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+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.
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+- Fastqc
+- Cutadapt / Trim Galore!
+- Tophat2
+- FeatureCounts (summary file with the column header in the first line or as metadata)
+- Samtools (stats, flagstat, dxstats)
+- Picard (MarkDuplicatesMetrics, CollectGCBiasMetrics, CollectInsertSizeMetrics, CollectAlignmentSummaryMetrics, CollectRnaSeqMetrics)
+- Bismark (Alignment report file)
+- Bowtie2 (Metrics file)
+- HTSeq-count ("no feature" file; although the "Assigned" metric is always 0)
+- RNA STAR (Alignment from Log.final.out, Gene counts from ReadsPerGene.out.tab)
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+----
+
+**Integrated by**
+
+Cyril Monjeaud and Yvan Le Bras
+`EnginesOn <http://engineson.fr/>`_ and Rennes GenOuest Bio-informatics Core Facility
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+ ]]>
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+ #if str($repeat.software) == "fastqc":
+ ## Searches for files named "fastqc_data.txt"
+ #for $k, $file in enumerate($repeat.input_file):
+ mkdir multiqc_WDir/${repeat.software}_${i}/file_${k} &&
+ ln -s '${file}' multiqc_WDir/fastqc_${i}/file_${k}/fastqc_data.txt &&
+ #end for
+ #else if str($repeat.software) == "tophat":
+ ## Searches for files ending in "align_summary.txt"
+ #for $file in $repeat.input_file:
+ ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}align_summary.txt' &&
+ #end for
+ #else if str($repeat.software) == "bowtie2":
+ ## Searches for files containing 'reads; of these;'
+ #for $file in $repeat.input_file:
+ ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.txt' &&
+ #end for
+ #else if str($repeat.software) == "cutadapt":
+ ## Searches for files containing 'This is cutadapt'
+ #for $file in $repeat.input_file:
+ cat '${file}' > 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.txt' &&
+ ## replace header for old cutadapt release
+ sed -i .old 's/You are running/This is/' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.txt' &&
+ #end for
+ #else if str($repeat.software) == "featurecounts":
+ ## Checks for files ending in '.summary'
+ #for $file in $repeat.input_file
+ #if $file.metadata.column_names and $file.metadata.column_names.find(',') != -1
+ echo '$file.metadata.column_names.replace(',','\t').replace('__ob__u','').replace('u__sq__','').replace('__sq__','').replace('__cb__','')' >> 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.summary' &&
+ cat '$file' >> 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.summary' &&
+ #else
+ ln -s '$file' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.summary' &&
+ #end if
+ #end for
+ #else if str($repeat.software) == "bismark":
+ ## Checks for files ending in _SE_report.txt
+ #for $file in $repeat.input_file
+ ln -s ${file} 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}_SE_report.txt' &&
+ #end for
+ #else if str($repeat.software) == "samtools":
+ ## Checks for files containing 'This file was produced by samtools stats'
+ #for $file in $repeat.input_file
+ ln -s ${file} 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' &&
+ #end for
+ #else if str($repeat.software) == "picard":
+ #for $file in $repeat.input_file
+ ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' &&
+ #end for
+ #else if str($repeat.software) == "samtools_idxstats":
+ ## Checks for files containing "idxstats" in the name
+ #for $file in $repeat.input_file
+ ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}_idxstats.txt' &&
+ #end for
+ #else if str($repeat.software) == "htseq":
+ ## Checks for files containing "__too_low_aQual"
+ #for $file in $repeat.input_file
+ ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' &&
+ #end for
+ #else if str($repeat.software) == "rnastar_log":
+ ## Checks for files named Log.final.out
+ #for $k, $file in enumerate($repeat.input_file):
+ mkdir 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' &&
+ ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}/Log.final.out' &&
+ #end for
+ #else if str($repeat.software) == "rnastar_counts":
+ ## Checks for files named ReadsPerGene.out.tab
+ #for $k, $file in enumerate($repeat.input_file):
+ mkdir 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' &&
+ ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}/ReadsPerGene.out.tab' &&
+ #end for
+ #end if
+#end for
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+multiqc multiqc_WDir
+ ]]>
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-
-
- | - | <tool id="multiqc" name="multiqc" version="@WRAPPER_VERSION@.0"> | -
| - | <description>aggregate results from bioinformatics analyses into a single report</description> | -
| - | <macros> | -
| - | <token name="@WRAPPER_VERSION@">1.0.0</token> | -
| - | </macros> | -
| - | <requirements> | -
| - | <requirement type="package" version="@WRAPPER_VERSION@">multiqc</requirement> | -
| - | </requirements> | -
| - | <version_command>@WRAPPER_VERSION@</version_command> | -
| - | <command detect_errors="aggressive"> | -
| - | <![CDATA[ | -
| - | mkdir multiqc_WDir && | -
| - | - |
| - | #for $i, $repeat in enumerate( $results ) | -
| - | mkdir multiqc_WDir/${repeat.software}_${i} && | -
| - | - |
| - | #if str($repeat.software) == "fastqc": | -
| - | ## Searches for files named "fastqc_data.txt" | -
| - | #for $k, $file in enumerate($repeat.input_file): | -
| - | mkdir multiqc_WDir/${repeat.software}_${i}/file_${k} && | -
| - | ln -s '${file}' multiqc_WDir/fastqc_${i}/file_${k}/fastqc_data.txt && | -
| - | #end for | -
| - | #else if str($repeat.software) == "tophat": | -
| - | ## Searches for files ending in "align_summary.txt" | -
| - | #for $file in $repeat.input_file: | -
| - | ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}align_summary.txt' && | -
| - | #end for | -
| - | #else if str($repeat.software) == "bowtie2": | -
| - | ## Searches for files containing 'reads; of these;' | -
| - | #for $file in $repeat.input_file: | -
| - | ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.txt' && | -
| - | #end for | -
| - | #else if str($repeat.software) == "cutadapt": | -
| - | ## Searches for files containing 'This is cutadapt' | -
| - | #for $file in $repeat.input_file: | -
| - | cat '${file}' > 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.txt' && | -
| - | ## replace header for old cutadapt release | -
| - | sed -i .old 's/You are running/This is/' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.txt' && | -
| - | #end for | -
| - | #else if str($repeat.software) == "featurecounts": | -
| - | ## Checks for files ending in '.summary' | -
| - | #for $file in $repeat.input_file | -
| - | #if $file.metadata.column_names and $file.metadata.column_names.find(',') != -1 | -
| - | echo '$file.metadata.column_names.replace(',','\t').replace('__ob__u','').replace('u__sq__','').replace('__sq__','').replace('__cb__','')' >> 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.summary' && | -
| - | cat '$file' >> 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.summary' && | -
| - | #else | -
| - | ln -s '$file' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}.summary' && | -
| - | #end if | -
| - | #end for | -
| - | #else if str($repeat.software) == "bismark": | -
| - | ## Checks for files ending in _SE_report.txt | -
| - | #for $file in $repeat.input_file | -
| - | ln -s ${file} 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}_SE_report.txt' && | -
| - | #end for | -
| - | #else if str($repeat.software) == "samtools": | -
| - | ## Checks for files containing 'This file was produced by samtools stats' | -
| - | #for $file in $repeat.input_file | -
| - | ln -s ${file} 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' && | -
| - | #end for | -
| - | #else if str($repeat.software) == "picard": | -
| - | #for $file in $repeat.input_file | -
| - | ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' && | -
| - | #end for | -
| - | #else if str($repeat.software) == "samtools_idxstats": | -
| - | ## Checks for files containing "idxstats" in the name | -
| - | #for $file in $repeat.input_file | -
| - | ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}_idxstats.txt' && | -
| - | #end for | -
| - | #else if str($repeat.software) == "htseq": | -
| - | ## Checks for files containing "__too_low_aQual" | -
| - | #for $file in $repeat.input_file | -
| - | ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' && | -
| - | #end for | -
| - | #else if str($repeat.software) == "rnastar_log": | -
| - | ## Checks for files named Log.final.out | -
| - | #for $k, $file in enumerate($repeat.input_file): | -
| - | mkdir 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' && | -
| - | ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}/Log.final.out' && | -
| - | #end for | -
| - | #else if str($repeat.software) == "rnastar_counts": | -
| - | ## Checks for files named ReadsPerGene.out.tab | -
| - | #for $k, $file in enumerate($repeat.input_file): | -
| - | mkdir 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}' && | -
| - | ln -s '${file}' 'multiqc_WDir/${repeat.software}_${i}/${file.element_identifier}/ReadsPerGene.out.tab' && | -
| - | #end for | -
| - | #end if | -
| - | #end for | -
| - | - |
| - | multiqc multiqc_WDir | -
| - | ]]></command> | -
| - | <inputs> | -
| - | <repeat name="results" title="Results" min="1"> | -
| - | <param name="software" type="select" label="Software name" help="Which tool was used generate logs?"> | -
| - | <option value="fastqc">FastQC</option> | -
| - | <option value="cutadapt">Cutadapt/Trim Galore!</option> | -
| - | <option value="tophat">Tophat2</option> | -
| - | <option value="featurecounts">FeatureCounts (Summary file)</option> | -
| - | <option value="samtools">Samtools (Stats, Flagstat)</option> | -
| - | <option value="samtools_idxstats">Samtools (Idxstats)</option> | -
| - | <option value="picard">Picard</option> | -
| - | <option value="bismark">Bismark</option> | -
| - | <option value="bowtie2">Bowtie2</option> | -
| - | <option value="htseq">HTSeq-Count</option> | -
| - | <option value="rnastar_log">RNA STAR (log)</option> | -
| - | <option value="rnastar_counts">RNA STAR (reads per gene)</option> | -
| - | </param> | -
| - | <param name="input_file" type="data" format="txt, tabular" multiple="true" label="Result file" help="Select input datasets"/> | -
| - | </repeat> | -
| - | <param name="saveLog" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Save log file" help="Save the multiQC log file to the history. This is mostly useful for debugging purposes."/> | -
| - | </inputs> | -
| - | <outputs> | -
| - | <data format="html" from_work_dir="multiqc_report.html" name="html_file" label="${tool.name} on ${on_string}: Webpage" /> | -
| - | <data format="txt" name="text_file" from_work_dir="multiqc_data/multiqc.log" label="${tool.name} on ${on_string}: Log"> | -
| - | <filter>saveLog</filter> | -
| - | </data> | -
| - | </outputs> | -
| - | <tests> | -
| - | <test> | -
| - | <repeat name="results"> | -
| - | <param name="software" value="fastqc" /> | -
| - | <param name="input_file" value="fastqc_data.txt" /> | -
| - | </repeat> | -
| - | <param name="saveLog" value="True"/> | -
| - | <output name="html_file" file="report_fastqc.html" compare="sim_size" delta="1000"/> | -
| - | <output name="text_file" file="log_fastqc.txt" compare="sim_size" delta="1000"/> | -
| - | </test> | -
| - | <test> | -
| - | <repeat name="results"> | -
| - | <param name="software" value="fastqc" /> | -
| - | <param name="input_file" value="fastqc_data.txt,fastqc_data_2.txt" /> | -
| - | </repeat> | -
| - | <output name="html_file" file="report_fastqc_2.html" compare="sim_size" delta="1000"/> | -
| - | </test> | -
| - | <test> | -
| - | <repeat name="results"> | -
| - | <param name="software" value="cutadapt" /> | -
| - | <param name="input_file" value="cutadapt.txt" /> | -
| - | </repeat> | -
| - | <output name="html_file" file="report_cutadapt.html" compare="sim_size" delta="1000"/> | -
| - | </test> | -
| - | <test> | -
| - | <repeat name="results"> | -
| - | <param name="software" value="tophat" /> | -
| - | <param name="input_file" value="tophat_data.txt" /> | -
| - | </repeat> | -
| - | <output name="html_file" file="report_tophat.html" compare="sim_size" delta="1000"/> | -
| - | </test> | -
| - | <test> | -
| - | <repeat name="results"> | -
| - | <param name="software" value="bowtie2" /> | -
| - | <param name="input_file" value="bowtie2SE1.txt,bowtie2SE2.txt" /> | -
| - | </repeat> | -
| - | <output name="html_file" file="report_bowtie2SE.html" compare="sim_size" delta="1000"/> | -
| - | </test> | -
| - | <test> | -
| - | <repeat name="results"> | -
| - | <param name="software" value="featurecounts" /> | -
| - | <param name="input_file" value="featurecounts_data.txt" /> | -
| - | </repeat> | -
| - | <output name="html_file" file="report_featurecounts.html" compare="sim_size" delta="1000"/> | -
| - | </test> | -
| - | <test> | -
| - | <repeat name="results"> | -
| - | <param name="software" value="picard" /> | -
| - | <param name="input_file" value="collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt,picard_CollectBaseDistributionByCycle.txt,picard_CollectRnaSeqMetrics.txt,picard_CollectAlignmentSummaryMetrics.txt" /> | -
| - | </repeat> | -
| - | <output name="html_file" file="report_picard.html" compare="sim_size" delta="10000"/> | -
| - | </test> | -
| - | <test> | -
| - | <repeat name="results"> | -
| - | <param name="software" value="htseq" /> | -
| - | <param name="input_file" value="htseq_data.txt" /> | -
| - | </repeat> | -
| - | <output name="html_file" file="report_htseq.html" compare="sim_size" delta="1000"/> | -
| - | </test> | -
| - | <test> | -
| - | <repeat name="results"> | -
| - | <param name="software" value="rnastar_log" /> | -
| - | <param name="input_file" value="rnastar_log.txt" /> | -
| - | </repeat> | -
| - | <output name="html_file" file="report_rnastar_log.html" compare="sim_size" delta="1000"/> | -
| - | </test> | -
| - | <test> | -
| - | <repeat name="results"> | -
| - | <param name="software" value="rnastar_counts" /> | -
| - | <param name="input_file" value="rnastar_counts.txt" /> | -
| - | </repeat> | -
| - | <output name="html_file" file="report_rnastar_counts.html" compare="sim_size" delta="1000"/> | -
| - | </test> | -
| - | <test> | -
| - | <repeat name="results"> | -
| - | <param name="software" value="bismark" /> | -
| - | <param name="input_file" value="bismark_data.txt" /> | -
| - | </repeat> | -
| - | <output name="html_file" file="report_bismark.html" compare="sim_size" delta="1000"/> | -
| - | </test> | -
| - | <test> | -
| - | <repeat name="results"> | -
| - | <param name="software" value="samtools" /> | -
| - | <param name="input_file" value="samtools_stats.txt,samtools_flagstat.txt" /> | -
| - | </repeat> | -
| - | <output name="html_file" file="report_samtools.html" compare="sim_size" delta="1000"/> | -
| - | </test> | -
| - | <test> | -
| - | <repeat name="results"> | -
| - | <param name="software" value="samtools_idxstats" /> | -
| - | <param name="input_file" value="samtools_idxstats.txt" /> | -
| - | </repeat> | -
| - | <output name="html_file" file="report_samtools_idxstats.html" compare="sim_size" delta="1000"/> | -
| - | </test> | -
| - | <test> | -
| - | <repeat name="results"> | -
| - | <param name="software" value="fastqc" /> | -
| - | <param name="input_file" value="fastqc_data.txt,fastqc_data_2.txt" /> | -
| - | </repeat> | -
| - | <repeat name="results"> | -
| - | <param name="software" value="cutadapt" /> | -
| - | <param name="input_file" value="cutadapt.txt" /> | -
| - | </repeat> | -
| - | <repeat name="results"> | -
| - | <param name="software" value="tophat" /> | -
| - | <param name="input_file" value="tophat_data.txt" /> | -
| - | </repeat> | -
| - | <repeat name="results"> | -
| - | <param name="software" value="featurecounts" /> | -
| - | <param name="input_file" value="featurecounts_data.txt" /> | -
| - | </repeat> | -
| - | <repeat name="results"> | -
| - | <param name="software" value="picard" /> | -
| - | <param name="input_file" value="collectGcBias_data.txt,CollectInsertSizeMetrics.txt,MarkDuplicates_data.txt" /> | -
| - | </repeat> | -
| - | <repeat name="results"> | -
| - | <param name="software" value="bismark" /> | -
| - | <param name="input_file" value="bismark_data.txt" /> | -
| - | </repeat> | -
| - | <repeat name="results"> | -
| - | <param name="software" value="samtools" /> | -
| - | <param name="input_file" value="samtools_stats.txt,samtools_flagstat.txt" /> | -
| - | </repeat> | -
| - | <output name="html_file" file="report_all.html" compare="sim_size" delta="5000"/> | -
| - | </test> | -
| - | </tests> | -
| - | - | -
| - | <help><![CDATA[ | -
| - | **What it does** | -
| - | - |
| - | 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 the following Galaxy tools produce logs that can used with MultiQC. There are: | -
| - | - |
| - | - Fastqc | -
| - | - Cutadapt / Trim Galore! | -
| - | - Tophat2 | -
| - | - FeatureCounts (summary file with the column header in the first line or as metadata) | -
| - | - Samtools (stats, flagstat, dxstats) | -
| - | - Picard (MarkDuplicatesMetrics, CollectGCBiasMetrics, CollectInsertSizeMetrics, CollectAlignmentSummaryMetrics, CollectRnaSeqMetrics) | -
| - | - Bismark (Alignment report file) | -
| - | - Bowtie2 (Metrics file) | -
| - | - HTSeq-count ("no feature" file; although the "Assigned" metric is always 0) | -
| - | - RNA STAR (Alignment from Log.final.out, Gene counts from ReadsPerGene.out.tab) | -
| - | - |
| - | ---- | -
| - | - |
| - | **Integrated by** | -
| - | - |
| - | Cyril Monjeaud and Yvan Le Bras | -
| - | - |
| - | `EnginesOn <http://engineson.fr/>`_ and Rennes GenOuest Bio-informatics Core Facility | -
| - | - |
| - | ]]></help> | -
| - | <citations> | -
| - | <citation type="doi">10.1093/bioinformatics/btw354</citation> | -
| - | </citations> | -
| - | </tool> | -