Mercurial > repos > iuc > multiqc
diff macros.xml @ 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 |
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--- 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>