diff multiqc.xml @ 16:9c1131228d96 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4eb6628314458d9426ea9e6fbf6e225d93e3d0fc"

--- a/multiqc.xml	Sat Jan 18 08:08:15 2020 +0000
+++ b/multiqc.xml	Fri Oct 09 14:56:00 2020 +0000
@@ -1,7 +1,7 @@
-<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.1">
+<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@+galaxy1">
     <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($file.element_identifier))
@@ -115,7 +115,7 @@
             #end if
         #end for
     #elif str($repeat.software_cond.software) == "bowtie2"
-        #set $pattern = "reads; of these:"
+        #set $pattern = "% overall alignment rate"
         @LN_FILES@
     #elif str($repeat.software_cond.software) == "busco"
         ## Searches for files "short_summary_[samplename].txt"
@@ -250,7 +250,7 @@
                 #set $pattern = "picard.analysis.InsertSizeMetrics"
                 @LN_2_FILES@
             #elif str($repeat2.type) == "markdups"
-                #set $pattern = "picard.sam.DuplicationMetrics"
+                #set $pattern = "MarkDuplicates"
                 @LN_2_FILES@
             #elif str($repeat2.type) == "oxogmetrics"
                 #set $pattern = "picard.analysis.CollectOxoGMetrics"
@@ -272,6 +272,28 @@
     #elif str($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">
@@ -1262,7 +1301,9 @@
 
 ----
 
-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>`_.
+The first integration of this tool was made by
+`@cmonjeau <https://github.com/cmonjeau>`_ and `@yvanlebras <https://github.com/yvanlebras>`_.
+It is now maintained by the `Intergalactic Utilities Commission <https://galaxyproject.org/iuc>`_.
     ]]></help>
     <citations>
         <citation type="doi">10.1093/bioinformatics/btw354</citation>