# HG changeset patch
# User iuc
# Date 1589636445 14400
# Node ID bf675f34b0560b29f3eca1a4a15b4e1218d09590
# Parent  3d93dd18d9f8491e8e601889bc7596056c1015b2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875"

diff -r 3d93dd18d9f8 -r bf675f34b056 multiqc.xml
--- a/multiqc.xml	Sat Jan 18 03:08:54 2020 -0500
+++ b/multiqc.xml	Sat May 16 09:40:45 2020 -0400
@@ -1,7 +1,7 @@
-<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.1">
+<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@+galaxy0">
     <description>aggregate results from bioinformatics analyses into a single report</description>
     <macros>
-        <token name="@WRAPPER_VERSION@">1.7</token>
+        <token name="@WRAPPER_VERSION@">1.8</token>
         <token name="@ESCAPE_IDENTIFIER@">
 <![CDATA[
 #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier))
@@ -272,6 +272,28 @@
     #elif str($repeat.software_cond.software) == "prokka"
         #set $pattern = "contigs:"
         @LN_FILES@
+    #elif str($repeat.software_cond.software) == "qualimap"
+        #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 '$file' \${filepath_3} &&
+            #else
+                #pass
+            #end if
+        #end for
     #elif str($repeat.software_cond.software) == "quast"
         #for $k, $file in enumerate($repeat.software_cond.input)
             #set file_dir = os.path.join($software_dir, 'file_' + str($k))
@@ -499,6 +521,7 @@
                     <!--<option value="bbmap">BBMap</option>-->
                     <option value="bcftools">Bcftools</option>
                     <!--<option value="bcl2fastq">bcl2fastq</option>-->
+                    <!--<option value="biobambam2">biobambam2</option>-->
                     <!--<option value="biobloomtools">BioBloom Tools</option>-->
                     <option value="bismark">Bismark</option>
                     <!--<option value="bowtie1">Bowtie 1</option>-->
@@ -515,6 +538,7 @@
                     <option value="fastp">fastp</option>
                     <option value="fastqc">FastQC</option>
                     <option value="featureCounts">featureCounts</option>
+                    <!--<option value="fgbio">fgbio</option>-->
                     <option value="flexbar">Flexbar</option>
                     <option value="gatk">GATK</option>
                     <!--<option value="goleft_indexcov">goleft indexcov</option>-->
@@ -529,12 +553,14 @@
                     <!--<option value="leehom">leeHom</option>-->
                     <option value="macs2">MACS2</option>
                     <!--<option value="methylQA">methylQA</option>-->
+                    <!--<option value="mosdepth">mostdepth</option>-->
+                    <!--<option value="mtnucratio">mtnucratio</option>-->
                     <!--<option value="peddy">Peddy</option>-->
                     <option value="picard">Picard</option>
                     <!--<option value="preseq">Preseq</option>-->
                     <option value="prokka">Prokka</option>
                     <!--<option value="qorts">QoRTs</option>-->
-                    <!--<option value="qualimap">Qualimap (BamQC or RNASeq output)</option>-->
+                    <option value="qualimap">Qualimap (BamQC or RNASeq output)</option>
                     <option value="quast">QUAST</option>
                     <!--<option value="rna_seqc">RNA-SeQC</option>-->
                     <!--<option value="rsem">RSEM (rsem-calculate-regex output)</option>-->
@@ -543,6 +569,8 @@
                     <option value="samblaster">Samblaster</option>
                     <option value="samtools">Samtools</option>
                     <!--<option value="sargasso">Sargasso</option>-->
+                    <!--<option value="seqyclean">SeqyClean</option>-->
+                    <!--<option value="sexdeterrmine">SexDetErrmine</option>-->
                     <!--<option value="skewer">Skewer</option>-->
                     <option value="slamdunk">Slamdunk</option>
                     <option value="snpeff">SnpEff</option>
@@ -663,6 +691,9 @@
                 <when value="prokka">
                     <param name="input" type="data" format="txt" multiple="true" label="Output of Prokka" help="It should contain 'contigs:'"/>
                 </when>
+                <when value="qualimap">
+                    <param name="input" type="data" format="txt,tabular,tsv" multiple="true" label="Output of Qualimap BamQC" help="First result input should be genome_coverage (default from tool output). Run the Flatten Collection tool to keep all output in one report" />
+                </when>
                 <when value="quast">
                     <param name="input" type="data" format="tabular,tsv" multiple="true" label="Output of Quast"/>
                 </when>
@@ -1100,6 +1131,12 @@
             </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>
@@ -1177,6 +1214,7 @@
                     <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" />
@@ -1197,6 +1235,7 @@
                 <element name="picard_dups" file="picard_dups_stats.tabular" compare="sim_size" delta="0"/>
                 <element name="picard_insertSize" file="picard_insertSize_stats.tabular" compare="sim_size" delta="0"/>
                 <element name="prokka" file="prokka_stats.tabular" compare="sim_size" delta="0"/>
+                <element name="qualimap_bamqc_genome_results" file="qualimap_bamqc_genome_results.tabular" compare="sim_size" delta="0"/>
                 <element name="quast" file="quast_stats.tabular" compare="sim_size" delta="0"/>
                 <element name="samblaster" file="samblaster_stats.tabular" compare="sim_size" delta="0"/>
                 <element name="samtools_flagstat">
diff -r 3d93dd18d9f8 -r bf675f34b056 test-data/genome_results.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome_results.txt	Sat May 16 09:40:45 2020 -0400
@@ -0,0 +1,135 @@
+BamQC report
+-----------------------------------
+
+>>>>>>> Input
+
+     bam file = x_bam
+     outfile = results/genome_results.txt
+
+
+>>>>>>> Reference
+
+     number of bases = 1,817,261 bp
+     number of contigs = 1
+
+
+>>>>>>> Globals
+
+     number of windows = 400
+
+     number of reads = 1,248,774
+     number of mapped reads = 1,242,183 (99.47%)
+     number of supplementary alignments = 3,386 (0.27%)
+     number of secondary alignments = 0
+
+     number of mapped paired reads (first in pair) = 623,192
+     number of mapped paired reads (second in pair) = 618,991
+     number of mapped paired reads (both in pair) = 1,237,764
+     number of mapped paired reads (singletons) = 4,419
+     number of overlapping read pairs = 463,596
+
+     number of mapped bases = 366,875,582 bp
+     number of sequenced bases = 366,823,893 bp
+     number of aligned bases = 0 bp
+     number of duplicated reads (estimated) = 673,527
+     duplication rate = 47.01%
+
+
+>>>>>>> Insert size
+
+     mean insert size = 1,097.678
+     std insert size = 27,365.2401
+     median insert size = 524
+
+
+>>>>>>> Mapping quality
+
+     mean mapping quality = 58.4552
+
+
+>>>>>>> ACTG content
+
+     number of A's = 109,576,306 bp (29.87%)
+     number of C's = 73,524,910 bp (20.04%)
+     number of T's = 111,308,231 bp (30.34%)
+     number of G's = 72,414,446 bp (19.74%)
+     number of N's = 0 bp (0%)
+
+     GC percentage = 39.78%
+
+
+>>>>>>> Mismatches and indels
+
+    general error rate = 0.0098
+    number of mismatches = 3,560,959
+    number of insertions = 7,229
+    mapped reads with insertion percentage = 0.56%
+    number of deletions = 14,669
+    mapped reads with deletion percentage = 1.15%
+    homopolymer indels = 46.92%
+
+
+>>>>>>> Coverage
+
+     mean coverageData = 201.8838X
+     std coverageData = 112.2733X
+     paired-end adapted mean coverage = 177.4988X
+
+     There is a 99.81% of reference with a coverageData >= 1X
+     There is a 99.77% of reference with a coverageData >= 2X
+     There is a 99.74% of reference with a coverageData >= 3X
+     There is a 99.7% of reference with a coverageData >= 4X
+     There is a 99.66% of reference with a coverageData >= 5X
+     There is a 99.6% of reference with a coverageData >= 6X
+     There is a 99.53% of reference with a coverageData >= 7X
+     There is a 99.41% of reference with a coverageData >= 8X
+     There is a 99.3% of reference with a coverageData >= 9X
+     There is a 99.21% of reference with a coverageData >= 10X
+     There is a 99.11% of reference with a coverageData >= 11X
+     There is a 98.99% of reference with a coverageData >= 12X
+     There is a 98.87% of reference with a coverageData >= 13X
+     There is a 98.76% of reference with a coverageData >= 14X
+     There is a 98.63% of reference with a coverageData >= 15X
+     There is a 98.5% of reference with a coverageData >= 16X
+     There is a 98.35% of reference with a coverageData >= 17X
+     There is a 98.16% of reference with a coverageData >= 18X
+     There is a 97.97% of reference with a coverageData >= 19X
+     There is a 97.79% of reference with a coverageData >= 20X
+     There is a 97.59% of reference with a coverageData >= 21X
+     There is a 97.37% of reference with a coverageData >= 22X
+     There is a 97.16% of reference with a coverageData >= 23X
+     There is a 96.95% of reference with a coverageData >= 24X
+     There is a 96.71% of reference with a coverageData >= 25X
+     There is a 96.48% of reference with a coverageData >= 26X
+     There is a 96.24% of reference with a coverageData >= 27X
+     There is a 95.99% of reference with a coverageData >= 28X
+     There is a 95.73% of reference with a coverageData >= 29X
+     There is a 95.49% of reference with a coverageData >= 30X
+     There is a 95.23% of reference with a coverageData >= 31X
+     There is a 94.99% of reference with a coverageData >= 32X
+     There is a 94.75% of reference with a coverageData >= 33X
+     There is a 94.51% of reference with a coverageData >= 34X
+     There is a 94.27% of reference with a coverageData >= 35X
+     There is a 94.01% of reference with a coverageData >= 36X
+     There is a 93.8% of reference with a coverageData >= 37X
+     There is a 93.55% of reference with a coverageData >= 38X
+     There is a 93.31% of reference with a coverageData >= 39X
+     There is a 93.04% of reference with a coverageData >= 40X
+     There is a 92.77% of reference with a coverageData >= 41X
+     There is a 92.52% of reference with a coverageData >= 42X
+     There is a 92.27% of reference with a coverageData >= 43X
+     There is a 91.99% of reference with a coverageData >= 44X
+     There is a 91.72% of reference with a coverageData >= 45X
+     There is a 91.44% of reference with a coverageData >= 46X
+     There is a 91.17% of reference with a coverageData >= 47X
+     There is a 90.9% of reference with a coverageData >= 48X
+     There is a 90.64% of reference with a coverageData >= 49X
+     There is a 90.4% of reference with a coverageData >= 50X
+     There is a 90.15% of reference with a coverageData >= 51X
+
+
+>>>>>>> Coverage per contig
+
+	NZ_CP031250.1	1817261	366875582	201.88381415768015	112.27329056357358
+
+
diff -r 3d93dd18d9f8 -r bf675f34b056 test-data/qualimap_bamqc_genome_results.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/qualimap_bamqc_genome_results.tabular	Sat May 16 09:40:45 2020 -0400
@@ -0,0 +1,2 @@
+Sample	bam_file	total_reads	mapped_reads	mapped_bases	sequenced_bases	mean_insert_size	median_insert_size	mean_mapping_quality	general_error_rate	percentage_aligned
+x_bam	x_bam	1248774.0	1242183.0	366875582.0	366823893.0	1097.678	524.0	58.4552	0.0098	99.4722023360512