Repository 'multiqc'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/multiqc

Changeset 18:c19b16e5729c (2020-11-19)
Previous changeset 17:5e33b465d8d5 (2020-10-09) Next changeset 19:f7985e0479b9 (2020-11-21)
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9"
modified:
multiqc.xml
removed:
test-data/pre_alignment_soft_log.txt
b
diff -r 5e33b465d8d5 -r c19b16e5729c multiqc.xml
--- a/multiqc.xml Fri Oct 09 14:56:59 2020 +0000
+++ b/multiqc.xml Thu Nov 19 21:54:37 2020 +0000
[
b'@@ -1,4 +1,4 @@\n-<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@+galaxy1">\n+<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@+galaxy2">\n     <description>aggregate results from bioinformatics analyses into a single report</description>\n     <macros>\n         <token name="@WRAPPER_VERSION@">1.8</token>\n@@ -842,8 +842,8 @@\n         </repeat>\n         <param name="title" type="text" value="" optional="true" label="Report title" help="It is printed as page header"/>\n         <param name="comment" type="text" value="" optional="true" label="Custom comment" help="It will be printed at the top of the report"/>\n-        <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."/>\n-        <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"/>\n+        <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."/>\n+        <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"/>\n     </inputs>\n     <outputs>\n         <data name="html_report" format="html" from_work_dir="report.html" label="${tool.name} on ${on_string}: Webpage" />\n@@ -854,11 +854,12 @@\n             <discover_datasets pattern="multiqc_(?P&lt;designation&gt;.+)\\.txt" format="tabular" directory="report_data" />\n         </collection>\n         <collection name="plots" type="list" label="${tool.name} on ${on_string}: Plots">\n-            <discover_datasets pattern="mqc_(?P&lt;designation&gt;.+_plot_.+)\\.txt" format="tabular" directory="report_data" />\n+            <discover_datasets pattern="mqc_(?P&lt;designation&gt;.+)\\.txt" format="tabular" directory="report_data" />\n+            <filter>flat</filter>\n         </collection>\n     </outputs>\n     <tests>\n-        <test>\n+        <test expect_num_outputs="4">\n             <repeat name="results">\n                 <conditional name="software_cond">\n                     <param name="software" value="cutadapt" />\n@@ -906,7 +907,8 @@\n             </repeat>\n             <param name="title" value="Title of the report"/>\n             <param name="comment" value="Commment for the report"/>\n-            <param name="saveLog" value="True"/>\n+            <param name="flat" value="true"/>\n+            <param name="saveLog" value="true"/>\n             <output name="html_report">\n                 <assert_contents>\n                     <has_text text="Title of the report" />\n@@ -920,8 +922,12 @@\n                     <has_text text="trimmomatic_plot" />\n                 </assert_contents>\n             </output>\n-            <output name="log" file="pre_alignment_soft_log.txt" compare="sim_size"/>\n-            <output_collection name="stats" type="list">\n+            <output name="log">\n+                <assert_contents>\n+                    <has_text_matching expression="\\[INFO   \\]  MultiQC complete$"/>\n+                </assert_contents>\n+            </output>\n+            <output_collection name="stats" type="list" count="11">\n                 <element name="cutadapt" file="cutadapt_stats.tabular" compare="sim_size" delta="10"/>\n                 <element name="fastp" file="fastp_stats.tabular" compare="sim_size" delta="10"/>\n                 <element name="fastqc" file="fastqc_stats.tabular" compare="sim_size" delta="10"/>\n@@ -931,8 +937,9 @@\n                 <element name="sortmerna" file="sortmerna_stats.tabular" compare="sim_size" delta="30"/>\n                 <element name="trimmomatic'..b'ion name="plots" type="list" count="29"/>\n         </test>\n-        <test>\n+        <test expect_num_outputs="2">\n             <repeat name="results">\n                 <conditional name="software_cond">\n                     <param name="software" value="bismark" />\n@@ -995,7 +1002,7 @@\n                     <param name="input" value="tophat.txt" />\n                 </conditional>\n             </repeat>\n-            <param name="saveLog" value="False"/>\n+            <param name="saveLog" value="false"/>\n             <output name="html_report">\n                 <assert_contents>\n                     <has_text text="bismark-alignment" />\n@@ -1009,7 +1016,7 @@\n                     <has_text text="hicexplorer1_log_1" />\n                 </assert_contents>\n             </output>\n-            <output_collection name="stats" type="list">\n+            <output_collection name="stats" type="list" count="8">\n                 <element name="bismark_alignment" file="bismark_stats.tabular" compare="sim_size" delta="10"/>\n                 <element name="bowtie2" file="bowtie2_stats.tabular" compare="sim_size" delta="20"/>\n                 <element name="general_stats" file="aligner_soft_stats.tabular" compare="sim_size" delta="50"/>\n@@ -1021,7 +1028,7 @@\n                 <element name="tophat.txt" file="tophat_stats.tabular" compare="sim_size" delta="10"/>\n             </output_collection>\n         </test>\n-        <test>\n+        <test expect_num_outputs="2">\n             <repeat name="results">\n                 <conditional name="software_cond">\n                     <param name="software" value="bamtools" />\n@@ -1221,7 +1228,7 @@\n                     <has_text text="snpeff" />\n                 </assert_contents>\n             </output>\n-            <output_collection name="stats" type="list">\n+            <output_collection name="stats" type="list" count="19">\n                 <element name="bamtools_stats" file="bamtools_stats.tabular" compare="sim_size" delta="10"/>\n                 <element name="bcftools_stats" file="bcftools_stats.tabular" compare="sim_size" delta="0"/>\n                 <element name="busco" file="busco_stats.tabular" compare="sim_size" delta="10"/>\n@@ -1249,7 +1256,7 @@\n                 <element name="snpeff" file="snpeff_stats.tabular" compare="sim_size" delta="10"/>\n             </output_collection>\n         </test>\n-        <test>\n+        <test expect_num_outputs="2">\n             <repeat name="results">\n                 <conditional name="software_cond">\n                     <param name="software" value="custom_content" />\n@@ -1264,8 +1271,9 @@\n                 </conditional>\n             </repeat>\n             <output name="html_report" file="report_manual_custom_content.html" compare="sim_size"/>\n+\t    <output_collection name="stats" type="list" count="1"/>\n         </test>\n-        <test>\n+        <test expect_num_outputs="3">\n             <repeat name="results">\n                 <conditional name="software_cond">\n                     <param name="software" value="fastqc" />\n@@ -1277,7 +1285,7 @@\n             </repeat>\n             <param name="title" value="Title of the report"/>\n             <param name="comment" value="Commment for the report"/>\n-            <param name="flat" value="True"/>\n+            <param name="flat" value="true"/>\n             <output name="html_report">\n                 <assert_contents>\n                     <has_text text="Title of the report" />\n@@ -1285,7 +1293,8 @@\n                     <has_text text="fastqc_seq_heatmap_key_t" />\n                 </assert_contents>\n             </output>\n-            <output_collection name="plots" type="list">\n+\t    <output_collection name="stats" type="list" count="1"/>\n+            <output_collection name="plots" type="list" count="1">\n                 <element name="fastqc_per_base_sequence_quality_plot_1" file="mqc_fastqc_per_base_sequence_quality_plot_1.txt" compare="sim_size" delta="10"/>\n             </output_collection>\n         </test>\n'
b
diff -r 5e33b465d8d5 -r c19b16e5729c test-data/pre_alignment_soft_log.txt
--- 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
[
b"@@ -1,85 +0,0 @@\n-[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\n-[2018-04-05 12:06:46,534] multiqc                                            [DEBUG  ]  No MultiQC config found: /Users/bebatut/.multiqc_config.yaml\n-[2018-04-05 12:06:46,534] multiqc                                            [DEBUG  ]  No MultiQC config found: multiqc_config.yaml\n-[2018-04-05 12:06:46,534] multiqc                                            [DEBUG  ]  Command used: /Users/bebatut/miniconda3/envs/multiqc/bin/multiqc multiqc_WDir\n-[2018-04-05 12:06:47,547] multiqc                                            [DEBUG  ]  Latest MultiQC version is v1.5\n-[2018-04-05 12:06:47,547] multiqc                                            [INFO   ]  This is MultiQC v1.5\n-[2018-04-05 12:06:47,548] multiqc                                            [DEBUG  ]  Command     : /Users/bebatut/miniconda3/envs/multiqc/bin/multiqc multiqc_WDir\n-[2018-04-05 12:06:47,548] multiqc                                            [DEBUG  ]  Working dir : /Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc\n-[2018-04-05 12:06:47,548] multiqc                                            [INFO   ]  Template    : default\n-[2018-04-05 12:06:47,548] multiqc                                            [INFO   ]  Searching 'multiqc_WDir'\n-[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\n-[2018-04-05 12:06:47,554] multiqc                                            [DEBUG  ]  Using temporary directory for creating report: /var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmpd75q9s93\n-[2018-04-05 12:06:48,019] multiqc                                            [DEBUG  ]  No samples found: custom_content\n-[2018-04-05 12:06:48,025] multiqc                                            [DEBUG  ]  No samples found: conpair\n-[2018-04-05 12:06:48,030] multiqc                                            [DEBUG  ]  No samples found: peddy\n-[2018-04-05 12:06:48,035] multiqc                                            [DEBUG  ]  No samples found: methylQA\n-[2018-04-05 12:06:48,040] multiqc                                            [DEBUG  ]  No samples found: qualimap\n-[2018-04-05 12:06:48,045] multiqc                                            [DEBUG  ]  No samples found: preseq\n-[2018-04-05 12:06:48,050] multiqc                                            [DEBUG  ]  No samples found: quast\n-[2018-04-05 12:06:48,054] multiqc                                            [DEBUG  ]  No samples found: qorts\n-[2018-04-05 12:06:48,059] multiqc                                            [DEBUG  ]  No samples found: rna_seqc\n-[2018-04-05 12:06:48,063] multiqc                                            [DEBUG  ]  No samples found: rsem\n-[2018-04-05 12:06:48,070] multiqc                                            [DEBUG  ]  No samples found: rseqc\n-[2018-04-05 12:06:48,074] multiqc                                            [DEBUG  ]  No samples found: busco\n-[2018-04-05 12:06:48,079] multiqc                                            [DEBUG  ]  No samples found: goleft_indexcov\n-[2018-04-05 12:06:48,083] multiqc                                            [DEBUG  ]  No samples found: disambiguate\n-[2018-04-05 12:06:48,08"..b"orts\n-[2018-04-05 12:06:48,307] multiqc.modules.flexbar.flexbar                    [INFO   ]  Found 1 logs\n-[2018-04-05 12:06:48,318] multiqc.modules.trimmomatic.trimmomatic            [INFO   ]  Found 1 logs\n-[2018-04-05 12:06:48,325] multiqc                                            [DEBUG  ]  No samples found: skewer\n-[2018-04-05 12:06:48,334] multiqc.modules.sortmerna.sortmerna                [INFO   ]  Found 1 logs\n-[2018-04-05 12:06:48,339] multiqc                                            [DEBUG  ]  No samples found: biobloomtools\n-[2018-04-05 12:06:48,346] multiqc                                            [DEBUG  ]  No samples found: fastq_screen\n-[2018-04-05 12:06:48,352] multiqc                                            [DEBUG  ]  No samples found: afterqc\n-[2018-04-05 12:06:48,434] multiqc.modules.fastqc.fastqc                      [INFO   ]  Found 2 reports\n-[2018-04-05 12:06:48,495] multiqc                                            [DEBUG  ]  No samples found: clusterflow\n-[2018-04-05 12:06:48,500] multiqc                                            [DEBUG  ]  No samples found: bcl2fastq\n-[2018-04-05 12:06:48,505] multiqc                                            [DEBUG  ]  No samples found: interop\n-[2018-04-05 12:06:48,514] multiqc                                            [INFO   ]  Compressing plot data\n-[2018-04-05 12:06:48,596] multiqc                                            [INFO   ]  Report      : multiqc_report.html\n-[2018-04-05 12:06:48,597] multiqc                                            [INFO   ]  Data        : multiqc_data\n-[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'\n-[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'\n-[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'\n-[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'\n-[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'\n-[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'\n-[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'\n-[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'\n-[2018-04-05 12:06:48,809] multiqc                                            [INFO   ]  MultiQC complete\n"