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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
author | iuc |
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date | Mon, 02 Sep 2024 14:22:54 +0000 |
parents | abfd8a6544d7 |
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<macros> <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> </xrefs> </xml> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">multiqc</requirement> </requirements> </xml> <xml name="citations"> <citations> <citation type="doi">10.1101/gr.244293.118</citation> </citations> </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 #set $file_path += '_' + str($file_paths.count($file_path)) #end if #set $file_paths += [$file_path] 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_2@"> <![CDATA[ #set repeat_dir = os.path.join($software_dir, str($repeat2.type.type) + '_' + str($j)) mkdir '$repeat_dir' && ]]></token> <token name="@LN_FILES@"> <![CDATA[ #set file_paths = [] #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 = [] @CREATE_REPEAT_DIR_1@ #for $file in $repeat2.input #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier)) #set file_path = os.path.join($repeat_dir, str($identifier)) @CHECK_LN_FILE@ #end for ]]></token> <token name="@LN_3_FILES@"> <![CDATA[ #set file_paths = [] #for $file in $repeat2.type.input #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier)) #set file_path = os.path.join($repeat_dir, str($identifier)) @CHECK_LN_FILE@ #end for ]]></token> <!-- is currently not used --> <xml name="element_assert" token_name="" token_lines="" token_columns="" token_text=""> <element name="@NAME@"> <assert_contents> <has_n_columns n="@COLUMNS@"/> <has_n_lines n="@LINES@"/> <has_text text="@TEXT@"/> <yield/> </assert_contents> </element> </xml> <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>