# HG changeset patch
# User iuc
# Date 1725286939 0
# Node ID 0771dee34cff6a8b61a282435c98b21a09ba5686
# Parent d01bcfd0418926ee66881c52090366b5bb3b7932
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
diff -r d01bcfd04189 -r 0771dee34cff bamtools_plugin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bamtools_plugin.xml Mon Sep 02 14:22:19 2024 +0000
@@ -0,0 +1,39 @@
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diff -r d01bcfd04189 -r 0771dee34cff bcftools_plugin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bcftools_plugin.xml Mon Sep 02 14:22:19 2024 +0000
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diff -r d01bcfd04189 -r 0771dee34cff bismark_plugin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bismark_plugin.xml Mon Sep 02 14:22:19 2024 +0000
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diff -r d01bcfd04189 -r 0771dee34cff bowtie2_plugin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bowtie2_plugin.xml Mon Sep 02 14:22:19 2024 +0000
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diff -r d01bcfd04189 -r 0771dee34cff busco_plugin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/busco_plugin.xml Mon Sep 02 14:22:19 2024 +0000
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diff -r d01bcfd04189 -r 0771dee34cff cutadapt_plugin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/cutadapt_plugin.xml Mon Sep 02 14:22:19 2024 +0000
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diff -r d01bcfd04189 -r 0771dee34cff deeptools_plugin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/deeptools_plugin.xml Mon Sep 02 14:22:19 2024 +0000
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diff -r d01bcfd04189 -r 0771dee34cff fastp_plugin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fastp_plugin.xml Mon Sep 02 14:22:19 2024 +0000
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diff -r d01bcfd04189 -r 0771dee34cff fastqc_plugin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fastqc_plugin.xml Mon Sep 02 14:22:19 2024 +0000
@@ -0,0 +1,71 @@
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+ value is not None and value.extension != "html"
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diff -r d01bcfd04189 -r 0771dee34cff featurecounts_plugin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/featurecounts_plugin.xml Mon Sep 02 14:22:19 2024 +0000
@@ -0,0 +1,50 @@
+
+ '${file_prefix}.summary';
+ cat '$file' >> '${file_prefix}.summary';
+ fi &&
+ #end for
+ ]]>
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diff -r d01bcfd04189 -r 0771dee34cff flexbar_plugin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/flexbar_plugin.xml Mon Sep 02 14:22:19 2024 +0000
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diff -r d01bcfd04189 -r 0771dee34cff gatk_plugin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gatk_plugin.xml Mon Sep 02 14:22:19 2024 +0000
@@ -0,0 +1,59 @@
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diff -r d01bcfd04189 -r 0771dee34cff macros.xml
--- a/macros.xml Sat Dec 10 11:20:55 2022 +0000
+++ b/macros.xml Mon Sep 02 14:22:19 2024 +0000
@@ -1,6 +1,6 @@
- 1.11
- 1
+ 1.24.1
+ 0
multiqc
@@ -9,14 +9,46 @@
multiqc
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+ 10.1101/gr.244293.118
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diff -r d01bcfd04189 -r 0771dee34cff multiqc.xml
--- a/multiqc.xml Sat Dec 10 11:20:55 2022 +0000
+++ b/multiqc.xml Mon Sep 02 14:22:19 2024 +0000
@@ -1,11 +1,31 @@
aggregate results from bioinformatics analyses into a single report
-
macros.xml
+ bamtools_plugin.xml
+ bcftools_plugin.xml
+ bismark_plugin.xml
+ bowtie2_plugin.xml
+ busco_plugin.xml
+ cutadapt_plugin.xml
+ deeptools_plugin.xml
+ fastqc_plugin.xml
+ fastp_plugin.xml
+ featurecounts_plugin.xml
+ flexbar_plugin.xml
+ gatk_plugin.xml
+ picard_plugin.xml
+ pycoqc_plugin.xml
+ qualimap_plugin.xml
+ rseqc_plugin.xml
+ salmon_plugin.xml
+ samtools_plugin.xml
+ star_plugin.xml
+ trimmomatic_plugin.xml
+ vcftools_plugin.xml
-
+
multiqc --version
'${file_prefix}.summary';
- cat '$file' >> '${file_prefix}.summary';
- fi &&
- #end for
+ @FEATURECOUNTS_COMMAND@
#elif str($repeat.software_cond.software) == "flexbar"
- #set $pattern = "flexible barcode and adapter removal"
- @LN_FILES@
+ @FLEXBAR_COMMAND@
#elif str($repeat.software_cond.software) == "gatk"
- #for $j, $repeat2 in enumerate( $repeat.software_cond.output )
- #if str($repeat2.type) == "varianteval"
- #set $pattern = "#:GATKTable:TiTvVariantEvaluator"
- @LN_2_FILES@
- #elif str($repeat2.type) == "base_recalibrator"
- #set $pattern = "#:GATKTable:Arguments:Recalibration"
- @LN_2_FILES@
- #end if
- #end for
+ @GATK_COMMAND@
#elif str($repeat.software_cond.software) == "hicup"
#for $file in $repeat.software_cond.input
@ESCAPE_IDENTIFIER@
@@ -112,15 +92,14 @@
ln -s '$file' '$file_path' &&
#end for
#elif str($repeat.software_cond.software) == "picard"
- @PICCARD_INPUT@
+ @PICARD_COMMAND@
#elif str($repeat.software_cond.software) == "prokka"
#set $pattern = "contigs:"
@LN_FILES@
#elif str($repeat.software_cond.software) == "pycoqc"
- #set $pattern = "\"pycoqc\":"
- @LN_FILES@
+ @PYCOQC_COMMAND@
#elif str($repeat.software_cond.software) == "qualimap"
- @QUALIMAP_INPUT@
+ @QUALIMAP_COMMAND@
#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))
@@ -135,14 +114,14 @@
ln -s '$file' '$file_path' &&
#end for
#elif str($repeat.software_cond.software) == "rseqc"
- @RSEQ_INPUT@
+ @RSEQC_COMMAND@
#elif str($repeat.software_cond.software) == "salmon"
- @SALMON_INPUT@
+ @SALMON_COMMAND@
#elif str($repeat.software_cond.software) == "samblaster"
#set $pattern = "samblaster: Version"
@LN_FILES@
#elif str($repeat.software_cond.software) == "samtools"
- @SAMTOOLS_INPUT@
+ @SAMTOOLS_COMMAND@
#elif str($repeat.software_cond.software) == "slamdunk"
#set $pattern = "# slamdunk"
@LN_FILES@
@@ -153,7 +132,7 @@
#set $pattern = "Minimal SW score based on E-value"
@LN_FILES@
#else if str($repeat.software_cond.software) == "star":
- @STAR_INPUT@
+ @STAR_COMMAND@
#elif str($repeat.software_cond.software) == "tophat"
#for $file in $repeat.software_cond.input
@ESCAPE_IDENTIFIER@
@@ -161,10 +140,9 @@
ln -s '$file' '$file_path' &&
#end for
#elif str($repeat.software_cond.software) == "trimmomatic"
- #set $pattern = "Trimmomatic"
- @LN_FILES@
+ @TRIMMOMATIC_COMMAND@
#elif str($repeat.software_cond.software) == "vcftools"
- @VCFTOOLS_INPUT@
+ @VCFTOOLS_COMMAND@
#else if str($repeat.software_cond.software) == "custom_content":
#set $configfile = "T"
#for $j, $file in enumerate( $repeat.software_cond.input )
@@ -191,34 +169,15 @@
#if $configfile == "T"
--config '$multiqc_config'
#end if
+
+&&
+mkdir -p ./plots &&
+ls -l ./report_data/ &&
+##cat ./report_data/multiqc_busco.txt &&
+cp ./report_data/*plot*.txt ./plots/ | true ## don't fail if no plot files are generated
+
]]>
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`_ aggregates results from bioinformatics analyses across many samples into a single report. It takes results of multiple analyses and creates a report that can be viewed as a single beautiful web-page. It's a general use tool, perfect for summarizing the output from numerous bioinformatics tools.
+`MultiQC `_ aggregates results from bioinformatics analyses across many samples into a single report.
+It takes results of multiple analyses and creates a report that can be viewed as a single beautiful web-page.
+It's a general use tool, perfect for summarizing the output from numerous bioinformatics tools.
**Inputs**
-MultiQC takes software output summaries/logs and creates a single report from them. You need to tell the tool which software was used to generate the report. This is done using the **Software name** dropdown. At present only the Galaxy tools found in the ToolShed produce logs that can used with MultiQC
-
-----
+MultiQC takes software output summaries/logs and creates a single report from them. You need to tell the tool which software was used to generate the report.
+This is done using the **Software name** dropdown. At present only the Galaxy tools found in the ToolShed produce logs that can used with MultiQC
-The first integration of this tool was made by
-`@cmonjeau `_ and `@yvanlebras `_.
-It is now maintained by the `Intergalactic Utilities Commission `_.
]]>
10.1093/bioinformatics/btw354
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diff -r d01bcfd04189 -r 0771dee34cff picard_plugin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_plugin.xml Mon Sep 02 14:22:19 2024 +0000
@@ -0,0 +1,119 @@
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diff -r d01bcfd04189 -r 0771dee34cff pycoqc_plugin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/pycoqc_plugin.xml Mon Sep 02 14:22:19 2024 +0000
@@ -0,0 +1,39 @@
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diff -r d01bcfd04189 -r 0771dee34cff qualimap_plugin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qualimap_plugin.xml Mon Sep 02 14:22:19 2024 +0000
@@ -0,0 +1,62 @@
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diff -r d01bcfd04189 -r 0771dee34cff rseqc_plugin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rseqc_plugin.xml Mon Sep 02 14:22:19 2024 +0000
@@ -0,0 +1,133 @@
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diff -r d01bcfd04189 -r 0771dee34cff salmon_plugin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/salmon_plugin.xml Mon Sep 02 14:22:19 2024 +0000
@@ -0,0 +1,62 @@
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diff -r d01bcfd04189 -r 0771dee34cff samtools_plugin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_plugin.xml Mon Sep 02 14:22:19 2024 +0000
@@ -0,0 +1,97 @@
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diff -r d01bcfd04189 -r 0771dee34cff star_plugin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/star_plugin.xml Mon Sep 02 14:22:19 2024 +0000
@@ -0,0 +1,77 @@
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diff -r d01bcfd04189 -r 0771dee34cff template_plugin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/template_plugin.xml Mon Sep 02 14:22:19 2024 +0000
@@ -0,0 +1,59 @@
+
+
+
+ #set $pattern = "Trimmomatic"
+ @LN_FILES@f
+ ]]>
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diff -r d01bcfd04189 -r 0771dee34cff test-data/mqc_fastqc_per_base_sequence_quality_plot_1.txt
--- a/test-data/mqc_fastqc_per_base_sequence_quality_plot_1.txt Sat Dec 10 11:20:55 2022 +0000
+++ b/test-data/mqc_fastqc_per_base_sequence_quality_plot_1.txt Mon Sep 02 14:22:19 2024 +0000
@@ -1,3 +1,3 @@
-Sample 1 2 3 4 5 6 7 8 9 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72 74 76 78 80 82 84 86 88 90 92 94 96 98 100
-poulet5_1 20.91988023102569 20.71684045861661 20.351574954545285 22.531542025544244 24.673566076408722 25.813099918237516 27.587864804423386 27.598941941168345 27.07115949658203 27.129873548155864 27.009298149330405 27.123565889736383 27.086309823818645 27.07924614241606 27.082520375286073 27.054301117420636 27.06350966402712 27.082996389756914 27.065495857740743 27.09608772106672 27.087097581099798 27.098251253504774 27.05184077595959 27.06521958267531 27.072148859992012 27.065725464720796 27.07168031241483 27.048083061725073 27.04642354460909 27.062865644448927 27.01859629866081 26.994157155710866 27.110127347871376 26.995846540401494 27.00461640700544 26.981614641085088 26.98900313236189 27.001189102815392 26.917739099268616 26.98481793846533 26.89518908041471 26.93677034448514 26.87640237596556 26.906094478605482 26.80463992772047 26.717012197170796 26.46960974280285 26.442842795754324 26.34282375517549 26.03493946215965 25.833215729758187 25.503102494315826 24.52807178671565 23.202399486277717 23.72906749698524
-poulet5_2 20.590586487162543 20.458478471078855 20.178608096352797 22.495204387546714 24.59397272343746 25.77560491172265 26.651378201897337 27.54968284369178 27.089005372429988 27.058984726469017 26.954911162632676 27.066410552214123 27.04552938409328 27.025118630273028 27.019042445557012 27.010315513591614 27.03931879529138 26.978450544896567 27.003714779595967 27.025971722873706 27.017791740868923 27.00628899118533 27.00906294218011 27.034922661648913 27.005346295860726 27.000909094303132 27.004913216028434 26.979999925331065 26.941037674211962 26.99995146519121 26.95084543903468 26.97609847339359 26.99262270906369 26.942271578389317 26.88024222603034 26.866450873439888 26.947610407356386 26.975012040366025 26.966286975124042 26.917634562757375 26.885127441207544 26.846286527110426 26.769134848366058 26.709703975000842 26.551336760637525 26.42626069165836 26.309463541024982 26.127226534353312 25.91885539987082 25.674260497519125 25.371903572535274 24.758753999454918 23.84710415196622 22.40618968149965 23.009550156991438
+Sample 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54
+poulet5_1 (1, 20.91988023102569) (2, 20.71684045861661) (3, 20.351574954545285) (4, 22.531542025544244) (5, 24.673566076408722) (6, 25.813099918237516) (7, 27.587864804423386) (8, 27.598941941168345) (9, 27.07115949658203) (10, 27.129873548155864) (12, 27.009298149330405) (14, 27.123565889736383) (16, 27.086309823818645) (18, 27.07924614241606) (20, 27.082520375286073) (22, 27.054301117420636) (24, 27.06350966402712) (26, 27.082996389756914) (28, 27.065495857740743) (30, 27.09608772106672) (32, 27.087097581099798) (34, 27.098251253504774) (36, 27.05184077595959) (38, 27.06521958267531) (40, 27.072148859992012) (42, 27.065725464720796) (44, 27.07168031241483) (46, 27.048083061725073) (48, 27.04642354460909) (50, 27.062865644448927) (52, 27.01859629866081) (54, 26.994157155710866) (56, 27.110127347871376) (58, 26.995846540401494) (60, 27.00461640700544) (62, 26.981614641085088) (64, 26.98900313236189) (66, 27.001189102815392) (68, 26.917739099268616) (70, 26.98481793846533) (72, 26.89518908041471) (74, 26.93677034448514) (76, 26.87640237596556) (78, 26.906094478605482) (80, 26.80463992772047) (82, 26.717012197170796) (84, 26.46960974280285) (86, 26.442842795754324) (88, 26.34282375517549) (90, 26.03493946215965) (92, 25.833215729758187) (94, 25.503102494315826) (96, 24.52807178671565) (98, 23.202399486277717) (100, 23.72906749698524)
+poulet5_2 (1, 20.590586487162543) (2, 20.458478471078855) (3, 20.178608096352797) (4, 22.495204387546714) (5, 24.59397272343746) (6, 25.77560491172265) (7, 26.651378201897337) (8, 27.54968284369178) (9, 27.089005372429988) (10, 27.058984726469017) (12, 26.954911162632676) (14, 27.066410552214123) (16, 27.04552938409328) (18, 27.025118630273028) (20, 27.019042445557012) (22, 27.010315513591614) (24, 27.03931879529138) (26, 26.978450544896567) (28, 27.003714779595967) (30, 27.025971722873706) (32, 27.017791740868923) (34, 27.00628899118533) (36, 27.00906294218011) (38, 27.034922661648913) (40, 27.005346295860726) (42, 27.000909094303132) (44, 27.004913216028434) (46, 26.979999925331065) (48, 26.941037674211962) (50, 26.99995146519121) (52, 26.95084543903468) (54, 26.97609847339359) (56, 26.99262270906369) (58, 26.942271578389317) (60, 26.88024222603034) (62, 26.866450873439888) (64, 26.947610407356386) (66, 26.975012040366025) (68, 26.966286975124042) (70, 26.917634562757375) (72, 26.885127441207544) (74, 26.846286527110426) (76, 26.769134848366058) (78, 26.709703975000842) (80, 26.551336760637525) (82, 26.42626069165836) (84, 26.309463541024982) (86, 26.127226534353312) (88, 25.91885539987082) (90, 25.674260497519125) (92, 25.371903572535274) (94, 24.758753999454918) (96, 23.84710415196622) (98, 22.40618968149965) (100, 23.009550156991438)
diff -r d01bcfd04189 -r 0771dee34cff trimmomatic_plugin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimmomatic_plugin.xml Mon Sep 02 14:22:19 2024 +0000
@@ -0,0 +1,40 @@
+
+
+
+ #set $pattern = "Trimmomatic"
+ @LN_FILES@
+
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diff -r d01bcfd04189 -r 0771dee34cff vcftools_plugin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/vcftools_plugin.xml Mon Sep 02 14:22:19 2024 +0000
@@ -0,0 +1,94 @@
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