text="mqc-module-section-bowtie2"/> + <has_text text="hisat2_se_plot"/> + <has_text text="MACS2"/> + <has_text text="star_alignment_plot"/> + <has_text text="tophat_alignment"/> + <has_text text="hicexplorer"/> + <has_text text="hicexplorer1_log_1"/> + </assert_contents> + </output> + <output name="stats"> + <assert_contents> + <has_text text="bismark_txt_SE_report"/> + <has_text text="bowtie2_1_txt"/> + <has_text text="HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2"/> + <has_text text="treat2"/> + <has_text text="hicexplorer_3_hicexplorer2_log_small_test_rf"/> + <has_text text="hisat2_2_txt"/> + <has_text text="HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1"/> + <has_text text="treat2"/> + <has_text text="Cutadapt"/> + <has_text text="star_log_txt"/> + <has_text text="tophat_txtalign"/> + <has_n_lines n="17"/> + <has_n_columns n="23"/> + </assert_contents> + </output> + </test> + <!--Test 03--> + <test expect_num_outputs="2"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="bamtools"/> + <param name="input" value="bamtools.txt"/> + </conditional> + </repeat> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="bcftools"/> + <param name="input" value="bcftools.txt"/> + </conditional> + </repeat> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="busco"/> + <param name="input" value="busco.txt"/> + </conditional> + </repeat> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="deeptools"/> + <repeat name="output"> + <param name="type" value="bamPEFragmentSize"/> + <param name="input" value="deeptools_bamPEFragmentSize.txt"/> + </repeat> + <repeat name="output"> + <param name="type" value="estimateReadFiltering"/> + <param name="input" value="deeptools_estimateReadFiltering.txt"/> + </repeat> + <repeat name="output"> + <param name="type" value="plotCoverageStdout"/> + <param name="input" value="deeptools_plotCoverageStdout.txt"/> + </repeat> + <repeat name="output"> + <param name="type" value="plotCoverageOutRawCounts"/> + <param name="input" value="deeptools_plotCoverageOutRawCounts.txt"/> + </repeat> + <repeat name="output"> + <param name="type" value="plotEnrichment"/> + <param name="input" value="deeptools_plotEnrichment.txt"/> + </repeat> + <repeat name="output"> + <param name="type" value="plotFingerprintOutRawCounts"/> + <param name="input" value="deeptools_plotFingerprintOutRawCounts.txt"/> + </repeat> + </conditional> + </repeat> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="featureCounts"/> + <param name="input" value="featureCounts.txt"/> + </conditional> + </repeat> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="gatk"/> + <repeat name="output"> + <param name="type" value="base_recalibrator"/> + <param name="input" value="gatk_BaseRecalibrator.txt"/> + </repeat> + <repeat name="output"> + <param name="type" value="varianteval"/> + <param name="input" value="gatk_varianteval.txt"/> + </repeat> + </conditional> + </repeat> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="htseq"/> + <param name="input" value="htseq.txt"/> + </conditional> + </repeat> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="picard"/> + <repeat name="output"> + <param name="type" value="gcbias"/> + <param name="input" value="picard_collectGcBias.txt"/> + </repeat> + <repeat name="output"> + <param name="type" value="insertsize"/> + <param name="input" value="picard_CollectInsertSizeMetrics.txt"/> + </repeat> + <repeat name="output"> + <param name="type" value="markdups"/> + <param name="input" value="picard_MarkDuplicates.txt"/> + </repeat> + <repeat name="output"> + <param name="type" value="basedistributionbycycle"/> + <param name="input" value="picard_CollectBaseDistributionByCycle.txt"/> + </repeat> + <repeat name="output"> + <param name="type" value="rnaseqmetrics"/> + <param name="input" value="picard_CollectRnaSeqMetrics.txt"/> + </repeat> + <repeat name="output"> + <param name="type" value="alignment_metrics"/> + <param name="input" value="picard_CollectAlignmentSummaryMetrics.txt"/> + </repeat> + </conditional> + </repeat> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="prokka"/> + <param name="input" value="prokka_1.txt,prokka_2.txt"/> + </conditional> + </repeat> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="qualimap"/> + <param name="input" value="genome_results.txt"/> + </conditional> + </repeat> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="quast"/> + <param name="input" value="quast.tsv"/> + </conditional> + </repeat> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="rseqc"/> + <repeat name="output"> + <conditional name="type"> + <param name="type" value="read_gc"/> + <param name="input" value="rseqc.txt"/> + </conditional> + </repeat> + </conditional> + </repeat> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="samblaster"/> + <param name="input" value="samblaster.txt"/> + </conditional> + </repeat> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="samtools"/> + <repeat name="output"> + <conditional name="type"> + <param name="type" value="stats"/> + <param name="input" value="samtools_stats.txt"/> + </conditional> + </repeat> + <repeat name="output"> + <conditional name="type"> + <param name="type" value="flagstat"/> + <param name="input" value="samtools_flagstat.txt"/> + </conditional> + </repeat> + <repeat name="output"> + <conditional name="type"> + <param name="type" value="idxstats"/> + <param name="input" value="samtools_idxstats.txt"/> + </conditional> + </repeat> + </conditional> + </repeat> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="snpeff"/> + <param name="input" value="snpeff.csv" ftype="csv"/> + </conditional> + </repeat> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="vcftools"/> + <repeat name="output"> + <conditional name="type"> + <param name="type" value="tstv_by_qual"/> + <param name="input" value="vcftools.txt"/> + </conditional> + </repeat> + <param name="input" value="vcftools.txt"/> + </conditional> + </repeat> + <output name="html_report"> + <assert_contents> + <has_text text="bamtools-stats"/> + <has_text text="bcftools_stats_indel-lengths"/> + <has_text text="busco-lineage-fungi_odb9"/> + <has_text text="deeptools"/> + <has_text text="featureCounts_assignment_plot"/> + <has_text text="gatk_varianteval_variant_plot"/> + <has_text text="htseq_assignment_plot"/> + <has_text text="picard_alignment_readlength"/> + <has_text text="picard-rna-assignment"/> + <has_text text="picard-markduplicates"/> + <has_text text="picard-insertsize"/> + <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="bamtools_txt"/> + <has_text text="Test1"/> + <has_text text="Prokka_mqc_generalstats_prokka_contigs"/> + <has_text text="5: TopHat on data 1, data 14, and data 13"/> + <has_text text="gatk_varianteval_txt"/> + <has_text text="x_bam"/> + <has_text text="htseq_txt"/> + <has_text text="picard_CollectRnaSeqMetrics_bam"/> + <has_text text="dataset_114"/> + <has_text text="Helicobacter pylori"/> + <has_text text="Sample2"/> + <has_text text="14892_1#15"/> + <has_text text="samtools_flagstat_txt"/> + <has_text text="mapped_passed"/> + <has_text text="stats_mqc_generalstats_samtools_stats_error_rate"/> + <has_text text="samtools_stats_txt"/> + <has_text text="snpeff_csv"/> + <has_text text="Bamtools"/> + <has_n_lines n="22"/> + <has_n_columns n="46"/> + </assert_contents> + </output> + </test> + <!--Test 04--> + <test expect_num_outputs="2"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="custom_content"/> + <param name="cc_select" value="manual"/> + <param name="plot_type" value="linegraph"/> + <param name="section_name" value="BPC"/> + <param name="description" value="Sum of intensity (Y) of the most intense peaks at each retention time(X)"/> + <param name="xlab" value="Retention Time"/> + <param name="ylab" value="Base Peak Intensity"/> + <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="4594258" delta="500"/> + </assert_contents> + </output> + <!--output name="stats" ftype="tabular"> + Not created anymore. Proper test needed. + <assert_contents> + <has_n_lines n="2" /> + </assert_contents> + </output--> + </test> + <!--Test 05--> + <test expect_num_outputs="3"> + <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> + </conditional> + </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> + <param name="flat" value="true"/> + <param name="export" value="true"/> + <output name="html_report"> + <assert_contents> + <has_text text="Title of the report"/> + <has_text text="Commment for the report"/> + <has_text text="fastqc_seq_heatmap_key_t"/> + </assert_contents> + </output> + <output name="stats" ftype="tabular"> + <assert_contents> + <has_text text="poulet5_2"/> + <has_text text="FastQC"/> + <has_n_lines n="3"/> + <has_n_columns n="7"/> + </assert_contents> + </output> + <output_collection name="plots" type="list" count="7"> + <element name="fastqc_per_base_sequence_quality_plot" file="mqc_fastqc_per_base_sequence_quality_plot_1.txt"> + <assert_contents> + <has_size size="2877" delta="200"/> + </assert_contents> + </element> + </output_collection> + </test> + <!--Test 06--> + <test expect_num_outputs="2"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="pycoqc"/> + <param name="input" value="pycoqc.json"/> + </conditional> + </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> + <!-- <param name="flat" value="true"/> --> + <output name="html_report"> + <assert_contents> + <has_text text="Title of the report"/> + <has_text text="Commment for the report"/> + <has_text text="General Statistics"/> + <has_text text="pycoqc_count_plot"/> + <has_text text="pycoqc_read_len_plot"/> + <has_text text="pycoqc_read_qual_plot"/> + </assert_contents> + </output> + <output name="stats" ftype="tabular"> + <assert_contents> + <has_text text="pycoQC_mqc_generalstats_pycoqc_passed_median_read_length"/> + <has_text text="pycoqc_json"/> + </assert_contents> + </output> + </test> </xml> </macros>
--- a/multiqc.xml Sat Dec 10 11:22:18 2022 +0000 +++ b/multiqc.xml Mon Sep 02 14:22:54 2024 +0000 @@ -1,11 +1,31 @@ <tool id="multiqc" name="MultiQC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> <description>aggregate results from bioinformatics analyses into a single report</description> - <macros> <import>macros.xml</import> + <import>bamtools_plugin.xml</import> + <import>bcftools_plugin.xml</import> + <import>bismark_plugin.xml</import> + <import>bowtie2_plugin.xml</import> + <import>busco_plugin.xml</import> + <import>cutadapt_plugin.xml</import> + <import>deeptools_plugin.xml</import> + <import>fastqc_plugin.xml</import> + <import>fastp_plugin.xml</import> + <import>featurecounts_plugin.xml</import> + <import>flexbar_plugin.xml</import> + <import>gatk_plugin.xml</import> + <import>picard_plugin.xml</import> + <import>pycoqc_plugin.xml</import> + <import>qualimap_plugin.xml</import> + <import>rseqc_plugin.xml</import> + <import>salmon_plugin.xml</import> + <import>samtools_plugin.xml</import> + <import>star_plugin.xml</import> + <import>trimmomatic_plugin.xml</import> + <import>vcftools_plugin.xml</import> </macros> <expand macro="bio_tools"/> - <expand macro='requirements' /> + <expand macro="requirements"/> <version_command>multiqc --version</version_command> <command detect_errors="aggressive"> <![CDATA[ @@ -22,69 +42,29 @@ #set software_dir = os.path.join('multiqc_WDir', str($repeat.software_cond.software) + '_' + str($i)) mkdir $software_dir && #if str($repeat.software_cond.software) == "bamtools" - #set $pattern = "Stats for BAM file(s)" - @LN_FILES@ + @BAMTOOLS_COMMAND@ #elif str($repeat.software_cond.software) == "bcftools" - #set $pattern = "This file was produced by bcftools stats" - @LN_FILES@ + @BCFTOOLS_COMMAND@ #elif str($repeat.software_cond.software) == "bismark" - @BISMARK_INPUT@ + @BISMARK_COMMAND@ #elif str($repeat.software_cond.software) == "bowtie2" - #set $pattern = "% overall alignment rate" - @LN_FILES@ + @BOWTIE2_COMMAND@ #elif str($repeat.software_cond.software) == "busco" - ## Searches for files "short_summary_[samplename].txt" - #for $file in $repeat.software_cond.input - @ESCAPE_IDENTIFIER@ - #set file_path = os.path.join($software_dir, 'short_summary_' + str($identifier)) - ln -s '$file' '$file_path' && - #end for + @BUSCO_COMMAND@ #elif str($repeat.software_cond.software) == "cutadapt" - #set $pattern = "This is cutadapt" - #for $file in $repeat.software_cond.input - @ESCAPE_IDENTIFIER@ - #set file_path = os.path.join($software_dir, str($identifier) + '.txt') - ln -s '$file' '$file_path' && - ## replace header for old cutadapt release - sed -i.old 's/You are running/This is/' '$file_path' && - grep -q "$pattern" '$file_path' || die "'$pattern' or 'You are running cutadapt' not found in the file" && - #end for + @CUTADAPT_COMMAND@ #elif str($repeat.software_cond.software) == "deeptools" - @DEEPTOOLS_INPUT@ + @DEEPTOOLS_COMMAND@ #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 + @FASTP_COMMAND@ #elif str($repeat.software_cond.software) == "fastqc" - @FASTQC_INPUT@ + @FASTQC_COMMAND@ #elif str($repeat.software_cond.software) == "featureCounts" - #for $file in $repeat.software_cond.input - @ESCAPE_IDENTIFIER@ - #set file_prefix = os.path.join($software_dir, str($identifier)) - if grep -qw Status '$file'; then - ln -s '$file' '${file_prefix}.summary'; - else - echo -e 'Status\t${identifier}' > '${file_prefix}.summary'; - cat '$file' >> '${file_prefix}.summary'; - fi && - #end for + @FEATURECOUNTS_COMMAND@ #elif str($repeat.software_cond.software) == "flexbar" - #set $pattern = "flexible barcode and adapter removal" - @LN_FILES@ + @FLEXBAR_COMMAND@ #elif str($repeat.software_cond.software) == "gatk" - #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) - #if str($repeat2.type) == "varianteval" - #set $pattern = "#:GATKTable:TiTvVariantEvaluator" - @LN_2_FILES@ - #elif str($repeat2.type) == "base_recalibrator" - #set $pattern = "#:GATKTable:Arguments:Recalibration" - @LN_2_FILES@ - #end if - #end for + @GATK_COMMAND@ #elif str($repeat.software_cond.software) == "hicup" #for $file in $repeat.software_cond.input @ESCAPE_IDENTIFIER@ @@ -112,15 +92,14 @@ ln -s '$file' '$file_path' && #end for #elif str($repeat.software_cond.software) == "picard" - @PICCARD_INPUT@ + @PICARD_COMMAND@ #elif str($repeat.software_cond.software) == "prokka" #set $pattern = "contigs:" @LN_FILES@ #elif str($repeat.software_cond.software) == "pycoqc" - #set $pattern = "\"pycoqc\":" - @LN_FILES@ + @PYCOQC_COMMAND@ #elif str($repeat.software_cond.software) == "qualimap" - @QUALIMAP_INPUT@ + @QUALIMAP_COMMAND@ #elif str($repeat.software_cond.software) == "quast" #for $k, $file in enumerate($repeat.software_cond.input) #set file_dir = os.path.join($software_dir, 'file_' + str($k)) @@ -135,14 +114,14 @@ ln -s '$file' '$file_path' && #end for #elif str($repeat.software_cond.software) == "rseqc" - @RSEQ_INPUT@ + @RSEQC_COMMAND@ #elif str($repeat.software_cond.software) == "salmon" - @SALMON_INPUT@ + @SALMON_COMMAND@ #elif str($repeat.software_cond.software) == "samblaster" #set $pattern = "samblaster: Version" @LN_FILES@ #elif str($repeat.software_cond.software) == "samtools" - @SAMTOOLS_INPUT@ + @SAMTOOLS_COMMAND@ #elif str($repeat.software_cond.software) == "slamdunk" #set $pattern = "# slamdunk" @LN_FILES@ @@ -153,7 +132,7 @@ #set $pattern = "Minimal SW score based on E-value" @LN_FILES@ #else if str($repeat.software_cond.software) == "star": - @STAR_INPUT@ + @STAR_COMMAND@ #elif str($repeat.software_cond.software) == "tophat" #for $file in $repeat.software_cond.input @ESCAPE_IDENTIFIER@ @@ -161,10 +140,9 @@ ln -s '$file' '$file_path' && #end for #elif str($repeat.software_cond.software) == "trimmomatic" - #set $pattern = "Trimmomatic" - @LN_FILES@ + @TRIMMOMATIC_COMMAND@ #elif str($repeat.software_cond.software) == "vcftools" - @VCFTOOLS_INPUT@ + @VCFTOOLS_COMMAND@ #else if str($repeat.software_cond.software) == "custom_content": #set $configfile = "T" #for $j, $file in enumerate( $repeat.software_cond.input ) @@ -191,34 +169,15 @@ #if $configfile == "T" --config '$multiqc_config' #end if + +&& +mkdir -p ./plots && +ls -l ./report_data/ && +##cat ./report_data/multiqc_busco.txt && +cp ./report_data/*plot*.txt ./plots/ | true ## don't fail if no plot files are generated + ]]></command> - <configfiles> - <configfile name="multiqc_config"> -<![CDATA[ -custom_data: -#for $i, $repeat in enumerate( $results ) - #if str($repeat.software_cond.software) == "custom_content" - section_$i: - file_format: 'tsv' - section_name: '$repeat.software_cond.section_name' - title: '$repeat.software_cond.title' - description: '$repeat.software_cond.description' - plot_type: '$repeat.software_cond.plot_type' - pconfig: - id: 'section_${i}_${repeat.software_cond.plot_type}' - ylab: '$repeat.software_cond.ylab' - xlab: '$repeat.software_cond.xlab' - #end if -#end for -sp: -#for $i, $repeat in enumerate( $results ) - #if str($repeat.software_cond.software) == "custom_content" - section_$i: - fn: 'file_${i}_*' - #end if -#end for - ]]></configfile> - </configfiles> + <expand macro="configfile"/> <inputs> <repeat name="results" title="Results" min="1"> <conditional name="software_cond"> @@ -287,7 +246,7 @@ <option value="star">STAR</option> <!--<option value="supernova">Supernova</option>--> <!--<option value="theta2">THeTA2</option>--> - <option value="tophat">TopHat2</option> + <option value="tophat">TopHat2 (TopHat2 is deprecated you should not use it)</option> <option value="trimmomatic">Trimmomatic</option> <option value="vcftools">VCFTools</option> <!--<option value="verifybamid">VerifyBAMID</option>--> @@ -295,74 +254,40 @@ <option value="custom_content">Custom Content</option> </param> <when value="bamtools"> - <param name="input" type="data" format="txt" multiple="true" label="Output of BAMtools" help="It should contain 'Stats for BAM file(s)'"/> + <expand macro="bamtools_form"/> </when> <when value="bcftools"> - <param name="input" type="data" format="txt" multiple="true" label="Output of BAMtools" help="It should contain 'This file was produced by bcftools stats'"/> + <expand macro="bcftools_form"/> </when> <when value="bismark"> - <repeat name="output" title="Bismark output" min="1"> - <param name="type" type="select" label="Type of Bismark output?"> - <option value="align">Alignment file</option> - <option value="dedup">Deduplication file</option> - <option value="meth_extract">Methylation file</option> - <option value="m_bias">m_bias file</option> - <option value="bam2nuc">bam2nuc file</option> - </param> - <param name="input" type="data" format="txt" multiple="true" label="Bismark output"/> - </repeat> + <expand macro="bismark_form"/> </when> <when value="bowtie2"> - <param name="input" type="data" format="txt" multiple="true" label="Output of Bowtie 2" help="It should contain 'reads; of these:'"/> + <expand macro="bowtie2_form"/> </when> <when value="busco"> - <param name="input" type="data" format="txt" multiple="true" label="Output of BUSCO"/> + <expand macro="busco_form"/> </when> <when value="cutadapt"> - <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Cutadapt" help="It should contain 'This is cutadapt' or 'You are running cutadapt'"/> + <expand macro="cutadapt_form"/> </when> <when value="deeptools"> - <repeat name="output" title="deepTools output" min="1"> - <param name="type" type="select" label="deepTool used to generate the output?"> - <option value="bamPEFragmentSize">bamPEFragmentSize</option> - <option value="estimateReadFiltering">estimateReadFiltering</option> - <option value="plotCoverageStdout">plotCoverageStdout</option> - <option value="plotCoverageOutRawCounts">plotCoverageOutRawCounts</option> - <option value="plotEnrichment">plotEnrichment</option> - <option value="plotFingerprintOutRawCounts">plotFingerprintOutRawCounts</option> - <option value="plotFingerprintOutQualityMetrics">plotFingerprintOutQualityMetrics</option> - </param> - <param name="input" type="data" format="txt" multiple="true" label="Bismark output"/> - </repeat> + <expand macro="deeptools_form"/> </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'"/> + <expand macro="fastp_form"/> </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> - <param name="input" type="data" format="txt" multiple="true" label="FastQC output"> - <validator type="expression" message="MultiQC does not accept the HTML report generated by FastQC, only the Raw Data">value is not None and value.extension != "html"</validator> - </param> - </repeat> + <expand macro="fastqc_form"/> </when> <when value="featureCounts"> - <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of FeatureCounts"/> + <expand macro="featurecounts_form"/> </when> <when value="flexbar"> - <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Flexbar" help="It should contain 'Flexbar - flexible barcode and adapter removal'"/> + <expand macro="flexbar_form"/> </when> <when value="gatk"> - <repeat name="output" title="GATK output" min="1"> - <param name="type" type="select" label="Type of GATK output?"> - <option value="varianteval">Variant eval file</option> - <option value="base_recalibrator">Base recalibrator file</option> - </param> - <param name="input" type="data" format="txt" multiple="true" label="GATK output"/> - </repeat> + <expand macro="gatk_form"/> </when> <when value="hicexplorer"> <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of HiCExplorer" help="It should contain 'Min rest. site distance'"/> @@ -380,105 +305,28 @@ <param name="input" type="data" format="txt,tabular,tsv" multiple="true" label="Output of MACS2" help="It should be a tabular file containing '# This file is generated by MACS'"/> </when> <when value="picard"> - <repeat name="output" title="Picard output" min="1"> - <param name="type" type="select" label="Type of Picard output?"> - <option value="alignment_metrics">Alignment metrics</option> - <option value="basedistributionbycycle">Base distribution by cycle</option> - <option value="gcbias">GC bias</option> - <option value="hsmetrics">HS Metrics</option> - <option value="insertsize">Insert size</option> - <option value="markdups">Markdups</option> - <option value="oxogmetrics">Oxog metrics</option> - <option value="pcr_metrics">PCR metrics</option> - <option value="rnaseqmetrics">RNA Seq metrics</option> - <option value="rrbs_metrics">RRBS metrics</option> - <option value="wgs_metrics">WGS metrics</option> - </param> - <param name="input" type="data" format="txt" multiple="true" label="Picard output"/> - </repeat> + <expand macro="picard_form"/> </when> <when value="prokka"> <param name="input" type="data" format="txt" multiple="true" label="Output of Prokka" help="It should contain 'contigs:'"/> </when> <when value="pycoqc"> - <param name="input" type="data" format="txt,json" multiple="true" label="Output of PycoQC"/> + <expand macro="pycoqc_form"/> </when> <when value="qualimap"> - <param name="input" type="data" format="txt,tabular,tsv" multiple="true" label="Output of Qualimap BamQC" help="First result input should be genome_coverage (default from tool output). Run the Flatten Collection tool to keep all output in one report" /> + <expand macro="qualimap_form"/> </when> <when value="quast"> <param name="input" type="data" format="tabular,tsv" multiple="true" label="Output of Quast"/> </when> <when value="rseqc"> - <repeat name="output" title="RSeQC output" min="1"> - <conditional name="type"> - <param name="type" type="select" label="Type of RSeQC output?"> - <option value="bam_stat">BAM/SAM mapping stats</option> - <option value="gene_body_coverage">Gene body coverage</option> - <option value="infer_experiment">Infer experiment</option> - <option value="inner_distance">Inner distance</option> - <option value="junction_annotation">Junction annotation</option> - <option value="junction_saturation">Junction saturation</option> - <option value="read_distribution">Read distribution</option> - <option value="read_duplication_pos">Read duplication</option> - <option value="read_gc">Read GC</option> - </param> - <when value="bam_stat"> - <param name="input" type="data" format="txt,tabular" multiple="true" label="RSeQC BAM stat: output file" help="It should contain 'Proper-paired reads map to different chrom:'"/> - </when> - <when value="gene_body_coverage"> - <param name="input" type="data" format="txt" multiple="true" label="RSeQC gene body coverage: stats file"/> - </when> - <when value="infer_experiment"> - <param name="input" type="data" format="txt" multiple="true" label="RSeQC infer experiment: configuration output" help="It should contain 'Fraction of reads explained by'"/> - </when> - <when value="inner_distance"> - <param name="input" type="data" format="txt" multiple="true" label="RSeQC inner distance: frequency file"/> - </when> - <when value="junction_annotation"> - <param name="input" type="data" format="txt" multiple="true" label="RSeQC junction annotation: stats file" help="It should contain 'Partial Novel Splicing Junctions:'"/> - </when> - <when value="junction_saturation"> - <param name="input" type="data" format="txt" multiple="true" label="RSeQC junction saturation: junction saturation plot Rscript file"/> - </when> - <when value="read_distribution"> - <param name="input" type="data" format="txt" multiple="true" label="RSeQC read distribution: stats output" help="It should contain 'Group Total_bases Tag_count Tags/Kb'"/> - </when> - <when value="read_duplication_pos"> - <param name="input" type="data" format="xls" multiple="true" label="RSeQC read duplication: positions XLS file"/> - </when> - <when value="read_gc"> - <param name="input" type="data" format="csv,xls,tabular" multiple="true" label="RSeQC read GC output"/> - </when> - </conditional> - </repeat> + <expand macro="rseqc_form"/> </when> <when value="samblaster"> <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Samblaster" help="It should contain 'samblaster: Version'"/> </when> <when value="samtools"> - <repeat name="output" title="Samtools output" min="1"> - <conditional name="type"> - <param name="type" type="select" label="Type of Samtools output?"> - <option value="stats">stats</option> - <option value="flagstat">flagstat</option> - <option value="idxstats">idxstats</option> - <option value="rmdup">rmdup</option> - </param> - <when value="stats"> - <param name="input" type="data" format="txt" multiple="true" label="Samtools stats output" help="It should contain 'This file was produced by samtools stats'"/> - </when> - <when value="flagstat"> - <param name="input" type="data" format="txt" multiple="true" label="Samtools flagstat output" help="It should contain 'in total (QC-passed reads + QC-failed reads)'"/> - </when> - <when value="idxstats"> - <param name="input" type="data" format="txt" multiple="true" label="Samtools idxstats output"/> - </when> - <when value="rmdup"> - <param name="input" type="data" format="txt" multiple="true" label="Samtools rmdup output" help="It should contain '[bam_rmdup'"/> - </when> - </conditional> - </repeat> + <expand macro="samtools_form"/> </when> <when value="slamdunk"> <param name="input" type="data" format="txt,tabular" multiple="true" label="Output of Slamdunk Alleyoop" help="It should contain '# slamdunk'"/> @@ -490,50 +338,16 @@ <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?"> - <option value="log">Log</option> - <option value="genecounts">Gene counts</option> - </param> - <when value="log"> - <param name="input" type="data" format="txt" multiple="true" label="STAR log output"/> - </when> - <when value="genecounts"> - <param name="input" type="data" format="tabular,tsv" multiple="true" label="STAR gene count output"/> - </when> - </conditional> - </repeat> + <expand macro="star_form"/> </when> <when value="tophat"> <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of TopHat2"/> </when> <when value="trimmomatic"> - <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Trimmomatic" help="It should contain 'TTrimmomatic'"/> + <expand macro="trimmomatic_form"/> </when> <when value="vcftools"> - <repeat name="output" title="VCFTools output" min="1"> - <conditional name="type"> - <param name="type" type="select" label="Type of VCFTools output?"> - <option value="relatedness2">relatedness2</option> - <option value="tstv_by_count">tstv_by_count</option> - <option value="tstv_by_qual">tstv_by_qual</option> - <option value="tstv_summary">tstv_summary</option> - </param> - <when value="relatedness2"> - <param name="input" type="data" format="txt" multiple="true" label="VCFTools relatedness2 output"/> - </when> - <when value="tstv_by_count"> - <param name="input" type="data" format="tabular,tsv" multiple="true" label="VCFTools TsTV count output"/> - </when> - <when value="tstv_by_qual"> - <param name="input" type="data" format="tabular" multiple="true" label="VCFTools TsTV qual output"/> - </when> - <when value="tstv_summary"> - <param name="input" type="data" format="txt" multiple="true" label="VCFTools TsTV summary output"/> - </when> - </conditional> - </repeat> + <expand macro="vcftools_form"/> </when> <when value="custom_content"> <param argument="plot_type" label="The plot type to visualise the data with" type="select"> @@ -543,11 +357,11 @@ <option value="generalstats">generalstats</option> <option value="table">table</option> </param> - <param argument="section_name" label="Section name" type="text" help="Nice name used for the report section header" /> - <param argument="title" label="Title" type="text" help="Plot title" /> - <param argument="description" label="Description" type="text" help="Introductory text to be printed under the section header" /> - <param argument="xlab" label="X axis label" type="text" /> - <param argument="ylab" label="Y axis label" type="text" /> + <param argument="section_name" label="Section name" type="text" help="Nice name used for the report section header"/> + <param argument="title" label="Title" type="text" help="Plot title"/> + <param argument="description" label="Description" type="text" help="Introductory text to be printed under the section header"/> + <param argument="xlab" label="X axis label" type="text"/> + <param argument="ylab" label="Y axis label" type="text"/> <param name="input" type="data" format="tabular,tsv" multiple="true" label="Data files"/> </when> </conditional> @@ -555,12 +369,12 @@ <param name="title" type="text" value="" optional="true" label="Report title" help="It is printed as page header"> <sanitizer invalid_char=""> <valid initial="string.letters,string.digits"> - <add value="," /> - <add value=":" /> - <add value="-" /> - <add value="_" /> - <add value=" " /> - <add value="." /> + <add value=","/> + <add value=":"/> + <add value="-"/> + <add value="_"/> + <add value=" "/> + <add value="."/> </valid> </sanitizer> <validator type="regex">[0-9a-zA-Z,: _.-]+</validator> @@ -568,561 +382,73 @@ <param name="comment" type="text" value="" optional="true" label="Custom comment" help="It will be printed at the top of the report"> <sanitizer invalid_char=""> <valid initial="string.letters,string.digits"> - <add value="," /> - <add value=":" /> - <add value="-" /> - <add value="_" /> - <add value=" " /> - <add value="." /> + <add value=","/> + <add value=":"/> + <add value="-"/> + <add value="_"/> + <add value=" "/> + <add value="."/> </valid> </sanitizer> <validator type="regex">[0-9a-zA-Z,: _.-]+</validator> </param> <param argument="--flat" type="boolean" truevalue="--flat" falsevalue="" checked="false" label="Use only flat plots (non-interactive images)" help="To consume less disk space and resources to display. Used by default when there are 100 or more samples."/> <param argument="--export" type="boolean" truevalue="--export" falsevalue="" checked="false" label="Output the multiQC plots raw data?" help="This will output a file for each plot containing the raw data used to generate the plot"/> - <param name="saveLog" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output the multiQC log file?" help="This is mostly useful for debugging purposes"/> </inputs> <outputs> - <data name="html_report" format="html" from_work_dir="report.html" label="${tool.name} on ${on_string}: Webpage" /> - <data name="log" format="txt" from_work_dir="report_data/multiqc.log" label="${tool.name} on ${on_string}: Log"> - <filter>saveLog</filter> - </data> - <collection name="stats" type="list" label="${tool.name} on ${on_string}: Stats"> - <discover_datasets pattern="multiqc_(?P<designation>.+)\.txt" format="tabular" directory="report_data" /> - </collection> + <data name="html_report" format="html" from_work_dir="report.html" label="${tool.name} on ${on_string}: Webpage"/> + <data name="stats" format="tabular" from_work_dir="report_data/multiqc_general_stats.txt" label="${tool.name} on ${on_string}: Stats"/> <collection name="plots" type="list" label="${tool.name} on ${on_string}: Plots"> - <discover_datasets pattern="mqc_(?P<designation>.+)\.txt" format="tabular" directory="report_data" /> + <discover_datasets pattern="(?P<designation>.+)\.txt" format="tabular" directory="plots"/> <filter>export</filter> </collection> </outputs> <tests> - <!--Test 01--> - <test expect_num_outputs="4"> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="cutadapt" /> - <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> - </conditional> - </repeat> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="flexbar" /> - <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"> - <conditional name="software_cond"> - <param name="software" value="trimmomatic" /> - <param name="input" value="trimmomatic.txt" /> - </conditional> - </repeat> - <param name="title" value="Title of the report"/> - <param name="comment" value="Commment for the report"/> - <param name="flat" value="true"/> - <param name="export" value="true"/> - <param name="saveLog" value="true"/> - <output name="html_report"> - <assert_contents> - <has_text text="Title of the report" /> - <has_text text="Commment for the report" /> - <has_text text="cutadapt_trimmed_sequences_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"> - <assert_contents> - <has_text_matching expression="\[INFO \] MultiQC complete$"/> - </assert_contents> - </output> - <output_collection name="stats" type="list" count="10"> - <expand macro="element_assert" name="cutadapt" columns="9" lines="2" text="dataset_33"/> - <expand macro="element_assert" name="fastp" columns="2" lines="3" text="R1_fq"/> - <expand macro="element_assert" name="fastqc" columns="22" lines="3" text="poulet5_1"/> - <expand macro="element_assert" name="flexbar" columns="11" lines="2" text="result_right"/> - <expand macro="element_assert" name="general_stats" columns="20" lines="11" text="bwa-mem-fastq1_fq"/> - <expand macro="element_assert" name="slamdunk_readrates_plus" columns="13" lines="3" text="slamdunk_reads1_overallrates_csv"/> - <expand macro="element_assert" name="slamdunk_readrates_minus" columns="13" lines="3" text="slamdunk_reads1_overallrates_csv"/> - <expand macro="element_assert" name="sortmerna" columns="22" lines="2" text="25839_merged"/> - <expand macro="element_assert" name="sources" columns="4" lines="7" text="Module"/> - <expand macro="element_assert" name="trimmomatic" columns="6" lines="2" text="C2"/> - </output_collection> - <output_collection name="plots" type="list" count="29"/> - </test> - <!--Test 02--> - <test expect_num_outputs="2"> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="bismark" /> - <repeat name="output"> - <param name="type" value="align"/> - <param name="input" value="bismark.txt"/> - </repeat> - </conditional> - </repeat> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="bowtie2" /> - <param name="input" value="bowtie2_1.txt,bowtie2_2.txt" /> - </conditional> - </repeat> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="hisat2" /> - <param name="input" value="hisat2_1.txt,hisat2_2.txt" /> - </conditional> - </repeat> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="hicexplorer" /> - <param name="input" value="hicexplorer1.log,hicexplorer1.log,hicexplorer2.log" /> - </conditional> - </repeat> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="kallisto" /> - <param name="input" value="kallisto_1.txt,kallisto_2.txt" /> - </conditional> - </repeat> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="macs2" /> - <param name="input" value="macs_1.txt,macs_2.txt" /> - </conditional> - </repeat> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="star" /> - <repeat name="output"> - <conditional name="type"> - <param name="type" value="log"/> - <param name="input" value="star_log.txt" /> - </conditional> - </repeat> - <repeat name="output"> - <conditional name="type"> - <param name="type" value="genecounts"/> - <param name="input" value="star_counts.txt" /> - </conditional> - </repeat> - </conditional> - </repeat> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="tophat" /> - <param name="input" value="tophat.txt" /> - </conditional> - </repeat> - <param name="saveLog" value="false"/> - <output name="html_report"> - <assert_contents> - <has_text text="bismark-alignment" /> - <has_text text="bowtie2_se_plot" /> - <has_text text="hisat2_se_plot" /> - <has_text text="kallisto_alignment" /> - <has_text text="MACS2" /> - <has_text text="star_alignment_plot" /> - <has_text text="tophat_alignment" /> - <has_text text="hicexplorer" /> - <has_text text="hicexplorer1_log_1" /> - </assert_contents> - </output> - <output_collection name="stats" type="list" count="11"> - <expand macro="element_assert" name="bismark_alignment" columns="21" lines="2" text="bismark_txt_SE_report"/> - <expand macro="element_assert" name="bowtie2" columns="7" lines="3" text="bowtie2_1_txt"/> - <expand macro="element_assert" name="cutadapt" columns="9" lines="5" text="HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2"/> - <expand macro="element_assert" name="general_stats" columns="22" lines="19" text="treat2"/> - <expand macro="element_assert" name="hicexplorer" columns="41" lines="4" text="hicexplorer_3_hicexplorer2_log_small_test_rf"/> - <expand macro="element_assert" name="hisat2" columns="6" lines="3" text="hisat2_2_txt"/> - <expand macro="element_assert" name="kallisto" columns="6" lines="3" text="HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1"/> - <expand macro="element_assert" name="macs" columns="12" lines="3" text="treat2"/> - <expand macro="element_assert" name="sources" columns="4" lines="18" text="Cutadapt"/> - <expand macro="element_assert" name="star" columns="27" lines="2" text="star_log_txt"/> - <expand macro="element_assert" name="tophat.txt" columns="9" lines="2" text="tophat_txtalign"/> - </output_collection> - </test> - <!--Test 03--> - <test expect_num_outputs="2"> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="bamtools" /> - <param name="input" value="bamtools.txt" /> - </conditional> - </repeat> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="bcftools" /> - <param name="input" value="bcftools.txt" /> - </conditional> - </repeat> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="busco" /> - <param name="input" value="busco.txt" /> - </conditional> - </repeat> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="deeptools" /> - <repeat name="output"> - <param name="type" value="bamPEFragmentSize"/> - <param name="input" value="deeptools_bamPEFragmentSize.txt"/> - </repeat> - <repeat name="output"> - <param name="type" value="estimateReadFiltering"/> - <param name="input" value="deeptools_estimateReadFiltering.txt"/> - </repeat> - <repeat name="output"> - <param name="type" value="plotCoverageStdout"/> - <param name="input" value="deeptools_plotCoverageStdout.txt"/> - </repeat> - <repeat name="output"> - <param name="type" value="plotCoverageOutRawCounts"/> - <param name="input" value="deeptools_plotCoverageOutRawCounts.txt"/> - </repeat> - <repeat name="output"> - <param name="type" value="plotEnrichment"/> - <param name="input" value="deeptools_plotEnrichment.txt"/> - </repeat> - <repeat name="output"> - <param name="type" value="plotFingerprintOutRawCounts"/> - <param name="input" value="deeptools_plotFingerprintOutRawCounts.txt"/> - </repeat> - </conditional> - </repeat> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="featureCounts" /> - <param name="input" value="featureCounts.txt" /> - </conditional> - </repeat> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="gatk" /> - <repeat name="output"> - <param name="type" value="base_recalibrator"/> - <param name="input" value="gatk_BaseRecalibrator.txt"/> - </repeat> - <repeat name="output"> - <param name="type" value="varianteval"/> - <param name="input" value="gatk_varianteval.txt"/> - </repeat> - </conditional> - </repeat> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="htseq" /> - <param name="input" value="htseq.txt" /> - </conditional> - </repeat> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="picard" /> - <repeat name="output"> - <param name="type" value="gcbias"/> - <param name="input" value="picard_collectGcBias.txt"/> - </repeat> - <repeat name="output"> - <param name="type" value="insertsize"/> - <param name="input" value="picard_CollectInsertSizeMetrics.txt"/> - </repeat> - <repeat name="output"> - <param name="type" value="markdups"/> - <param name="input" value="picard_MarkDuplicates.txt"/> - </repeat> - <repeat name="output"> - <param name="type" value="basedistributionbycycle"/> - <param name="input" value="picard_CollectBaseDistributionByCycle.txt"/> - </repeat> - <repeat name="output"> - <param name="type" value="rnaseqmetrics"/> - <param name="input" value="picard_CollectRnaSeqMetrics.txt"/> - </repeat> - <repeat name="output"> - <param name="type" value="alignment_metrics"/> - <param name="input" value="picard_CollectAlignmentSummaryMetrics.txt"/> - </repeat> - </conditional> - </repeat> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="prokka" /> - <param name="input" value="prokka_1.txt,prokka_2.txt" /> - </conditional> - </repeat> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="qualimap" /> - <param name="input" value="genome_results.txt" /> - </conditional> - </repeat> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="quast" /> - <param name="input" value="quast.tsv" /> - </conditional> - </repeat> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="rseqc" /> - <repeat name="output"> - <conditional name="type"> - <param name="type" value="read_gc"/> - <param name="input" value="rseqc.txt"/> - </conditional> - </repeat> - </conditional> - </repeat> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="samblaster" /> - <param name="input" value="samblaster.txt" /> - </conditional> - </repeat> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="samtools" /> - <repeat name="output"> - <conditional name="type"> - <param name="type" value="stats"/> - <param name="input" value="samtools_stats.txt"/> - </conditional> - </repeat> - <repeat name="output"> - <conditional name="type"> - <param name="type" value="flagstat"/> - <param name="input" value="samtools_flagstat.txt"/> - </conditional> - </repeat> - <repeat name="output"> - <conditional name="type"> - <param name="type" value="idxstats"/> - <param name="input" value="samtools_idxstats.txt"/> - </conditional> - </repeat> - </conditional> - </repeat> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="snpeff" /> - <param name="input" value="snpeff.csv" ftype="csv" /> - </conditional> - </repeat> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="vcftools" /> - <repeat name="output"> - <conditional name="type"> - <param name="type" value="tstv_by_qual"/> - <param name="input" value="vcftools.txt"/> - </conditional> - </repeat> - <param name="input" value="vcftools.txt" /> - </conditional> - </repeat> - <output name="html_report"> - <assert_contents> - <has_text text="bamtools-stats" /> - <has_text text="bcftools_stats_indel-lengths" /> - <has_text text="busco-lineage-fungi_odb9" /> - <has_text text="deeptools" /> - <has_text text="featureCounts_assignment_plot" /> - <has_text text="gatk_varianteval_variant_plot" /> - <has_text text="htseq_assignment_plot" /> - <has_text text="picard_alignment_readlength" /> - <has_text text="picard-rna-assignment" /> - <has_text text="picard-markduplicates" /> - <has_text text="picard-insertsize" /> - <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_collection name="stats" type="list" count="21"> - <expand macro="element_assert" name="bamtools_stats" columns="20" lines="2" text="bamtools_txt"/> - <expand macro="element_assert" name="bcftools_stats" columns="28" lines="2" text="Test1"/> - <expand macro="element_assert" name="busco" columns="8" lines="2" text="busco_txt"/> - <expand macro="element_assert" name="featureCounts" columns="14" lines="7" text="5: TopHat on data 1, data 14, and data 13"/> - <expand macro="element_assert" name="gatk_varianteval" columns="12" lines="2" text="gatk_varianteval_txt"/> - <expand macro="element_assert" name="general_stats" columns="44" lines="23" text="x_bam"/> - <expand macro="element_assert" name="htseq" columns="9" lines="2" text="htseq_txt"/> - <expand macro="element_assert" name="picard_AlignmentSummaryMetrics" columns="26" lines="2" text="D11_H4K16ac_Rep1_R1_fastq_gz"/> - <expand macro="element_assert" name="picard_RnaSeqMetrics" columns="27" lines="2" text="picard_CollectRnaSeqMetrics_bam"/> - <expand macro="element_assert" name="picard_baseContent" columns="11" lines="2" text="D11_H4K16ac_Rep1_R1_fastq_gz"/> - <expand macro="element_assert" name="picard_dups" columns="10" lines="2" text="dataset_114"/> - <expand macro="element_assert" name="picard_insertSize" columns="23" lines="2" text="dataset_197_FR"/> - <expand macro="element_assert" name="prokka" columns="11" lines="3" text="Sample2"/> - <expand macro="element_assert" name="qualimap_bamqc_genome_results" columns="12" lines="2" text="x_bam"/> - <expand macro="element_assert" name="quast" columns="50" lines="2" text="14892_1#15"/> - <expand macro="element_assert" name="samblaster" columns="5" lines="2" text="virtual-normal"/> - <expand macro="element_assert" name="samtools_flagstat" columns="34" lines="2" text="samtools_flagstat_txt"> - <has_text text="samtools_flagstat" /> - <has_text text="mapped_passed" /> - <has_text text="20689039" /> - </expand> - <expand macro="element_assert" name="samtools_idxstats" columns="68" lines="2" text="samtools_idxstats_txt_idxstat"/> - <expand macro="element_assert" name="samtools_stats" columns="40" lines="2" text="samtools_stats_txt"/> - <expand macro="element_assert" name="snpeff" columns="169" lines="2" text="snpeff_csv"/> - <expand macro="element_assert" name="sources" columns="4" lines="33" text="Bamtools"/> - </output_collection> - </test> - <!--Test 04--> - <test expect_num_outputs="2"> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="custom_content" /> - <param name="cc_select" value="manual" /> - <param name="plot_type" value="linegraph" /> - <param name="section_name" value="BPC" /> - <param name="description" value="Sum of intensity (Y) of the most intense peaks at each retention time(X)" /> - <param name="xlab" value="Retention Time" /> - <param name="ylab" value="Base Peak Intensity" /> - <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="1110578" delta="500" /> - </assert_contents> - </output> - <output_collection name="stats" type="list" count="1"/> - </test> - <!--Test 05--> - <test expect_num_outputs="3"> - <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> - </conditional> - </repeat> - <param name="title" value="Title of the report"/> - <param name="comment" value="Commment for the report"/> - <param name="flat" value="true"/> - <param name="export" value="true"/> - <output name="html_report"> - <assert_contents> - <has_text text="Title of the report" /> - <has_text text="Commment for the report" /> - <has_text text="fastqc_seq_heatmap_key_t" /> - </assert_contents> - </output> - <output_collection name="stats" type="list" count="3"> - <expand macro="element_assert" name="fastqc" columns="22" lines="3" text="poulet5_2"/> - <expand macro="element_assert" name="general_stats" columns="6" lines="3" text="poulet5_2"/> - <expand macro="element_assert" name="sources" columns="4" lines="3" text="FastQC"/> - </output_collection> - <output_collection name="plots" type="list" count="7"> - <element name="fastqc_per_base_sequence_quality_plot_1" file="mqc_fastqc_per_base_sequence_quality_plot_1.txt" compare="sim_size" delta="10"/> - </output_collection> - </test> - <!--Test 06--> - <test expect_num_outputs="2"> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="pycoqc" /> - <param name="input" value="pycoqc.json"/> - </conditional> - </repeat> - <param name="title" value="Title of the report"/> - <param name="comment" value="Commment for the report"/> - <!-- <param name="flat" value="true"/> --> - <output name="html_report"> - <assert_contents> - <has_text text="Title of the report" /> - <has_text text="Commment for the report" /> - <has_text text="General Statistics" /> - <has_text text="pycoqc_count_plot" /> - <has_text text="pycoqc_read_len_plot" /> - <has_text text="pycoqc_read_qual_plot" /> - </assert_contents> - </output> - <output_collection name="stats" type="list" count="2"/> - </test> - <!--Test 07--> - <test expect_num_outputs="2"> - <repeat name="results"> - <conditional name="software_cond"> - <param name="software" value="rseqc" /> - <repeat name="output"> - <conditional name="type"> - <param name="type" value="junction_annotation"/> - <param name="input" value="junction_annotation.txt"/> - </conditional> - </repeat> - <repeat name="output"> - <conditional name="type"> - <param name="type" value="junction_saturation"/> - <param name="input" value="junction_saturation.txt"/> - </conditional> - </repeat> - </conditional> - </repeat> - <param name="title" value="RSEQC report"/> - <!-- <param name="flat" value="true"/> --> - <output name="html_report"> - <assert_contents> - <has_text text="RSEQC report" /> - <has_text text="Junction Annotation" /> - <has_text text="Junction Saturation" /> - </assert_contents> - </output> - <output_collection name="stats" type="list" count="2"/> - </test> + <expand macro="general_tests"/> + <expand macro="bcftools_test"/> + <expand macro="bowtie2_test"/> + <expand macro="fastqc_test"/> + <expand macro="trimmomatic_test"/> + <!-- Test 10 --> + <expand macro="flexbar_test"/> + <expand macro="fastp_test"/> + <expand macro="bismark_test"/> + <expand macro="rseqc_test"/> + <expand macro="star_test"/> + <expand macro="cutadapt_test"/> + <expand macro="samtools_test"/> + <expand macro="busco_test"/> + <expand macro="featurecounts_test"/> + <expand macro="picard_test"/> + <!-- Test 20 --> + <expand macro="qualimap_test"/> + <expand macro="gatk_test"/> + <expand macro="bamtools_test"/> + <expand macro="pycoqc_test"/> + + <!--expand macro="vcftools_test"/> Does not work, did it ever worked? --> + </tests> <help><![CDATA[ **What it does** -`MultiQC <http://multiqc.info/>`_ aggregates results from bioinformatics analyses across many samples into a single report. It takes results of multiple analyses and creates a report that can be viewed as a single beautiful web-page. It's a general use tool, perfect for summarizing the output from numerous bioinformatics tools. +`MultiQC <http://multiqc.info/>`_ aggregates results from bioinformatics analyses across many samples into a single report. +It takes results of multiple analyses and creates a report that can be viewed as a single beautiful web-page. +It's a general use tool, perfect for summarizing the output from numerous bioinformatics tools. **Inputs** -MultiQC takes software output summaries/logs and creates a single report from them. You need to tell the tool which software was used to generate the report. This is done using the **Software name** dropdown. At present only the Galaxy tools found in the ToolShed produce logs that can used with MultiQC - ----- +MultiQC takes software output summaries/logs and creates a single report from them. You need to tell the tool which software was used to generate the report. +This is done using the **Software name** dropdown. At present only the Galaxy tools found in the ToolShed produce logs that can used with MultiQC -The first integration of this tool was made by -`@cmonjeau <https://github.com/cmonjeau>`_ and `@yvanlebras <https://github.com/yvanlebras>`_. -It is now maintained by the `Intergalactic Utilities Commission <https://galaxyproject.org/iuc>`_. ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/btw354</citation> </citations> + <creator> + <person givenName="Cyril" familyName="Monjeaud" url="https://github.com/cmonjeau"/> + <person givenName="Yvan" familyName="Le Bras" url="https://github.com/yvanlebras"/> + <person givenName="Bérénice" familyName="Batut" url="https://github.com/bebatut"/> + <person givenName="Björn" familyName="Grüning" url="https://github.com/bgruening"/> + </creator> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_plugin.xml Mon Sep 02 14:22:54 2024 +0000 @@ -0,0 +1,119 @@ +<macros> + <token name="@PICARD_COMMAND@"><![CDATA[ + #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) + #if str($repeat2.type) == "alignment_metrics" + #set $pattern = "picard.analysis.AlignmentSummaryMetrics" + @LN_2_FILES@ + #elif str($repeat2.type) == "basedistributionbycycle" + #set $pattern = "picard.analysis.BaseDistributionByCycleMetrics" + @LN_2_FILES@ + #elif str($repeat2.type) == "gcbias" + #set $pattern = "picard.analysis.GcBias" + @LN_2_FILES@ + #elif str($repeat2.type) == "hsmetrics" + #set $pattern = "picard.analysis.directed.HsMetrics" + @ @ + #elif str($repeat2.type) == "insertsize" + #set $pattern = "picard.analysis.InsertSizeMetrics" + @LN_2_FILES@ + #elif str($repeat2.type) == "markdups" + #set $pattern = "MarkDuplicates" + @LN_2_FILES@ + #elif str($repeat2.type) == "oxogmetrics" + #set $pattern = "picard.analysis.CollectOxoGMetrics" + @LN_2_FILES@ + #elif str($repeat2.type) == "pcr_metrics" + #set $pattern = "picard.analysis.directed.TargetedPcrMetrics" + @LN_2_FILES@ + #elif str($repeat2.type) == "rnaseqmetrics" + #set $pattern = "Collect" + @LN_2_FILES@ + #elif str($repeat2.type) == "rrbs_metrics" + #set $pattern = "picard.analysis.RrbsSummaryMetrics" + @LN_2_FILES@ + #elif str($repeat2.type) == "wgs_metrics" + #set $pattern = "picard.analysis.CollectWgsMetrics$WgsMetrics" + @LN_2_FILES@ + #end if + #end for + ]]></token> + <xml name="picard_form"> + <repeat name="output" title="Picard output" min="1"> + <param name="type" type="select" label="Type of Picard output?"> + <option value="alignment_metrics">Alignment metrics</option> + <option value="basedistributionbycycle">Base distribution by cycle</option> + <option value="gcbias">GC bias</option> + <option value="hsmetrics">HS Metrics</option> + <option value="insertsize">Insert size</option> + <option value="markdups">Markdups</option> + <option value="oxogmetrics">Oxog metrics</option> + <option value="pcr_metrics">PCR metrics</option> + <option value="rnaseqmetrics">RNA Seq metrics</option> + <option value="rrbs_metrics">RRBS metrics</option> + <option value="wgs_metrics">WGS metrics</option> + </param> + <param name="input" type="data" format="txt" multiple="true" label="Picard output"/> + </repeat> + </xml> + <xml name="picard_test"> + <test expect_num_outputs="3"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="picard"/> + <repeat name="output"> + <param name="type" value="gcbias"/> + <param name="input" value="picard_collectGcBias.txt"/> + </repeat> + <repeat name="output"> + <param name="type" value="insertsize"/> + <param name="input" value="picard_CollectInsertSizeMetrics.txt"/> + </repeat> + <repeat name="output"> + <param name="type" value="markdups"/> + <param name="input" value="picard_MarkDuplicates.txt"/> + </repeat> + <repeat name="output"> + <param name="type" value="basedistributionbycycle"/> + <param name="input" value="picard_CollectBaseDistributionByCycle.txt"/> + </repeat> + <repeat name="output"> + <param name="type" value="rnaseqmetrics"/> + <param name="input" value="picard_CollectRnaSeqMetrics.txt"/> + </repeat> + <repeat name="output"> + <param name="type" value="alignment_metrics"/> + <param name="input" value="picard_CollectAlignmentSummaryMetrics.txt"/> + </repeat> + </conditional> + </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> + <param name="flat" value="true"/> + <param name="export" value="true"/> + <output name="html_report"> + <assert_contents> + <has_text text="Title of the report"/> + <has_text text="Commment for the report"/> + <has_text text="picard_CollectRnaSeqMetrics_bam"/> + <has_text text="picard_alignment_readlength"/> + <has_text text="picard-rna-assignment"/> + <has_text text="picard-markduplicates"/> + <has_text text="picard-insertsize"/> + <has_text text="picard-gcbias"/> + </assert_contents> + </output> + <output name="stats"> + <assert_contents> + <has_text text="picard_CollectRnaSeqMetrics_bam"/> + <has_text text="InsertSizeMetrics_mqc_generalstats_picard_insertsizemetrics_summed_median"/> + <has_text text="picard_CollectRnaSeqMetrics_bam"/> + <has_text text="RnaSeqMetrics_mqc_generalstats_picard_rnaseqmetrics_PCT_MRNA_BASES"/> + <has_text text="NA"/> + <has_n_lines n="4"/> + <has_n_columns n="6"/> + </assert_contents> + </output> + <output_collection name="plots" type="list" count="3"/> + </test> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pycoqc_plugin.xml Mon Sep 02 14:22:54 2024 +0000 @@ -0,0 +1,39 @@ +<macros> + <token name="@PYCOQC_COMMAND@"><![CDATA[ + #set $pattern = "\"pycoqc\":" + @LN_FILES@ + ]]></token> + <xml name="pycoqc_form"> + <param name="input" type="data" format="txt,json" multiple="true" label="Output of PycoQC"/> + </xml> + <!-- add here your test files and tests, the more stringent the better --> + <xml name="pycoqc_test"> + <test expect_num_outputs="2"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="pycoqc"/> + <param name="input" value="pycoqc.json"/> + </conditional> + </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> + <!-- <param name="flat" value="true"/> --> + <output name="html_report"> + <assert_contents> + <has_text text="Title of the report"/> + <has_text text="Commment for the report"/> + <has_text text="General Statistics"/> + <has_text text="pycoqc_count_plot"/> + <has_text text="pycoqc_read_len_plot"/> + <has_text text="pycoqc_read_qual_plot"/> + </assert_contents> + </output> + <output name="stats" ftype="tabular"> + <assert_contents> + <has_text text="pycoQC_mqc_generalstats_pycoqc_passed_median_read_length"/> + <has_text text="pycoqc_json"/> + </assert_contents> + </output> + </test> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qualimap_plugin.xml Mon Sep 02 14:22:54 2024 +0000 @@ -0,0 +1,62 @@ +<macros> + <token name="@QUALIMAP_COMMAND@"><![CDATA[ + #for $file in $repeat.software_cond.input + #if re.search("genome_results", str($file.element_identifier)) + sample="\$(grep 'bam file = ' $file | sed 's/bam file = //g' | sed 's: ::g')" && + dir_name="$software_dir/\${sample}" && + mkdir -p \${dir_name} && + filepath_1="\${dir_name}/genome_results.txt" && + ln -sf '$file' \${filepath_1} && + #elif re.search("coverage_histogram", str($file.element_identifier)) + nested_dir_name="\${dir_name}/raw_data_qualimapReport/" && + mkdir -p \${nested_dir_name} && + filepath_2="\${nested_dir_name}/coverage_histogram.txt" && + ln -sf '$file' \${filepath_2} && + #elif re.search("gc-content_distribution", str($file.element_identifier)) + nested_dir_name="\${dir_name}/raw_data_qualimapReport/" && + mkdir -p \${nested_dir_name} && + filepath_3="\${nested_dir_name}/mapped_reads_gc-content_distribution.txt" && + ln -sf '$file' \${filepath_3} && + #else + #pass + #end if + #end for + ]]></token> + <xml name="qualimap_form"> + <param name="input" type="data" format="txt,tabular,tsv" multiple="true" label="Output of Qualimap BamQC" help="First result input should be genome_coverage (default from tool output). Run the Flatten Collection tool to keep all output in one report"/> + </xml> + <!-- add here your test files and tests, the more stringent the better --> + <xml name="qualimap_test"> + <test expect_num_outputs="3"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="qualimap"/> + <param name="input" value="genome_results.txt"/> + </conditional> + </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> + <param name="flat" value="true"/> + <param name="export" value="true"/> + <output name="html_report"> + <assert_contents> + <has_text text="Title of the report"/> + <has_text text="Commment for the report"/> + <has_text text="qualimap"/> + </assert_contents> + </output> + <output name="stats"> + <assert_contents> + <has_text text="BamQC_mqc_generalstats_qualimap_bamqc_mean_coverage"/> + <has_text text="BamQC_mqc_generalstats_qualimap_bamqc_mapped_reads"/> + <has_text text="BamQC_mqc_generalstats_qualimap_bamqc_total_reads"/> + <has_text text="x_bam"/> + <has_text text="0.98"/> + <has_n_lines n="2"/> + <has_n_columns n="6"/> + </assert_contents> + </output> + <output_collection name="plots" type="list" count="0"/> + </test> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rseqc_plugin.xml Mon Sep 02 14:22:54 2024 +0000 @@ -0,0 +1,133 @@ +<macros> + <token name="@RSEQC_COMMAND@"><![CDATA[ + #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) + @CREATE_REPEAT_DIR_2@ + #if str($repeat2.type.type) == "bam_stat" + #set $pattern = "Proper-paired reads map to different chrom:" + @LN_3_FILES@ + #elif str($repeat2.type.type) == "gene_body_coverage" + #for $k, $file in enumerate($repeat2.type.input) + #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.geneBodyCoverage.txt') + ln -s '$file' '$file_path' && + #end for + #elif str($repeat2.type.type) == "inner_distance" + #for $k, $file in enumerate($repeat2.type.input) + #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.inner_distance_freq.txt') + ln -s '${file}' '$file_path' && + #end for + #elif str($repeat2.type.type) == "junction_annotation" + #set $pattern = "Partial Novel Splicing Junctions:" + @LN_3_FILES@ + #elif str($repeat2.type.type) == "read_gc" + #for $k, $file in enumerate($repeat2.type.input) + #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.GC.xls') + ln -s '$file' '$file_path' && + #end for + #elif str($repeat2.type.type) == "junction_saturation" + #for $k, $file in enumerate($repeat2.type.input) + #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.junctionSaturation_plot.r') + ln -s '${file}' '$file_path' && + #end for + #elif str($repeat2.type.type) == "read_distribution" + #set $pattern = "Group Total_bases Tag_count Tags/Kb" + @LN_3_FILES@ + #elif str($repeat2.type.type) == "read_duplication_pos" + #for $k, $file in enumerate($repeat2.type.input) + #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.pos.DupRate.xls') + ln -s '$file' '$file_path' && + #end for + #elif str($repeat2.type.type) == "infer_experiment" + #set $pattern = "Fraction of reads explained by" + #for $file in $repeat2.type.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier)) + grep -q "$pattern" $file || die "'$pattern' not found in the file" && + ln -s '$file' '$file_path' && + #end for + #end if + #end for + ]]></token> + <xml name="rseqc_form"> + <repeat name="output" title="RSeQC output" min="1"> + <conditional name="type"> + <param name="type" type="select" label="Type of RSeQC output?"> + <option value="bam_stat">BAM/SAM mapping stats</option> + <option value="gene_body_coverage">Gene body coverage</option> + <option value="infer_experiment">Infer experiment</option> + <option value="inner_distance">Inner distance</option> + <option value="junction_annotation">Junction annotation</option> + <option value="junction_saturation">Junction saturation</option> + <option value="read_distribution">Read distribution</option> + <option value="read_duplication_pos">Read duplication</option> + <option value="read_gc">Read GC</option> + </param> + <when value="bam_stat"> + <param name="input" type="data" format="txt,tabular" label="RSeQC BAM stat: output file" help="It should contain 'Proper-paired reads map to different chrom:" multiple="true"/> + </when> + <when value="gene_body_coverage"> + <param name="input" type="data" format="txt" label="RSeQC gene body coverage: stats file" multiple="true"/> + </when> + <when value="infer_experiment"> + <param name="input" type="data" format="txt" label="RSeQC infer experiment: configuration output" help="It should contain 'Fraction of reads explained by" multiple="true"/> + </when> + <when value="inner_distance"> + <param name="input" type="data" format="txt" label="RSeQC inner distance: frequency file" multiple="true"/> + </when> + <when value="junction_annotation"> + <param name="input" type="data" format="txt" label="RSeQC junction annotation: stats file" help="It should contain 'Partial Novel Splicing Junctions:" multiple="true"/> + </when> + <when value="junction_saturation"> + <param name="input" type="data" format="txt" label="RSeQC junction saturation: junction saturation plot Rscript file" multiple="true"/> + </when> + <when value="read_distribution"> + <param name="input" type="data" format="txt" label="RSeQC read distribution: stats output" help="It should contain 'Group Total_bases Tag_count Tags/Kb" multiple="true"/> + </when> + <when value="read_duplication_pos"> + <param name="input" type="data" format="xls" label="RSeQC read duplication: positions XLS file" multiple="true"/> + </when> + <when value="read_gc"> + <param name="input" type="data" format="csv,xls,tabular" label="RSeQC read GC output" multiple="true"/> + </when> + </conditional> + </repeat> + </xml> + <xml name="rseqc_test"> + <test expect_num_outputs="3"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="rseqc"/> + <repeat name="output"> + <conditional name="type"> + <param name="type" value="junction_annotation"/> + <param name="input" value="junction_annotation.txt"/> + </conditional> + </repeat> + <repeat name="output"> + <conditional name="type"> + <param name="type" value="junction_saturation"/> + <param name="input" value="junction_saturation.txt"/> + </conditional> + </repeat> + </conditional> + </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> + <param name="flat" value="true"/> + <param name="export" value="true"/> + <output name="html_report"> + <assert_contents> + <has_text text="Title of the report"/> + <has_text text="Commment for the report"/> + <has_text text="rseqc_junction_annotation"/> + <has_text text="rseqc_junction_annotation_junctions_plot"/> + </assert_contents> + </output> + <!-- for unknown reason empty + <output name="stats"> + <assert_contents> + </assert_contents> + </output> --> + <output_collection name="plots" type="list" count="5"/> + </test> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/salmon_plugin.xml Mon Sep 02 14:22:54 2024 +0000 @@ -0,0 +1,62 @@ +<macros> + <!-- not yet finished --> + <token name="@SALMON_COMMAND@"><![CDATA[ + #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) + @CREATE_REPEAT_DIR_2@ + #if str($repeat2.type.type) == "meta" + #for $k, $file in enumerate($repeat2.type.input) + #set file_dir = os.path.join($repeat_dir, 'file_' + str($k)) + #set file_path = os.path.join($file_dir, 'meta_info.json') + mkdir '$file_dir' && + ln -s '$file' '$file_path' && + #end for + #elif str($repeat2.type.type) == "fld" + #for $k, $file in enumerate($repeat2.type.input) + #set file_dir = os.path.join($repeat_dir, 'file_' + str($k)) + #set file_path = os.path.join($file_dir,'flenDist.txt') + mkdir '$file_dir' && + ln -s '$file' '$file_path' && + #end for + #end if + #end for + ]]></token> + <xml name="salmon_form"> + + </xml> + <!-- add here your test files and tests, the more stringent the better --> + <xml name="salmon_test"> + <test expect_num_outputs="3"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="trimmomatic"/> + <param name="input" value="trimmomatic.txt"/> + </conditional> + </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> + <param name="flat" value="true"/> + <param name="export" value="true"/> + <output name="html_report"> + <assert_contents> + <has_text text="Title of the report"/> + <has_text text="Commment for the report"/> + <has_text text="cutadapt_trimmed_sequences_plot"/> + <has_text text="All-in-one FASTQ preprocessor"/> + <has_text text="trimmomatic_plot"/> + </assert_contents> + </output> + <output name="stats"> + <assert_contents> + <has_text text="dataset_33"/> + <has_text text="R1_fq"/> + <has_text text="result_right"/> + <has_text text="25839_merged"/> + <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"/> + </test> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_plugin.xml Mon Sep 02 14:22:54 2024 +0000 @@ -0,0 +1,97 @@ +<macros> + <token name="@SAMTOOLS_COMMAND@"><![CDATA[ + #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) + @CREATE_REPEAT_DIR_2@ + #if str($repeat2.type.type) == "stats" + #set $pattern = "This file was produced by samtools stats" + @LN_3_FILES@ + #elif str($repeat2.type.type) == "flagstat" + #set $pattern = "in total (QC-passed reads + QC-failed reads)" + @LN_3_FILES@ + #elif str($repeat2.type.type) == "idxstats" + #for $file in $repeat2.type.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '_idxstat') + ln -s '$file' '$file_path' && + #end for + #elif str($repeat2.type.type) == "rmdup" + #set $pattern = "[bam_rmdup" + @LN_3_FILES@ + #end if + #end for + ]]></token> + <xml name="samtools_form"> + <repeat name="output" title="Samtools output" min="1"> + <conditional name="type"> + <param name="type" type="select" label="Type of Samtools output?"> + <option value="stats">stats</option> + <option value="flagstat">flagstat</option> + <option value="idxstats">idxstats</option> + <option value="rmdup">rmdup</option> + </param> + <when value="stats"> + <param name="input" type="data" format="txt" multiple="true" label="Samtools stats output" help="It should contain 'This file was produced by samtools stats'"/> + </when> + <when value="flagstat"> + <param name="input" type="data" format="txt" multiple="true" label="Samtools flagstat output" help="It should contain 'in total (QC-passed reads + QC-failed reads)'"/> + </when> + <when value="idxstats"> + <param name="input" type="data" format="txt" multiple="true" label="Samtools idxstats output"/> + </when> + <when value="rmdup"> + <param name="input" type="data" format="txt" multiple="true" label="Samtools rmdup output" help="It should contain '[bam_rmdup'"/> + </when> + </conditional> + </repeat> + </xml> + <!-- add here your test files and tests, the more stringent the better --> + <xml name="samtools_test"> + <test expect_num_outputs="3"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="samtools"/> + <repeat name="output"> + <conditional name="type"> + <param name="type" value="stats"/> + <param name="input" value="samtools_stats.txt"/> + </conditional> + </repeat> + <repeat name="output"> + <conditional name="type"> + <param name="type" value="flagstat"/> + <param name="input" value="samtools_flagstat.txt"/> + </conditional> + </repeat> + <repeat name="output"> + <conditional name="type"> + <param name="type" value="idxstats"/> + <param name="input" value="samtools_idxstats.txt"/> + </conditional> + </repeat> + </conditional> + </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> + <param name="flat" value="true"/> + <param name="export" value="true"/> + <output name="html_report"> + <assert_contents> + <has_text text="Title of the report"/> + <has_text text="Commment for the report"/> + <has_text text="samtools-flagstat-dp"/> + </assert_contents> + </output> + <output name="stats"> + <assert_contents> + <has_text text="samtools_flagstat_txt"/> + <has_text text="mapped_passed"/> + <has_text text="stats_mqc_generalstats_samtools_stats_error_rate"/> + <has_text text="samtools_stats_txt"/> + <has_n_lines n="3"/> + <has_n_columns n="11"/> + </assert_contents> + </output> + <output_collection name="plots" type="list" count="5"/> + </test> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/star_plugin.xml Mon Sep 02 14:22:54 2024 +0000 @@ -0,0 +1,77 @@ +<macros> + <token name="@STAR_COMMAND@"><![CDATA[ + #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) + @CREATE_REPEAT_DIR_2@ + #if str($repeat2.type.type) == "log" + #for $file in $repeat2.type.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '_Log.final.out') + ln -s '$file' '$file_path' && + #end for + #elif str($repeat2.type.type) == "genecounts" + #for $file in $repeat2.type.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '_ReadsPerGene.out.tab') + ln -s '$file' '$file_path' && + #end for + #end if + #end for + ]]></token> + <xml name="star_form"> + <repeat name="output" title="STAR output" min="1"> + <conditional name="type"> + <param name="type" type="select" label="Type of STAR output?"> + <option value="log">Log</option> + <option value="genecounts">Gene counts</option> + </param> + <when value="log"> + <param name="input" type="data" format="txt" label="STAR log output" multiple="true"/> + </when> + <when value="genecounts"> + <param name="input" type="data" format="tabular,tsv" label="STAR gene count output" multiple="true"/> + </when> + </conditional> + </repeat> + </xml> + <xml name="star_test"> + <test expect_num_outputs="3"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="star"/> + <repeat name="output"> + <conditional name="type"> + <param name="type" value="log"/> + <param name="input" value="star_log.txt"/> + </conditional> + </repeat> + <repeat name="output"> + <conditional name="type"> + <param name="type" value="genecounts"/> + <param name="input" value="star_counts.txt"/> + </conditional> + </repeat> + </conditional> + </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> + <param name="flat" value="true"/> + <param name="export" value="true"/> + <output name="html_report"> + <assert_contents> + <has_text text="Title of the report"/> + <has_text text="Commment for the report"/> + <has_text text="star_alignment_plot"/> + </assert_contents> + </output> + <output name="stats"> + <assert_contents> + <has_text text="STAR_mqc_generalstats_star_uniquely_mapped_percent"/> + <has_text text="star_log_txt"/> + <has_n_lines n="2"/> + <has_n_columns n="7"/> + </assert_contents> + </output> + <output_collection name="plots" type="list" count="1"/> + </test> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/template_plugin.xml Mon Sep 02 14:22:54 2024 +0000 @@ -0,0 +1,59 @@ +<macros> + <!-- + This is the TEMPLATE macro for MultiQC + 1. please copy this template_plugin.xml to your own file e.g. trimmomatic_plugin.xml + 2. Replace `TEMPLATE` with the name of the plugin, e.g. `fastqc`. The tokens and xml-names need to be called `trimmomatic_form` or `TRIMMOMATIC_COMMAND` + 3. import your new *_plugin.xml macro into the main multiqc.xml file at the top of the file + 4. add a new option to the main select element, e.g. `<option value="trimmomatic">Trimmomatic</option>` + 5. add the *_COMMAND token to the <command> section. + 6. add the *_test macro to the test section. + 7. remove all unused comments from your new file +--> + <token name="@TEMPLATE_COMMAND@"><![CDATA[ + <!--This pattern is used to check the file content in the @CHECK_LN_FILE@ token. The pattern should be included in the file. --> + #set $pattern = "Trimmomatic" + @LN_FILES@f + ]]></token> + <xml name="TEMPLATE_form"> + <!-- Please add here your input forms specific to your plugin. Keep the name as `input` if you have a single input. + If you have multiple inputs have a look at other plugins, e.g. fastqc + --> + <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Trimmomatic" help="It should contain 'TTrimmomatic'"/> + </xml> + <!-- add here your test files and tests, the more stringent the better --> + <xml name="TEMPLATE_test"> + <test expect_num_outputs="3"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="trimmomatic"/> + <param name="input" value="trimmomatic.txt"/> + </conditional> + </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> + <param name="flat" value="true"/> + <param name="export" value="true"/> + <output name="html_report"> + <assert_contents> + <has_text text="Title of the report"/> + <has_text text="Commment for the report"/> + <has_text text="cutadapt_trimmed_sequences_plot"/> + <has_text text="All-in-one FASTQ preprocessor"/> + <has_text text="trimmomatic_plot"/> + </assert_contents> + </output> + <output name="stats"> + <assert_contents> + <has_text text="dataset_33"/> + <has_text text="R1_fq"/> + <has_text text="result_right"/> + <has_text text="25839_merged"/> + <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"/> + </test> + </xml> +</macros>
--- a/test-data/mqc_fastqc_per_base_sequence_quality_plot_1.txt Sat Dec 10 11:22:18 2022 +0000 +++ b/test-data/mqc_fastqc_per_base_sequence_quality_plot_1.txt Mon Sep 02 14:22:54 2024 +0000 @@ -1,3 +1,3 @@ -Sample 1 2 3 4 5 6 7 8 9 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74 76 78 80 82 84 86 88 90 92 94 96 98 100 -poulet5_1 20.91988023102569 20.71684045861661 20.351574954545285 22.531542025544244 24.673566076408722 25.813099918237516 27.587864804423386 27.598941941168345 27.07115949658203 27.129873548155864 27.009298149330405 27.123565889736383 27.086309823818645 27.07924614241606 27.082520375286073 27.054301117420636 27.06350966402712 27.082996389756914 27.065495857740743 27.09608772106672 27.087097581099798 27.098251253504774 27.05184077595959 27.06521958267531 27.072148859992012 27.065725464720796 27.07168031241483 27.048083061725073 27.04642354460909 27.062865644448927 27.01859629866081 26.994157155710866 27.110127347871376 26.995846540401494 27.00461640700544 26.981614641085088 26.98900313236189 27.001189102815392 26.917739099268616 26.98481793846533 26.89518908041471 26.93677034448514 26.87640237596556 26.906094478605482 26.80463992772047 26.717012197170796 26.46960974280285 26.442842795754324 26.34282375517549 26.03493946215965 25.833215729758187 25.503102494315826 24.52807178671565 23.202399486277717 23.72906749698524 -poulet5_2 20.590586487162543 20.458478471078855 20.178608096352797 22.495204387546714 24.59397272343746 25.77560491172265 26.651378201897337 27.54968284369178 27.089005372429988 27.058984726469017 26.954911162632676 27.066410552214123 27.04552938409328 27.025118630273028 27.019042445557012 27.010315513591614 27.03931879529138 26.978450544896567 27.003714779595967 27.025971722873706 27.017791740868923 27.00628899118533 27.00906294218011 27.034922661648913 27.005346295860726 27.000909094303132 27.004913216028434 26.979999925331065 26.941037674211962 26.99995146519121 26.95084543903468 26.97609847339359 26.99262270906369 26.942271578389317 26.88024222603034 26.866450873439888 26.947610407356386 26.975012040366025 26.966286975124042 26.917634562757375 26.885127441207544 26.846286527110426 26.769134848366058 26.709703975000842 26.551336760637525 26.42626069165836 26.309463541024982 26.127226534353312 25.91885539987082 25.674260497519125 25.371903572535274 24.758753999454918 23.84710415196622 22.40618968149965 23.009550156991438 +Sample 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 +poulet5_1 (1, 20.91988023102569) (2, 20.71684045861661) (3, 20.351574954545285) (4, 22.531542025544244) (5, 24.673566076408722) (6, 25.813099918237516) (7, 27.587864804423386) (8, 27.598941941168345) (9, 27.07115949658203) (10, 27.129873548155864) (12, 27.009298149330405) (14, 27.123565889736383) (16, 27.086309823818645) (18, 27.07924614241606) (20, 27.082520375286073) (22, 27.054301117420636) (24, 27.06350966402712) (26, 27.082996389756914) (28, 27.065495857740743) (30, 27.09608772106672) (32, 27.087097581099798) (34, 27.098251253504774) (36, 27.05184077595959) (38, 27.06521958267531) (40, 27.072148859992012) (42, 27.065725464720796) (44, 27.07168031241483) (46, 27.048083061725073) (48, 27.04642354460909) (50, 27.062865644448927) (52, 27.01859629866081) (54, 26.994157155710866) (56, 27.110127347871376) (58, 26.995846540401494) (60, 27.00461640700544) (62, 26.981614641085088) (64, 26.98900313236189) (66, 27.001189102815392) (68, 26.917739099268616) (70, 26.98481793846533) (72, 26.89518908041471) (74, 26.93677034448514) (76, 26.87640237596556) (78, 26.906094478605482) (80, 26.80463992772047) (82, 26.717012197170796) (84, 26.46960974280285) (86, 26.442842795754324) (88, 26.34282375517549) (90, 26.03493946215965) (92, 25.833215729758187) (94, 25.503102494315826) (96, 24.52807178671565) (98, 23.202399486277717) (100, 23.72906749698524) +poulet5_2 (1, 20.590586487162543) (2, 20.458478471078855) (3, 20.178608096352797) (4, 22.495204387546714) (5, 24.59397272343746) (6, 25.77560491172265) (7, 26.651378201897337) (8, 27.54968284369178) (9, 27.089005372429988) (10, 27.058984726469017) (12, 26.954911162632676) (14, 27.066410552214123) (16, 27.04552938409328) (18, 27.025118630273028) (20, 27.019042445557012) (22, 27.010315513591614) (24, 27.03931879529138) (26, 26.978450544896567) (28, 27.003714779595967) (30, 27.025971722873706) (32, 27.017791740868923) (34, 27.00628899118533) (36, 27.00906294218011) (38, 27.034922661648913) (40, 27.005346295860726) (42, 27.000909094303132) (44, 27.004913216028434) (46, 26.979999925331065) (48, 26.941037674211962) (50, 26.99995146519121) (52, 26.95084543903468) (54, 26.97609847339359) (56, 26.99262270906369) (58, 26.942271578389317) (60, 26.88024222603034) (62, 26.866450873439888) (64, 26.947610407356386) (66, 26.975012040366025) (68, 26.966286975124042) (70, 26.917634562757375) (72, 26.885127441207544) (74, 26.846286527110426) (76, 26.769134848366058) (78, 26.709703975000842) (80, 26.551336760637525) (82, 26.42626069165836) (84, 26.309463541024982) (86, 26.127226534353312) (88, 25.91885539987082) (90, 25.674260497519125) (92, 25.371903572535274) (94, 24.758753999454918) (96, 23.84710415196622) (98, 22.40618968149965) (100, 23.009550156991438)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trimmomatic_plugin.xml Mon Sep 02 14:22:54 2024 +0000 @@ -0,0 +1,40 @@ +<macros> + <token name="@TRIMMOMATIC_COMMAND@"> + <!--This pattern is used to check the file content in the @CHECK_LN_FILE@ token. The pattern should be included in the file. --> + #set $pattern = "Trimmomatic" + @LN_FILES@ +</token> + <xml name="trimmomatic_form"> + <param name="input" type="data" format="txt,tabular,tsv,csv" label="Output of Trimmomatic" help="It should contain 'TTrimmomatic" multiple="true"/> + </xml> + <xml name="trimmomatic_test"> + <test expect_num_outputs="3"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="trimmomatic"/> + <param name="input" value="trimmomatic.txt"/> + </conditional> + </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> + <param name="flat" value="true"/> + <param name="export" value="true"/> + <output name="html_report"> + <assert_contents> + <has_text text="Title of the report"/> + <has_text text="Commment for the report"/> + <has_text text="trimmomatic_plot"/> + </assert_contents> + </output> + <output name="stats"> + <assert_contents> + <has_text text="Trimmomatic_mqc_generalstats_trimmomatic_dropped_pct"/> + <has_text text="C2"/> + <has_n_lines n="2"/> + <has_n_columns n="2"/> + </assert_contents> + </output> + <output_collection name="plots" type="list" count="1"/> + </test> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcftools_plugin.xml Mon Sep 02 14:22:54 2024 +0000 @@ -0,0 +1,94 @@ +<macros> + <token name="@VCFTOOLS_COMMAND@"><![CDATA[ + #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) + @CREATE_REPEAT_DIR_2@ + #if str($repeat2.type.type) == "relatedness2" + #for $file in $repeat2.type.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '.relatedness2') + ln -s '$file' '$file_path' && + #end for + #elif str($repeat2.type) == "tstv_by_count" + #for $file in $repeat2.type.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.count') + ln -s '$file' '$file_path' && + #end for + #elif str($repeat2.type) == "tstv_by_qual" + #for $file in $repeat2.type.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.qual') + ln -s '$file' '$file_path' && + #end for + #elif str($repeat2.type) == "tstv_summary" + #for $file in $repeat2.type.input + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.summary') + ln -s '$file' '$file_path' && + #end for + #end if + #end for + ]]></token> + <xml name="vcftools_form"> + <repeat name="output" title="VCFTools output" min="1"> + <conditional name="type"> + <param name="type" type="select" label="Type of VCFTools output?"> + <option value="relatedness2">relatedness2</option> + <option value="tstv_by_count">tstv_by_count</option> + <option value="tstv_by_qual">tstv_by_qual</option> + <option value="tstv_summary">tstv_summary</option> + </param> + <when value="relatedness2"> + <param name="input" type="data" format="txt" label="VCFTools relatedness2 output" multiple="true"/> + </when> + <when value="tstv_by_count"> + <param name="input" type="data" format="tabular,tsv" label="VCFTools TsTV count output" multiple="true"/> + </when> + <when value="tstv_by_qual"> + <param name="input" type="data" format="tabular" label="VCFTools TsTV qual output" multiple="true"/> + </when> + <when value="tstv_summary"> + <param name="input" type="data" format="txt" label="VCFTools TsTV summary output" multiple="true"/> + </when> + </conditional> + </repeat> + </xml> + <xml name="vcftools_test"> + <test expect_num_outputs="2"> + <repeat name="results"> + <conditional name="software_cond"> + <param name="software" value="vcftools"/> + <repeat name="output"> + <conditional name="type"> + <param name="type" value="tstv_by_qual"/> + <param name="input" value="vcftools.txt"/> + </conditional> + </repeat> + </conditional> + </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> + <output name="html_report"> + <assert_contents> + <has_text text="Title of the report"/> + <has_text text="Commment for the report"/> + <has_text text="cutadapt_trimmed_sequences_plot"/> + <has_text text="All-in-one FASTQ preprocessor"/> + <has_text text="trimmomatic_plot"/> + </assert_contents> + </output> + <output name="stats"> + <assert_contents> + <has_text text="dataset_33"/> + <has_text text="R1_fq"/> + <has_text text="result_right"/> + <has_text text="25839_merged"/> + <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"/> + </test> + </xml> +</macros>