# HG changeset patch
# User iuc
# Date 1605822877 0
# Node ID c19b16e5729c1411bdffea071b6739fab7c07a18
# Parent  5e33b465d8d52f36920006ab30f725da85c296bc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 263b1803fbf2622dbeb283b1d965690a5dc24ec9"

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
@@ -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 ${on_string}: Webpage" />
@@ -854,11 +854,12 @@
             <discover_datasets pattern="multiqc_(?P&lt;designation&gt;.+)\.txt" format="tabular" directory="report_data" />
         </collection>
         <collection name="plots" type="list" label="${tool.name} on ${on_string}: Plots">
-            <discover_datasets pattern="mqc_(?P&lt;designation&gt;.+_plot_.+)\.txt" format="tabular" directory="report_data" />
+            <discover_datasets pattern="mqc_(?P&lt;designation&gt;.+)\.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>
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
@@ -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