Mercurial > repos > iuc > multiqc
changeset 18:c19b16e5729c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9"
| author | iuc |
|---|---|
| date | Thu, 19 Nov 2020 21:54:37 +0000 |
| parents | 5e33b465d8d5 |
| children | f7985e0479b9 |
| files | multiqc.xml test-data/pre_alignment_soft_log.txt |
| diffstat | 2 files changed, 26 insertions(+), 102 deletions(-) [+] |
line wrap: on
line diff
--- a/multiqc.xml Fri Oct 09 14:56:59 2020 +0000 +++ b/multiqc.xml Thu Nov 19 21:54:37 2020 +0000 @@ -1,4 +1,4 @@ -<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@+galaxy1"> +<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@+galaxy2"> <description>aggregate results from bioinformatics analyses into a single report</description> <macros> <token name="@WRAPPER_VERSION@">1.8</token> @@ -842,8 +842,8 @@ </repeat> <param name="title" type="text" value="" optional="true" label="Report title" help="It is printed as page header"/> <param name="comment" type="text" value="" optional="true" label="Custom comment" help="It will be printed at the top of the report"/> - <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 name="saveLog" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output the multiQC log file?" help="This is mostly useful for debugging purposes"/> + <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 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 ${on_string}: Webpage" /> @@ -854,11 +854,12 @@ <discover_datasets pattern="multiqc_(?P<designation>.+)\.txt" format="tabular" directory="report_data" /> </collection> <collection name="plots" type="list" label="${tool.name} on ${on_string}: Plots"> - <discover_datasets pattern="mqc_(?P<designation>.+_plot_.+)\.txt" format="tabular" directory="report_data" /> + <discover_datasets pattern="mqc_(?P<designation>.+)\.txt" format="tabular" directory="report_data" /> + <filter>flat</filter> </collection> </outputs> <tests> - <test> + <test expect_num_outputs="4"> <repeat name="results"> <conditional name="software_cond"> <param name="software" value="cutadapt" /> @@ -906,7 +907,8 @@ </repeat> <param name="title" value="Title of the report"/> <param name="comment" value="Commment for the report"/> - <param name="saveLog" value="True"/> + <param name="flat" value="true"/> + <param name="saveLog" value="true"/> <output name="html_report"> <assert_contents> <has_text text="Title of the report" /> @@ -920,8 +922,12 @@ <has_text text="trimmomatic_plot" /> </assert_contents> </output> - <output name="log" file="pre_alignment_soft_log.txt" compare="sim_size"/> - <output_collection name="stats" type="list"> + <output name="log"> + <assert_contents> + <has_text_matching expression="\[INFO \] MultiQC complete$"/> + </assert_contents> + </output> + <output_collection name="stats" type="list" count="11"> <element name="cutadapt" file="cutadapt_stats.tabular" compare="sim_size" delta="10"/> <element name="fastp" file="fastp_stats.tabular" compare="sim_size" delta="10"/> <element name="fastqc" file="fastqc_stats.tabular" compare="sim_size" delta="10"/> @@ -931,8 +937,9 @@ <element name="sortmerna" file="sortmerna_stats.tabular" compare="sim_size" delta="30"/> <element name="trimmomatic" file="trimmomatic_stats.tabular" compare="sim_size" delta="0"/> </output_collection> + <output_collection name="plots" type="list" count="29"/> </test> - <test> + <test expect_num_outputs="2"> <repeat name="results"> <conditional name="software_cond"> <param name="software" value="bismark" /> @@ -995,7 +1002,7 @@ <param name="input" value="tophat.txt" /> </conditional> </repeat> - <param name="saveLog" value="False"/> + <param name="saveLog" value="false"/> <output name="html_report"> <assert_contents> <has_text text="bismark-alignment" /> @@ -1009,7 +1016,7 @@ <has_text text="hicexplorer1_log_1" /> </assert_contents> </output> - <output_collection name="stats" type="list"> + <output_collection name="stats" type="list" count="8"> <element name="bismark_alignment" file="bismark_stats.tabular" compare="sim_size" delta="10"/> <element name="bowtie2" file="bowtie2_stats.tabular" compare="sim_size" delta="20"/> <element name="general_stats" file="aligner_soft_stats.tabular" compare="sim_size" delta="50"/> @@ -1021,7 +1028,7 @@ <element name="tophat.txt" file="tophat_stats.tabular" compare="sim_size" delta="10"/> </output_collection> </test> - <test> + <test expect_num_outputs="2"> <repeat name="results"> <conditional name="software_cond"> <param name="software" value="bamtools" /> @@ -1221,7 +1228,7 @@ <has_text text="snpeff" /> </assert_contents> </output> - <output_collection name="stats" type="list"> + <output_collection name="stats" type="list" count="19"> <element name="bamtools_stats" file="bamtools_stats.tabular" compare="sim_size" delta="10"/> <element name="bcftools_stats" file="bcftools_stats.tabular" compare="sim_size" delta="0"/> <element name="busco" file="busco_stats.tabular" compare="sim_size" delta="10"/> @@ -1249,7 +1256,7 @@ <element name="snpeff" file="snpeff_stats.tabular" compare="sim_size" delta="10"/> </output_collection> </test> - <test> + <test expect_num_outputs="2"> <repeat name="results"> <conditional name="software_cond"> <param name="software" value="custom_content" /> @@ -1264,8 +1271,9 @@ </conditional> </repeat> <output name="html_report" file="report_manual_custom_content.html" compare="sim_size"/> + <output_collection name="stats" type="list" count="1"/> </test> - <test> + <test expect_num_outputs="3"> <repeat name="results"> <conditional name="software_cond"> <param name="software" value="fastqc" /> @@ -1277,7 +1285,7 @@ </repeat> <param name="title" value="Title of the report"/> <param name="comment" value="Commment for the report"/> - <param name="flat" value="True"/> + <param name="flat" value="true"/> <output name="html_report"> <assert_contents> <has_text text="Title of the report" /> @@ -1285,7 +1293,8 @@ <has_text text="fastqc_seq_heatmap_key_t" /> </assert_contents> </output> - <output_collection name="plots" type="list"> + <output_collection name="stats" type="list" count="1"/> + <output_collection name="plots" type="list" count="1"> <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>
--- a/test-data/pre_alignment_soft_log.txt Fri Oct 09 14:56:59 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,85 +0,0 @@ -[2018-04-05 12:06:46,534] multiqc [DEBUG ] No MultiQC config found: /Users/bebatut/miniconda3/envs/multiqc/lib/python3.5/site-packages/multiqc_config.yaml -[2018-04-05 12:06:46,534] multiqc [DEBUG ] No MultiQC config found: /Users/bebatut/.multiqc_config.yaml -[2018-04-05 12:06:46,534] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml -[2018-04-05 12:06:46,534] multiqc [DEBUG ] Command used: /Users/bebatut/miniconda3/envs/multiqc/bin/multiqc multiqc_WDir -[2018-04-05 12:06:47,547] multiqc [DEBUG ] Latest MultiQC version is v1.5 -[2018-04-05 12:06:47,547] multiqc [INFO ] This is MultiQC v1.5 -[2018-04-05 12:06:47,548] multiqc [DEBUG ] Command : /Users/bebatut/miniconda3/envs/multiqc/bin/multiqc multiqc_WDir -[2018-04-05 12:06:47,548] multiqc [DEBUG ] Working dir : /Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc -[2018-04-05 12:06:47,548] multiqc [INFO ] Template : default -[2018-04-05 12:06:47,548] multiqc [INFO ] Searching 'multiqc_WDir' -[2018-04-05 12:06:47,549] multiqc [DEBUG ] Analysing modules: custom_content, conpair, peddy, methylQA, qualimap, preseq, quast, qorts, rna_seqc, rsem, rseqc, busco, goleft_indexcov, disambiguate, supernova, deeptools, sargasso, verifybamid, homer, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, dedup, picard, prokka, samblaster, samtools, bamtools, jellyfish, vcftools, bbmap, bismark, hicexplorer, hicup, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, leehom, adapterRemoval, clipandmerge, cutadapt, flexbar, trimmomatic, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastqc, clusterflow, bcl2fastq, interop -[2018-04-05 12:06:47,554] multiqc [DEBUG ] Using temporary directory for creating report: /var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93 -[2018-04-05 12:06:48,019] multiqc [DEBUG ] No samples found: custom_content -[2018-04-05 12:06:48,025] multiqc [DEBUG ] No samples found: conpair -[2018-04-05 12:06:48,030] multiqc [DEBUG ] No samples found: peddy -[2018-04-05 12:06:48,035] multiqc [DEBUG ] No samples found: methylQA -[2018-04-05 12:06:48,040] multiqc [DEBUG ] No samples found: qualimap -[2018-04-05 12:06:48,045] multiqc [DEBUG ] No samples found: preseq -[2018-04-05 12:06:48,050] multiqc [DEBUG ] No samples found: quast -[2018-04-05 12:06:48,054] multiqc [DEBUG ] No samples found: qorts -[2018-04-05 12:06:48,059] multiqc [DEBUG ] No samples found: rna_seqc -[2018-04-05 12:06:48,063] multiqc [DEBUG ] No samples found: rsem -[2018-04-05 12:06:48,070] multiqc [DEBUG ] No samples found: rseqc -[2018-04-05 12:06:48,074] multiqc [DEBUG ] No samples found: busco -[2018-04-05 12:06:48,079] multiqc [DEBUG ] No samples found: goleft_indexcov -[2018-04-05 12:06:48,083] multiqc [DEBUG ] No samples found: disambiguate -[2018-04-05 12:06:48,088] multiqc [DEBUG ] No samples found: supernova -[2018-04-05 12:06:48,097] multiqc [DEBUG ] No samples found: deeptools -[2018-04-05 12:06:48,103] multiqc [DEBUG ] No samples found: sargasso -[2018-04-05 12:06:48,108] multiqc [DEBUG ] No samples found: verifybamid -[2018-04-05 12:06:48,113] multiqc [DEBUG ] No samples found: homer -[2018-04-05 12:06:48,118] multiqc [DEBUG ] No samples found: macs2 -[2018-04-05 12:06:48,124] multiqc [DEBUG ] No samples found: theta2 -[2018-04-05 12:06:48,130] multiqc [DEBUG ] No samples found: snpeff -[2018-04-05 12:06:48,136] multiqc [DEBUG ] No samples found: gatk -[2018-04-05 12:06:48,141] multiqc [DEBUG ] No samples found: htseq -[2018-04-05 12:06:48,145] multiqc [DEBUG ] No samples found: bcftools -[2018-04-05 12:06:48,151] multiqc [DEBUG ] No samples found: featureCounts -[2018-04-05 12:06:48,157] multiqc [DEBUG ] No samples found: dedup -[2018-04-05 12:06:48,166] multiqc [DEBUG ] No samples found: picard -[2018-04-05 12:06:48,170] multiqc [DEBUG ] No samples found: prokka -[2018-04-05 12:06:48,174] multiqc [DEBUG ] No samples found: samblaster -[2018-04-05 12:06:48,180] multiqc [DEBUG ] No samples found: samtools -[2018-04-05 12:06:48,184] multiqc [DEBUG ] No samples found: bamtools -[2018-04-05 12:06:48,189] multiqc [DEBUG ] No samples found: jellyfish -[2018-04-05 12:06:48,194] multiqc [DEBUG ] No samples found: vcftools -[2018-04-05 12:06:48,202] multiqc [DEBUG ] No samples found: bbmap -[2018-04-05 12:06:48,206] multiqc [DEBUG ] No samples found: bismark -[2018-04-05 12:06:48,211] multiqc [DEBUG ] No samples found: hicexplorer -[2018-04-05 12:06:48,215] multiqc [DEBUG ] No samples found: hicup -[2018-04-05 12:06:48,219] multiqc [DEBUG ] No samples found: salmon -[2018-04-05 12:06:48,225] multiqc [DEBUG ] No samples found: kallisto -[2018-04-05 12:06:48,231] multiqc [DEBUG ] No samples found: slamdunk -[2018-04-05 12:06:48,236] multiqc [DEBUG ] No samples found: star -[2018-04-05 12:06:48,242] multiqc [DEBUG ] No samples found: hisat2 -[2018-04-05 12:06:48,246] multiqc [DEBUG ] No samples found: tophat -[2018-04-05 12:06:48,250] multiqc [DEBUG ] No samples found: bowtie2 -[2018-04-05 12:06:48,255] multiqc [DEBUG ] No samples found: bowtie1 -[2018-04-05 12:06:48,259] multiqc [DEBUG ] No samples found: leehom -[2018-04-05 12:06:48,263] multiqc [DEBUG ] No samples found: adapterRemoval -[2018-04-05 12:06:48,268] multiqc [DEBUG ] No samples found: clipandmerge -[2018-04-05 12:06:48,276] multiqc.modules.cutadapt.cutadapt [INFO ] Found 1 reports -[2018-04-05 12:06:48,307] multiqc.modules.flexbar.flexbar [INFO ] Found 1 logs -[2018-04-05 12:06:48,318] multiqc.modules.trimmomatic.trimmomatic [INFO ] Found 1 logs -[2018-04-05 12:06:48,325] multiqc [DEBUG ] No samples found: skewer -[2018-04-05 12:06:48,334] multiqc.modules.sortmerna.sortmerna [INFO ] Found 1 logs -[2018-04-05 12:06:48,339] multiqc [DEBUG ] No samples found: biobloomtools -[2018-04-05 12:06:48,346] multiqc [DEBUG ] No samples found: fastq_screen -[2018-04-05 12:06:48,352] multiqc [DEBUG ] No samples found: afterqc -[2018-04-05 12:06:48,434] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports -[2018-04-05 12:06:48,495] multiqc [DEBUG ] No samples found: clusterflow -[2018-04-05 12:06:48,500] multiqc [DEBUG ] No samples found: bcl2fastq -[2018-04-05 12:06:48,505] multiqc [DEBUG ] No samples found: interop -[2018-04-05 12:06:48,514] multiqc [INFO ] Compressing plot data -[2018-04-05 12:06:48,596] multiqc [INFO ] Report : multiqc_report.html -[2018-04-05 12:06:48,597] multiqc [INFO ] Data : multiqc_data -[2018-04-05 12:06:48,597] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_cutadapt.txt' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data' -[2018-04-05 12:06:48,597] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_data.json' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data' -[2018-04-05 12:06:48,598] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_fastqc.txt' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data' -[2018-04-05 12:06:48,598] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_flexbar.txt' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data' -[2018-04-05 12:06:48,598] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_general_stats.txt' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data' -[2018-04-05 12:06:48,598] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_sortmerna.txt' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data' -[2018-04-05 12:06:48,598] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_sources.txt' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data' -[2018-04-05 12:06:48,599] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93/multiqc_data/multiqc_trimmomatic.txt' to '/Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_data' -[2018-04-05 12:06:48,809] multiqc [INFO ] MultiQC complete