Mercurial > repos > iuc > multiqc
changeset 25:a7e081ceb76a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 1805997f0c29291dd6fc96add4481422e28e6265
| author | iuc |
|---|---|
| date | Sat, 25 Jan 2025 17:24:12 +0000 |
| parents | f7e2f1eb3a16 |
| children | |
| files | bamtools_plugin.xml bcftools_plugin.xml cutadapt_plugin.xml fastp_plugin.xml fastqc_plugin.xml featurecounts_plugin.xml flexbar_plugin.xml macros.xml picard_plugin.xml pycoqc_plugin.xml qualimap_plugin.xml samtools_plugin.xml star_plugin.xml trimmomatic_plugin.xml |
| diffstat | 14 files changed, 33 insertions(+), 33 deletions(-) [+] |
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--- a/bamtools_plugin.xml Mon Sep 02 14:22:54 2024 +0000 +++ b/bamtools_plugin.xml Sat Jan 25 17:24:12 2025 +0000 @@ -28,7 +28,7 @@ <output name="stats"> <assert_contents> <has_text text="bamtools_txt"/> - <has_text text="Bamtools"/> + <has_text text="bamtools-duplicates_pct"/> <has_n_lines n="2"/> <has_n_columns n="3"/> </assert_contents>
--- a/bcftools_plugin.xml Mon Sep 02 14:22:54 2024 +0000 +++ b/bcftools_plugin.xml Sat Jan 25 17:24:12 2025 +0000 @@ -28,8 +28,8 @@ </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="bcftools_stats-number_of_records"/> + <has_text text="bcftools_stats-number_of_SNPs"/> <has_text text="Test1"/> <has_text text="72330"/> <has_n_lines n="2"/>
--- a/cutadapt_plugin.xml Mon Sep 02 14:22:54 2024 +0000 +++ b/cutadapt_plugin.xml Sat Jan 25 17:24:12 2025 +0000 @@ -34,10 +34,9 @@ </output> <output name="stats"> <assert_contents> - <has_text text="Cutadapt"/> - <has_text text="Cutadapt_mqc_generalstats_cutadapt_percent_trimmed"/> + <has_text text="Sample"/> + <has_text text="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>
--- a/fastp_plugin.xml Mon Sep 02 14:22:54 2024 +0000 +++ b/fastp_plugin.xml Sat Jan 25 17:24:12 2025 +0000 @@ -33,9 +33,9 @@ </output> <output name="stats"> <assert_contents> - <has_text text="fastp_mqc_generalstats_fastp_pct_duplication"/> + <has_text text="fastp-pct_duplication"/> <has_text text="R1_fq"/> - <has_text text="fastp_mqc_generalstats_fastp_after_filtering_q30_rate"/> + <has_text text="fastp-after_filtering_q30_rate"/> <has_text text="bwa-mem-fastq1_fq"/> <has_n_lines n="3"/> <has_n_columns n="8"/>
--- a/fastqc_plugin.xml Mon Sep 02 14:22:54 2024 +0000 +++ b/fastqc_plugin.xml Sat Jan 25 17:24:12 2025 +0000 @@ -58,7 +58,7 @@ <assert_contents> <has_text text="poulet5_1"/> <has_text text="poulet5_2"/> - <has_text text="FastQC_mqc_generalstats_fastqc_median_sequence_length"/> + <has_text text="fastqc-median_sequence_length"/> <has_n_lines n="3"/> <has_n_columns n="7"/> </assert_contents>
--- a/featurecounts_plugin.xml Mon Sep 02 14:22:54 2024 +0000 +++ b/featurecounts_plugin.xml Sat Jan 25 17:24:12 2025 +0000 @@ -36,10 +36,10 @@ </output> <output name="stats"> <assert_contents> - <has_text text="featureCounts_mqc_generalstats_featurecounts_Assigned"/> + <has_text text="featurecounts-Assigned"/> <has_text text="accepted_hits"/> <has_text text="TopHat"/> - <has_text text="featureCounts_mqc_generalstats_featurecounts_percent_assigned"/> + <has_text text="featurecounts-percent_assigned"/> <has_n_lines n="7"/> <has_n_columns n="3"/> </assert_contents>
--- a/flexbar_plugin.xml Mon Sep 02 14:22:54 2024 +0000 +++ b/flexbar_plugin.xml Sat Jan 25 17:24:12 2025 +0000 @@ -28,7 +28,7 @@ </output> <output name="stats"> <assert_contents> - <has_text text="Flexbar_mqc_generalstats_flexbar_removed_bases_pct"/> + <has_text text="flexbar-removed_bases_pct"/> <has_text text="result_right"/> <has_n_lines n="2"/> <has_n_columns n="2"/>
--- a/macros.xml Mon Sep 02 14:22:54 2024 +0000 +++ b/macros.xml Sat Jan 25 17:24:12 2025 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">1.24.1</token> + <token name="@TOOL_VERSION@">1.27</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="bio_tools"> <xrefs> @@ -180,7 +180,7 @@ <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="slamdunk-retained"/> <has_text text="C2"/> <has_n_lines n="11"/> <has_n_columns n="22"/> @@ -275,7 +275,7 @@ <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="cutadapt-percent_trimmed"/> <has_text text="star_log_txt"/> <has_text text="tophat_txtalign"/> <has_n_lines n="17"/> @@ -488,7 +488,7 @@ <assert_contents> <has_text text="bamtools_txt"/> <has_text text="Test1"/> - <has_text text="Prokka_mqc_generalstats_prokka_contigs"/> + <has_text text="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"/> @@ -500,12 +500,13 @@ <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-error_rate"/> <has_text text="samtools_stats_txt"/> <has_text text="snpeff_csv"/> - <has_text text="Bamtools"/> + <has_text text="bamtools-mapped_reads_pct"/> + <has_text text="bamtools-duplicates_pct"/> <has_n_lines n="22"/> - <has_n_columns n="46"/> + <has_n_columns n="50"/> </assert_contents> </output> </test> @@ -525,7 +526,7 @@ </repeat> <output name="html_report" ftype="html"> <assert_contents> - <has_size value="4594258" delta="500"/> + <has_size value="4766687" delta="500"/> </assert_contents> </output> <!--output name="stats" ftype="tabular"> @@ -560,7 +561,7 @@ <output name="stats" ftype="tabular"> <assert_contents> <has_text text="poulet5_2"/> - <has_text text="FastQC"/> + <has_text text="fastqc-percent_gc"/> <has_n_lines n="3"/> <has_n_columns n="7"/> </assert_contents> @@ -596,7 +597,7 @@ </output> <output name="stats" ftype="tabular"> <assert_contents> - <has_text text="pycoQC_mqc_generalstats_pycoqc_passed_median_read_length"/> + <has_text text="pycoqc-passed_median_read_length"/> <has_text text="pycoqc_json"/> </assert_contents> </output>
--- a/picard_plugin.xml Mon Sep 02 14:22:54 2024 +0000 +++ b/picard_plugin.xml Sat Jan 25 17:24:12 2025 +0000 @@ -105,9 +105,9 @@ <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_insertsizemetrics-summed_median"/> <has_text text="picard_CollectRnaSeqMetrics_bam"/> - <has_text text="RnaSeqMetrics_mqc_generalstats_picard_rnaseqmetrics_PCT_MRNA_BASES"/> + <has_text text="picard_rnaseqmetrics-PCT_MRNA_BASES"/> <has_text text="NA"/> <has_n_lines n="4"/> <has_n_columns n="6"/>
--- a/pycoqc_plugin.xml Mon Sep 02 14:22:54 2024 +0000 +++ b/pycoqc_plugin.xml Sat Jan 25 17:24:12 2025 +0000 @@ -30,7 +30,7 @@ </output> <output name="stats" ftype="tabular"> <assert_contents> - <has_text text="pycoQC_mqc_generalstats_pycoqc_passed_median_read_length"/> + <has_text text="pycoqc-passed_median_read_length"/> <has_text text="pycoqc_json"/> </assert_contents> </output>
--- a/qualimap_plugin.xml Mon Sep 02 14:22:54 2024 +0000 +++ b/qualimap_plugin.xml Sat Jan 25 17:24:12 2025 +0000 @@ -47,13 +47,13 @@ </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="qualimap_bamqc-mean_coverage"/> + <has_text text="qualimap_bamqc-mapped_reads"/> + <has_text text="qualimap_bamqc-total_reads"/> <has_text text="x_bam"/> <has_text text="0.98"/> <has_n_lines n="2"/> - <has_n_columns n="6"/> + <has_n_columns n="9"/> </assert_contents> </output> <output_collection name="plots" type="list" count="0"/>
--- a/samtools_plugin.xml Mon Sep 02 14:22:54 2024 +0000 +++ b/samtools_plugin.xml Sat Jan 25 17:24:12 2025 +0000 @@ -85,10 +85,10 @@ <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-error_rate"/> <has_text text="samtools_stats_txt"/> <has_n_lines n="3"/> - <has_n_columns n="11"/> + <has_n_columns n="12"/> </assert_contents> </output> <output_collection name="plots" type="list" count="5"/>
--- a/star_plugin.xml Mon Sep 02 14:22:54 2024 +0000 +++ b/star_plugin.xml Sat Jan 25 17:24:12 2025 +0000 @@ -65,7 +65,7 @@ </output> <output name="stats"> <assert_contents> - <has_text text="STAR_mqc_generalstats_star_uniquely_mapped_percent"/> + <has_text text="star-mapped_percent"/> <has_text text="star_log_txt"/> <has_n_lines n="2"/> <has_n_columns n="7"/>
--- a/trimmomatic_plugin.xml Mon Sep 02 14:22:54 2024 +0000 +++ b/trimmomatic_plugin.xml Sat Jan 25 17:24:12 2025 +0000 @@ -28,7 +28,7 @@ </output> <output name="stats"> <assert_contents> - <has_text text="Trimmomatic_mqc_generalstats_trimmomatic_dropped_pct"/> + <has_text text="trimmomatic-dropped_pct"/> <has_text text="C2"/> <has_n_lines n="2"/> <has_n_columns n="2"/>