Mercurial > repos > iuc > multiqc
diff multiqc.xml @ 8:e0f4a651c6b9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 13875b17a3a5259b9705529a3597bea12828cb20
| author | iuc |
|---|---|
| date | Fri, 20 Apr 2018 01:06:25 -0400 |
| parents | 467486f1c568 |
| children | df99138d2776 |
line wrap: on
line diff
--- a/multiqc.xml Sun Jan 14 09:55:46 2018 -0500 +++ b/multiqc.xml Fri Apr 20 01:06:25 2018 -0400 @@ -1,26 +1,49 @@ -<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.1"> +<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@">1.3</token> + <token name="@WRAPPER_VERSION@">1.5</token> + <token name="@ESCAPE_IDENTIFIER@"> +<![CDATA[ +#set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier)) + ]]></token> + <token name="@CHECK_LN_FILE@"> +<![CDATA[ +grep -q "$pattern" $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" && +ln -s '$file' '$file_path' && + ]]></token> + <token name="@CREATE_REPEAT_DIR_1@"> +<![CDATA[ +#set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j)) +mkdir '$repeat_dir' && + ]]></token> + <token name="@CREATE_REPEAT_DIR_2@"> +<![CDATA[ +#set repeat_dir = os.path.join($software_dir, str($repeat2.type.type) + '_' + str($j)) +mkdir '$repeat_dir' && + ]]></token> <token name="@LN_FILES@"> <![CDATA[ #for $file in $repeat.software_cond.input - grep -q "$pattern" $file || die "'$pattern' not found in the file" && - ln -s '$file' '$software_dir/${file.element_identifier}' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($software_dir, str($identifier)) + @CHECK_LN_FILE@ #end for ]]></token> <token name="@LN_2_FILES@"> <![CDATA[ -#for $file in $repeat2.input: - grep -q "$pattern" $file || die "'$pattern' not found in the file" && - ln -s '$file' '$software_dir/${repeat2.type}_${j}_${file.element_identifier}' && +@CREATE_REPEAT_DIR_1@ +#for $file in $repeat2.input + #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier)) + #set file_path = os.path.join($repeat_dir, str($identifier)) + @CHECK_LN_FILE@ #end for ]]></token> <token name="@LN_3_FILES@"> <![CDATA[ -#for $file in $repeat2.type.input: - grep -q "$pattern" $file || die "'$pattern' not found in the file" && - ln -s '$file' '$repeat_dir/${file.element_identifier}' && +#for $file in $repeat2.type.input + #set identifier = re.sub('[^\s\w\-]', '_', str($file.element_identifier)) + #set file_path = os.path.join($repeat_dir, str($identifier)) + @CHECK_LN_FILE@ #end for ]]></token> </macros> @@ -30,6 +53,9 @@ <version_command>multiqc --version</version_command> <command detect_errors="aggressive"> <![CDATA[ +#import re +#import os + die() { echo "$@" 1>&2 ; exit 1; } && mkdir multiqc_WDir && @@ -37,7 +63,7 @@ #set $configfile="F" #for $i, $repeat in enumerate( $results ) - #set software_dir = 'multiqc_WDir/' + str($repeat.software_cond.software) + '_' + str($i) + #set software_dir = os.path.join('multiqc_WDir', str($repeat.software_cond.software) + '_' + str($i)) mkdir $software_dir && #if str($repeat.software_cond.software) == "bamtools" @@ -48,26 +74,36 @@ @LN_FILES@ #elif str($repeat.software_cond.software) == "bismark" #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) - #set file_prefix = $software_dir + '/' + str($repeat2.type) + '_' + str($j) + @CREATE_REPEAT_DIR_1@ #if str($repeat2.type) == "align" #for $file in $repeat2.input - ln -s '$file' '${file_prefix}_${file.element_identifier}_SE_report.txt' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '_SE_report.txt') + ln -s '$file' '$file_path' && #end for #elif str($repeat2.type) == "dedup" #for $file in $repeat2.input - ln -s '$file' '${file_prefix}_${file.element_identifier}_deduplication_report.txt' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '_deduplication_report.txt') + ln -s '$file' '$file_path' && #end for #elif str($repeat2.type) == "meth_extract" #for $file in $repeat2.input - ln -s '$file' '${file_prefix}_${file.element_identifier}_splitting_report.txt' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '_splitting_report.txt') + ln -s '$file' '$file_path' && #end for #elif str($repeat2.type) == "m_bias" #for $file in $repeat2.input - ln -s '$file' '${file_prefix}_${file.element_identifier}_M-bias.txt' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '_M-bias.txt') + ln -s '$file' '$file_path' && #end for #elif str($repeat2.type) == "bam2nuc" #for $file in $repeat2.input - ln -s '$file' '${file_prefix}_${file.element_identifier}.nucleotide_stats.txt' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '.nucleotide_stats.txt') + ln -s '$file' '$file_path' && #end for #end if #end for @@ -77,40 +113,68 @@ #elif str($repeat.software_cond.software) == "busco" ## Searches for files "short_summary_[samplename].txt" #for $file in $repeat.software_cond.input - ln -s '$file' '$software_dir/short_summary_${file.element_identifier}' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($software_dir, 'short_summary_' + str($identifier)) + ln -s '$file' '$file_path' && #end for #elif str($repeat.software_cond.software) == "cutadapt" #set $pattern = "This is cutadapt" #for $file in $repeat.software_cond.input - #set file_path = $software_dir + '/' + str($file.element_identifier) + '.txt' + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($software_dir, str($identifier) + '.txt') ln -s '$file' '$file_path' && ## replace header for old cutadapt release sed -i.old 's/You are running/This is/' '$file_path' && grep -q "$pattern" '$file_path' || die "'$pattern' or 'You are running cutadapt' not found in the file" && #end for + #elif str($repeat.software_cond.software) == "deeptools" + #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) + #if str($repeat2.type) == "bamPEFragmentSize" + #set $pattern = "Frag." + @LN_2_FILES@ + #elif str($repeat2.type) == "estimateReadFiltering" + #set $pattern = "Internally-determined Duplicate" + @LN_2_FILES@ + #elif str($repeat2.type) == "plotCoverageStdout" + #set $pattern = "sample" + @LN_2_FILES@ + #elif str($repeat2.type) == "plotCoverageOutRawCounts" + #set $pattern = "#plotCoverage --outRawCounts" + @LN_2_FILES@ + #elif str($repeat2.type) == "plotEnrichment" + #set $pattern = "featureReadCount" + @LN_2_FILES@ + #elif str($repeat2.type) == "plotFingerprintOutRawCounts" + #set $pattern = "#plotFingerprint --outRawCounts" + @LN_2_FILES@ + #end if + #end for #elif str($repeat.software_cond.software) == "fastqc" #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) - #set repeat_dir = $software_dir + '/' + str($repeat2.type) + '_' + str($j) - mkdir '$repeat_dir' && + @CREATE_REPEAT_DIR_1@ #if str($repeat2.type) == "data" #for $k, $file in enumerate($repeat2.input) - #set file_dir = $repeat_dir + '/file_' + str($k) + #set file_dir = os.path.join($repeat_dir, 'file_' + str($k)) + #set file_path = os.path.join($file_dir, 'fastqc_data.txt') mkdir '$file_dir' && - ln -s '$file' '$file_dir/fastqc_data.txt' && + ln -s '$file' '$file_path' && #end for #elif str($repeat2.type) == "theoretical_gc" #for $file in $repeat2.input - ln -s '$file' '$repeat_dir/${file.element_identifier}_fastqc_theoretical_gc' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '_fastqc_theoretical_gc') + ln -s '$file' '$file_path' && #end for #end if #end for #elif str($repeat.software_cond.software) == "featureCounts" #for $file in $repeat.software_cond.input - #set file_prefix = $software_dir + '/' + str($file.element_identifier) + @ESCAPE_IDENTIFIER@ + #set file_prefix = os.path.join($software_dir, str($identifier)) if grep -qw Status '$file'; then ln -s '$file' '${file_prefix}.summary'; else - echo -e 'Status\t$file.element_identifier' > '${file_prefix}.summary'; + echo -e 'Status\t${identifier}' > '${file_prefix}.summary'; cat '$file' >> '${file_prefix}.summary'; fi && #end for @@ -129,7 +193,9 @@ #end for #elif str($repeat.software_cond.software) == "hicup" #for $file in $repeat.software_cond.input - ln -s '${file}' '$software_dir/HiCUP_summary_report_${file.element_identifier}' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($software_dir, 'HiCUP_summary_report_' + str($identifier)) + ln -s '${file}' '$file_path' && #end for #elif str($repeat.software_cond.software) == "hisat2" #set $pattern = "HISAT2 summary stats:" @@ -185,35 +251,40 @@ @LN_FILES@ #elif str($repeat.software_cond.software) == "quast" #for $k, $file in enumerate($repeat.software_cond.input) - #set file_dir = $software_dir + '/file_' + str($k) + #set file_dir = os.path.join($software_dir, 'file_' + str($k)) + #set file_path = os.path.join($file_dir, 'report.tsv') mkdir '$file_dir' && - ln -s '$file' '$file_dir/report.tsv' && + ln -s '$file' '$file_path' && #end for #elif str($repeat.software_cond.software) == "rsem" #for $file in $repeat.software_cond.input - ln -s '$file' '$software_dir/${file.element_identifier}.cnt' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($software_dir, str($identifier) + '.cnt') + ln -s '$file' '$file_path' && #end for #elif str($repeat.software_cond.software) == "rseqc" #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) - #set repeat_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j) - mkdir '$repeat_dir' && + @CREATE_REPEAT_DIR_2@ #if str($repeat2.type.type) == "bam_stat" #set $pattern = "Proper-paired reads map to different chrom:" @LN_3_FILES@ #elif str($repeat2.type.type) == "gene_body_coverage" #for $k, $file in enumerate($repeat2.type.input) - ln -s '$file' '$repeat_dir/file_${k}.geneBodyCoverage.txt' && + #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.geneBodyCoverage.txt') + ln -s '$file' '$file_path' && #end for #elif str($repeat2.type.type) == "inner_distance" #for $k, $file in enumerate($repeat2.type.input) - ln -s '${file}' '$repeat_dir/file_${k}.inner_distance_freq.txt' && + #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.inner_distance_freq.txt') + ln -s '${file}' '$file_path' && #end for #elif str($repeat2.type.type) == "junction_annotation" #set $pattern = "Partial Novel Splicing Junctions:" @LN_3_FILES@ #elif str($repeat2.type.type) == "read_gc" #for $k, $file in enumerate($repeat2.type.input) - ln -s '$file' '$repeat_dir/file_${k}.GC.xls' && + #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.GC.xls') + ln -s '$file' '$file_path' && #end for #elif str($repeat2.type.type) == "junction_annotation" #set $pattern = "Group Total_bases Tag_count Tags/Kb" @@ -223,31 +294,34 @@ @LN_3_FILES@ #elif str($repeat2.type.type) == "read_duplication_pos" #for $k, $file in enumerate($repeat2.type.input) - ln -s '$file' '$repeat_dir/file_${k}.pos.DupRate.xls' && + #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.pos.DupRate.xls') + ln -s '$file' '$file_path' && #end for #elif str($repeat2.type.type) == "infer_experiment" #set $pattern = "Fraction of reads explained by" #for $k, $file in enumerate($repeat2.type.input) + #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '_infer_experiment.txt') grep -q "$pattern" $file || die "'$pattern' not found in the file" && - ln -s '$file' '$repeat_dir/$file_${k}_infer_experiment.txt' && + ln -s '$file' '$file_path' && #end for #end if #end for #elif str($repeat.software_cond.software) == "salmon" #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) - #set repeat_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j) - mkdir '$repeat_dir' && + @CREATE_REPEAT_DIR_2@ #if str($repeat2.type.type) == "meta" #for $k, $file in enumerate($repeat2.type.input) - #set file_dir = $repeat_dir + '/file_' + str($k) + #set file_dir = os.path.join($repeat_dir, 'file_' + str($k)) + #set file_path = os.path.join($file_dir, 'meta_info.json') mkdir '$file_dir' && - ln -s '$file' '$file_dir/meta_info.json' && + ln -s '$file' '$file_path' && #end for #elif str($repeat2.type.type) == "fld" #for $k, $file in enumerate($repeat2.type.input) - #set file_dir = $repeat_dir + '/file_' + str($k) + #set file_dir = os.path.join($repeat_dir, 'file_' + str($k)) + #set file_path = os.path.join($file_dir,'flenDist.txt') mkdir '$file_dir' && - ln -s '$file' '$file_dir/flenDist.txt' && + ln -s '$file' '$file_path' && #end for #end if #end for @@ -256,8 +330,7 @@ @LN_FILES@ #elif str($repeat.software_cond.software) == "samtools" #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) - #set repeat_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j) - mkdir '$repeat_dir' && + @CREATE_REPEAT_DIR_2@ #if str($repeat2.type.type) == "stats" #set $pattern = "This file was produced by samtools stats" @LN_3_FILES@ @@ -266,7 +339,9 @@ @LN_3_FILES@ #elif str($repeat2.type.type) == "idxstats" #for $file in $repeat2.type.input - ln -s '$file' '$repeat_dir/${file.element_identifier}_idxstat' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '_idxstat') + ln -s '$file' '$file_path' && #end for #elif str($repeat2.type.type) == "rmdup" #set $pattern = "[bam_rmdup" @@ -281,60 +356,81 @@ @LN_FILES@ #else if str($repeat.software_cond.software) == "star": #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) - #set repeat_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j) - mkdir $repeat_dir && + @CREATE_REPEAT_DIR_2@ #if str($repeat2.type.type) == "log" #for $file in $repeat2.type.input - ln -s '$file' '${repeat_dir}/${file.element_identifier}_Log.final.out' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '_Log.final.out') + ln -s '$file' '$file_path' && #end for #elif str($repeat2.type.type) == "genecounts" #for $file in $repeat2.type.input - ln -s '$file' '${repeat_dir}/${file.element_identifier}_ReadsPerGene.out.tab' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '_ReadsPerGene.out.tab') + ln -s '$file' '$file_path' && #end for #end if #end for #elif str($repeat.software_cond.software) == "tophat" #for $file in $repeat.software_cond.input - ln -s '$file' '$software_dir/${file.element_identifier}align_summary.txt' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($software_dir, str($identifier) + 'align_summary.txt') + ln -s '$file' '$file_path' && #end for #elif str($repeat.software_cond.software) == "trimmomatic" #set $pattern = "Trimmomatic" @LN_FILES@ #elif str($repeat.software_cond.software) == "vcftools" #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) - #set file_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j) - mkdir $file_dir && + @CREATE_REPEAT_DIR_2@ #if str($repeat2.type.type) == "relatedness2" #for $file in $repeat2.type.input - ln -s '$file' '${repeat_dir}/${file.element_identifier}.relatedness2' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '.relatedness2') + ln -s '$file' '$file_path' && #end for #elif str($repeat2.type) == "tstv_by_count" #for $file in $repeat2.type.input - ln -s '$file' '${repeat_dir}/${file.element_identifier}.TsTv.count' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.count') + ln -s '$file' '$file_path' && #end for #elif str($repeat2.type) == "tstv_by_qual" #for $file in $repeat2.type.input - ln -s '$file' '${repeat_dir}/${file.element_identifier}.TsTv.qual' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.qual') + ln -s '$file' '$file_path' && #end for #elif str($repeat2.type) == "tstv_summary" #for $file in $repeat2.type.input - ln -s '$file' '${repeat_dir}/${file.element_identifier}.TsTv.summary' && + @ESCAPE_IDENTIFIER@ + #set file_path = os.path.join($repeat_dir, str($identifier) + '.TsTv.summary') + ln -s '$file' '$file_path' && #end for #end if #end for #else if str($repeat.software_cond.software) == "custom_content": #set $configfile = "T" #for $j, $file in enumerate( $repeat.software_cond.input ) - ln -s '$file' '${software_dir}/file_${i}_${j}' && + #set file_path = os.path.join($software_dir, 'file_' + str($i) + '_' + str($j)) + ln -s '$file' '$file_path' && more $file && #end for #end if #end for multiqc multiqc_WDir +--filename "report" + +#if str($title) + --title "$title" +#end if +#if str($comment) + --comment "$comment" +#end if #if $configfile == "T" - -c '$multiqc_config' + --config '$multiqc_config' #end if ]]></command> <configfiles> @@ -371,6 +467,7 @@ <!--<option value="adapterRemoval">Adapter Removal</option>--> <!--<option value="afterqc">AfterQC</option>--> <option value="bamtools">Bamtools</option> + <!--<option value="bbmap">BBMap</option>--> <option value="bcftools">Bcftools</option> <!--<option value="bcl2fastq">bcl2fastq</option>--> <!--<option value="biobloomtools">BioBloom Tools</option>--> @@ -380,19 +477,23 @@ <option value="busco">BUSCO</option> <!--<option value="clusterflow">Cluster Flow</option>--> <option value="cutadapt">Cutadapt/Trim Galore!</option> + <!--<option value="clipandmerge">ClipAndMerge</option>--> <!--<option value="conpair">Conpair</option>--> + <!--<option value="dedup">DeDup</option>--> + <option value="deeptools">deepTools</option> <!--<option value="disambiguate">Disambiguate</option>--> <!--<option value="fastq_screen">FastQ Screen</option>--> <option value="fastqc">FastQC</option> <option value="featureCounts">featureCounts</option> <option value="flexbar">Flexbar</option> - <option value="gatk">GATK (BaseRecalibrator or VariantEval output)</option> + <option value="gatk">GATK</option> <!--<option value="goleft_indexcov">goleft indexcov</option>--> <option value="hicexplorer">HiCExplorer</option> <!--<option value="hicup">HiCUP</option>--> <option value="hisat2">HISAT2</option> <!--<option value="homer">HOMER</option>--> <option value="htseq">HTSeq</option> + <!--<option value="interop">InterOp</option>--> <!--<option value="jellyfish">Jellyfish</option>--> <option value="kallisto">Kallisto</option> <!--<option value="leehom">leeHom</option>--> @@ -407,19 +508,22 @@ <option value="quast">QUAST</option> <!--<option value="rna_seqc">RNA-SeQC</option>--> <!--<option value="rsem">RSEM (rsem-calculate-regex output)</option>--> - <option value="rseqc">RSeQC (bam_stat, gene_body_coverage, infer_experiment, ...)</option> + <option value="rseqc">RSeQC</option> <!--<option value="salmon">Salmon</option>--> <option value="samblaster">Samblaster</option> <option value="samtools">Samtools</option> + <!--<option value="sargasso">Sargasso</option>--> <!--<option value="skewer">Skewer</option>--> - <option value="sortmerna">SortMeRNA</option> <!--<option value="slamdunk">Slamdunk</option>--> - <!--<option value="snpeff">SnpEff</option>--> + <option value="snpeff">SnpEff</option> + <option value="sortmerna">SortMeRNA</option> <option value="star">STAR</option> + <!--<option value="supernova">Supernova</option>--> <!--<option value="theta2">THeTA2</option>--> <option value="tophat">TopHat2</option> <option value="trimmomatic">Trimmomatic</option> <option value="vcftools">VCFTools</option> + <!--<option value="verifybamid">VerifyBAMID</option>--> <!--Custom--> <option value="custom_content">Custom Content</option> </param> @@ -450,13 +554,29 @@ <when value="cutadapt"> <param name="input" type="data" format="txt,tabular,tsv,csv" multiple="true" label="Output of Cutadapt" help="It should contain 'This is cutadapt' or 'You are running cutadapt'"/> </when> + <when value="deeptools"> + <repeat name="output" title="deepTools output" min="1"> + <param name="type" type="select" label="deepTool used to generate the output?"> + <option value="bamPEFragmentSize">bamPEFragmentSize</option> + <option value="estimateReadFiltering">estimateReadFiltering</option> + <option value="plotCoverageStdout">plotCoverageStdout</option> + <option value="plotCoverageOutRawCounts">plotCoverageOutRawCounts</option> + <option value="plotEnrichment">plotEnrichment</option> + <option value="plotFingerprintOutRawCounts">plotFingerprintOutRawCounts</option> + <option value="plotFingerprintOutQualityMetrics">plotFingerprintOutQualityMetrics</option> + </param> + <param name="input" type="data" format="txt" multiple="true" label="Bismark output"/> + </repeat> + </when> <when value="fastqc"> <repeat name="output" title="FastQC output" min="1"> <param name="type" type="select" label="Type of FastQC output?"> <option value="data">Raw data</option> <option value="theoretical_gc">Theorectical GC</option> </param> - <param name="input" type="data" format="txt" multiple="true" label="FastQC output"/> + <param name="input" type="data" format="txt" multiple="true" label="FastQC output"> + <validator type="expression" message="MultiQC does not accept the HTML report generated by FastQC, only the Raw Data">value is not None and value.extension != "html"</validator> + </param> </repeat> </when> <when value="featureCounts"> @@ -584,6 +704,9 @@ <when value="sortmerna"> <param name="input" type="data" format="txt" multiple="true" label="Log file of SortMeRNA" help="It should contain 'Minimal SW score based on E-value'"/> </when> + <when value="snpeff"> + <param name="input" type="data" format="csv" multiple="true" label="Output of SnpEff"/> + </when> <when value="star"> <repeat name="output" title="STAR output" min="1"> <conditional name="type"> @@ -647,15 +770,18 @@ </when> </conditional> </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 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 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="multiqc_report.html" label="${tool.name} on ${on_string}: Webpage" /> - <data name="log" format="txt" from_work_dir="multiqc_data/multiqc.log" label="${tool.name} on ${on_string}: Log"> + <data name="html_report" format="html" from_work_dir="report.html" label="${tool.name} on ${on_string}: Webpage" /> + <data name="log" format="txt" from_work_dir="report_data/multiqc.log" label="${tool.name} on ${on_string}: Log"> <filter>saveLog</filter> </data> <collection name="stats" type="list" label="${tool.name} on ${on_string}: Stats"> - <discover_datasets pattern="multiqc_(?P<designation>.+)\.txt" format="tabular" directory="multiqc_data" /> + <discover_datasets pattern="multiqc_(?P<designation>.+)\.txt" format="tabular" directory="report_data" /> </collection> </outputs> <tests> @@ -693,9 +819,13 @@ <param name="input" value="trimmomatic.txt" /> </conditional> </repeat> + <param name="title" value="Title of the report"/> + <param name="comment" value="Commment for the report"/> <param name="saveLog" value="True"/> <output name="html_report"> <assert_contents> + <has_text text="Title of the report" /> + <has_text text="Commment for the report" /> <has_text text="cutadapt_plot" /> <has_text text="fastqc_seq_heatmap_key_t" /> <has_text text="flexbar_plot" /> @@ -785,9 +915,9 @@ </output> <output_collection name="stats" type="list"> <element name="bismark_alignment" file="bismark_stats.tabular" compare="sim_size" delta="10"/> - <element name="bowtie2" file="bowtie2_stats.tabular" compare="sim_size" delta="0"/> + <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"/> - <element name="hisat2" file="hisat2_stats.tabular" compare="sim_size" delta="0"/> + <element name="hisat2" file="hisat2_stats.tabular" compare="sim_size" delta="20"/> <!-- <element name="hicexplorer" file="hicexplorer_stats.tabular" compare="sim_size" delta="0"/> --> <element name="kallisto" file="kallisto_stats.tabular" compare="sim_size" delta="10"/> <element name="star" file="star_stats.tabular" compare="sim_size" delta="10"/> @@ -815,6 +945,35 @@ </repeat> <repeat name="results"> <conditional name="software_cond"> + <param name="software" value="deeptools" /> + <repeat name="output"> + <param name="type" value="bamPEFragmentSize"/> + <param name="input" value="deeptools_bamPEFragmentSize.txt"/> + </repeat> + <repeat name="output"> + <param name="type" value="estimateReadFiltering"/> + <param name="input" value="deeptools_estimateReadFiltering.txt"/> + </repeat> + <repeat name="output"> + <param name="type" value="plotCoverageStdout"/> + <param name="input" value="deeptools_plotCoverageStdout.txt"/> + </repeat> + <repeat name="output"> + <param name="type" value="plotCoverageOutRawCounts"/> + <param name="input" value="deeptools_plotCoverageOutRawCounts.txt"/> + </repeat> + <repeat name="output"> + <param name="type" value="plotEnrichment"/> + <param name="input" value="deeptools_plotEnrichment.txt"/> + </repeat> + <repeat name="output"> + <param name="type" value="plotFingerprintOutRawCounts"/> + <param name="input" value="deeptools_plotFingerprintOutRawCounts.txt"/> + </repeat> + </conditional> + </repeat> + <repeat name="results"> + <conditional name="software_cond"> <param name="software" value="featureCounts" /> <param name="input" value="featureCounts.txt" /> </conditional> @@ -921,6 +1080,12 @@ </repeat> <repeat name="results"> <conditional name="software_cond"> + <param name="software" value="snpeff" /> + <param name="input" value="snpeff.csv" /> + </conditional> + </repeat> + <repeat name="results"> + <conditional name="software_cond"> <param name="software" value="vcftools" /> <repeat name="output"> <conditional name="type"> @@ -936,6 +1101,7 @@ <has_text text="bamtools-stats" /> <has_text text="bcftools_stats_indel-lengths" /> <has_text text="busco-lineage-fungi_odb9" /> + <has_text text="deeptools" /> <has_text text="featureCounts_assignment_plot" /> <has_text text="gatk_varianteval_variant_plot" /> <has_text text="htseq_assignment_plot" /> @@ -948,17 +1114,17 @@ <has_text text="samblaster_duplicates" /> <has_text text="quast-stats" /> <has_text text="samtools-flagstat-dp" /> - <has_text text="bamtools-stats" /> + <has_text text="snpeff" /> </assert_contents> </output> <output_collection name="stats" type="list"> - <element name="bamtools_stats" file="bamtools_stats.tabular" compare="sim_size" delta="0"/> + <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="0"/> + <element name="busco" file="busco_stats.tabular" compare="sim_size" delta="10"/> <element name="featureCounts" file="featureCounts_stats.tabular" compare="sim_size" delta="25"/> <element name="gatk_varianteval" file="gatk_varianteval_stats.tabular" compare="sim_size" delta="20"/> <element name="general_stats" file="post_aligner_soft_stats.tabular" compare="sim_size" delta="25"/> - <element name="htseq" file="htseq_stats.tabular" compare="sim_size" delta="0"/> + <element name="htseq" file="htseq_stats.tabular" compare="sim_size" delta="10"/> <element name="picard_AlignmentSummaryMetrics" file="picard_AlignmentSummaryMetrics_stats.tabular" compare="sim_size" delta="0"/> <element name="picard_RnaSeqMetrics" file="picard_RnaSeqMetrics_stats.tabular" compare="sim_size" delta="40"/> <element name="picard_baseContent" file="picard_baseContent_stats.tabular" compare="sim_size" delta="50"/> @@ -975,6 +1141,7 @@ </assert_contents> </element> <element name="samtools_stats" file="samtools_stats_stats.tabular" compare="sim_size" delta="15"/> + <element name="snpeff" file="snpeff_stats.tabular" compare="sim_size" delta="10"/> </output_collection> </test> <test> @@ -1005,7 +1172,7 @@ ---- -The first integration of this tool was made by Cyril Monjeaud and Yvan Le Bras (`Enancio <http://enancio.fr/>`_ and Rennes GenOuest Bio-informatics Core Facility). +The first integration of this tool was made by Cyril Monjeaud and Yvan Le Bras (`Enancio <http://enancio.fr/>`_ and Rennes GenOuest Bio-informatics Core Facility). It is now maintained by the `Intergalactic Utilities Commission <https://galaxyproject.org/iuc>`_. ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/btw354</citation>