Mercurial > repos > iuc > multiqc
diff multiqc.xml @ 16:bf675f34b056 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875"
| author | iuc |
|---|---|
| date | Sat, 16 May 2020 09:40:45 -0400 |
| parents | 3d93dd18d9f8 |
| children | 5e33b465d8d5 |
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--- 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">