# HG changeset patch
# User iuc
# Date 1630396739 0
# Node ID 0e56998aebc62c15e814c36bdceb015471e9b960
# Parent  eb4284f666b124cc77f304496668868053856590
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"

diff -r eb4284f666b1 -r 0e56998aebc6 cnv.xml.orig
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cnv.xml.orig	Tue Aug 31 07:58:59 2021 +0000
@@ -0,0 +1,207 @@
+<?xml version="1.0"?>
+<<<<<<< HEAD:tools/delly/cnv.xml
+<tool id="delly_cnv" name="Delly cnv" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
+    <description>discover and genotype copy-number variants</description>
+=======
+<tool id="delly_rd" name="Delly read-depth (rd)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
+    <description>normalization on read-depth profiles</description>
+    <expand macro="bio_tools"/>
+>>>>>>> 20ed9dd6f (add bio.tools ID):tools/delly/rd.xml
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+## run
+delly cnv
+## generic options
+--genome '$generic.genome'
+--quality '$generic.quality'
+--mappability '$generic.mappability'
+--ploidy $generic.ploidy
+--outfile 'result.bcf'
+--covfile 'result.gz'
+## cnv calling options
+--sdrd $cnv.sdrd
+--cn-offset $cnv.cnoffset
+--cnv-size $cnv.cnvsize
+#if $cnv.svfile
+    --svfile $cnv.svfile
+#end if
+#if $cnv.vcffile
+    --vcffile '$cnv.vcffile'
+#end if
+$cnv.segmentation
+## read-depth window options
+--window-size $read.windowsize
+--window-offset $read.windowoffset
+#if $read.bedintervals
+    --bed-intervals '$read.bedintervals'
+#end if
+--fraction-window $read.fractionwindow
+$read.adaptivewindowing
+## gc fragment normalization options
+--scan-window $gc.scanwindow
+--fraction-unique $gc.fractionunique
+#if $gc.scanregions
+    --scan-regions '$gc.scanregions'
+#end if
+--mad-cutoff $gc.madcutoff
+--percentile $gc.percentile
+$gc.nowindowselection
+## input
+'$input'
+
+## postprocessing
+@LOG@
+    ]]></command>
+    <inputs>
+        <expand macro="input" format="bam" label="Select input file"/>
+        <section name="generic" title="Generic options" expanded="true">
+            <expand macro="genome"/>
+            <param argument="--quality" type="integer" value="10" label="Set minimum mapping quality"/>
+            <param argument="--mappability" type="data" format="fasta" label="Select mappability map file"/>
+            <param argument="--ploidy" type="integer" value="2" label="Set baseline ploidy"/>
+        </section>
+        <section name="cnv" title="CNV calling options" expanded="true">
+            <param argument="--sdrd" type="integer" value="2" label="Set minimum SD read-depth shift"/>
+            <expand macro="cnoffset" default="0.1"/>
+            <param name="cnvsize" type="integer" value="1000" label="Set minimum CNV size" help="(--cnv-size)"/>
+            <param argument="--svfile" type="data" format="bcf" optional="true" label="Select delly SV file for breakpoint refinement"/> <!-- filetype sv.bcf not supported by galaxy -->
+            <expand macro="vcffile"/>
+            <param argument="--segmentation" type="boolean" truevalue="--segmentation" falsevalue="" label="Use copy-number segmentation?"/>
+        </section>
+        <section name="read" title="Read-depth window options" expanded="true">
+            <param name="windowsize" type="integer" value="10000" label="Set window size" help="(--window-size)"/>
+            <param name="windowoffset" type="integer" value="10000" label="Set window offset" help="(--window-offset)"/>
+            <param name="bedintervals" type="data" format="bed" optional="true" label="Select input BED file" help="(--bed-intervals)"/>
+            <param name="fractionwindow" type="float" min="0.0" max="1.0" value="0.25" label="Set minimum callable window fraction" help="(--fraction-window)"/>
+            <param name="adaptivewindowing" type="boolean" truevalue="-a" falsevalue="" label="Use mappable bases for window size?" help="(--adaptive-windowing)"/>
+        </section>
+        <section name="gc" title="GC fragment normalization options" expanded="true">
+            <param name="scanwindow" type="integer" value="10000" label="Set scan window size" help="(--scan-window)"/>
+            <param name="fractionunique" type="float" min="0.0" max="1.0" value="0.8" label="Set uniqueness filter for scan windows" help="(--fraction-unique)"/>
+            <param name="scanregions" type="data" format="bed" optional="true" label="Select file with scanning regions" help="(--scan-regions)"/>
+            <param name="madcutoff" type="integer" value="3" label="Set count cutoff" help="(median + 3 * mad) (--mad-cutoff)"/>
+            <param argument="--percentile" type="float" min="0.0" max="1.0" value="0.0005" label="Set threshold for excluding extreme GC fraction"/>
+            <param name="nowindowselection" type="boolean" truevalue="-n" falsevalue="" label="Skip scan window selection?" help="(--no-window-selection)"/>
+        </section>
+        <section name="oo" title="Output options" expanded="true">
+            <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">
+                <option value="cnv" selected="true">CNV</option>
+                <option value="coverage">Coverage</option>
+                <option value="log">Log</option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="out_cnv" format="bcf" from_work_dir="result.bcf" label="${tool.name} on ${on_string}: CNV">
+            <filter>'cnv' in oo['out']</filter>
+        </data>
+        <data name="out_coverage" format="tabular.gz" from_work_dir="result.gz" label="${tool.name} on ${on_string}: Coverage">
+            <filter>'coverage' in oo['out']</filter>
+        </data>
+        <expand macro="log"/>
+    </outputs>
+    <tests>
+        <!-- no test implemented for vcffile, svfile, bed-intervals, scanregions -->
+
+        <!-- #1 default; test data to small, results are empty -->
+        <test expect_num_outputs="3">
+            <param name="input" value="normal.bam"/>
+            <section name="generic">
+                <param name="genome" value="genome.fasta"/>
+                <param name="mappability" value="map.fasta"/>
+            </section>
+            <section name="oo">
+                <param name="out" value="cnv,coverage,log"/>
+            </section>
+            <output name="out_cnv">
+                <assert_contents>
+                    <has_size value="0"/>
+                </assert_contents>
+            </output>
+            <output name="out_coverage">
+                <assert_contents>
+                    <has_size value="0"/>
+                </assert_contents>
+            </output>
+            <output name="out_log">
+                <assert_contents>
+                    <has_text_matching expression=".+Scanning Windows"/>
+                    <has_line line="***************************************************"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #2 -->
+        <test expect_num_outputs="3">
+            <param name="input" value="normal.bam"/>
+            <section name="generic">
+                <param name="genome" value="genome.fasta"/>
+                <param name="quality" value="11"/>
+                <param name="mappability" value="map.fasta"/>
+                <param name="ploidy" value="3"/>
+            </section>
+            <section name="cnv">
+                <param name="sdrd" value="3"/>
+                <param name="cnoffset" value="0.2"/>
+                <param name="cnvsize" value="1001"/>
+                <param name="segmentation" value="true"/>
+            </section>
+            <section name="read">
+                <param name="windowsize" value="10001"/>
+                <param name="windowoffset" value="9999"/>
+                <param name="fractionwindow" value="0.24"/>
+                <param name="adaptivewindowing" value="true"/>
+            </section>
+            <section name="gc">
+                <param name="scanwindow" value="10001"/>
+                <param name="fractionunique" value="0.79"/>
+                <param name="madcutoff" value="2"/>
+                <param name="percentile" value="0.0006"/>
+                <param name="nowindowselection" value="true"/>
+            </section>
+            <section name="oo">
+                <param name="out" value="cnv,coverage,log"/>
+            </section>
+            <output name="out_cnv">
+                <assert_contents>
+                    <has_size value="700" delta="10"/>
+                </assert_contents>
+            </output>
+            <output name="out_coverage">
+                <assert_contents>
+                    <has_size value="61"/>
+                </assert_contents>
+            </output>
+            <output name="out_log">
+                <assert_contents>
+                    <has_text_matching expression=".+Done.+"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+@WID@
+
+**Input**
+
+Delly *cnv* requires are a sample (BAM), a genome (FASTA) and a mappability map (FASTA), which is available `here <https://gear.embl.de/data/delly/>`_. Intervals (BED), scanning regions (BED) and a delly SV file for breakpoint refinement (BCF) can be provided optionally.
+
+**Output**
+
+CNV (BCF) and coverage (compressed tabular) files are created.
+
+.. class:: infomark
+
+**References**
+
+@REFERENCES@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file
diff -r eb4284f666b1 -r 0e56998aebc6 lr.xml
--- a/lr.xml	Fri Jan 22 14:29:56 2021 +0000
+++ b/lr.xml	Tue Aug 31 07:58:59 2021 +0000
@@ -1,6 +1,7 @@
 <?xml version="1.0"?>
 <tool id="delly_lr" name="Delly long-read (lr)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
     <description>optimized calling and genotyping of structural variants</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
diff -r eb4284f666b1 -r 0e56998aebc6 macros.xml
--- a/macros.xml	Fri Jan 22 14:29:56 2021 +0000
+++ b/macros.xml	Tue Aug 31 07:58:59 2021 +0000
@@ -16,7 +16,11 @@
             <citation type="doi">10.1093/bioinformatics/bts378</citation>
         </citations>
     </xml>
-	
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">delly2</xref>
+        </xrefs>
+    </xml>
     <!-- command -->
 
     <token name="@BAM@"><![CDATA[
@@ -148,4 +152,4 @@
     <token name="@REFERENCES@"><![CDATA[
 More information are available on `GitHub <https://github.com/dellytools/delly>`_.
     ]]></token>
-</macros>
\ No newline at end of file
+</macros>
diff -r eb4284f666b1 -r 0e56998aebc6 macros.xml.orig
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml.orig	Tue Aug 31 07:58:59 2021 +0000
@@ -0,0 +1,162 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@TOOL_VERSION@">0.8.7</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">delly</requirement>
+            <requirement type="package" version="1.10.2">bcftools</requirement>
+        </requirements>
+    </xml>
+    <xml name="version_command">
+        <version_command><![CDATA[delly -v 2>&1 | grep 'Delly version' | cut -f 3 -d ' ']]></version_command>
+    </xml>
+	<xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/bioinformatics/bts378</citation>
+        </citations>
+    </xml>
+<<<<<<< HEAD
+	
+    <!-- command -->
+=======
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type='bio.tools'>delly2</xref>
+        </xrefs>
+    </xml>
+    <!--
+        command 
+    -->
+>>>>>>> 20ed9dd6f (add bio.tools ID)
+
+    <token name="@BAM@"><![CDATA[
+#for $i, $current in enumerate($input)
+    ln -s '${current}' 'input_${i}.bam' &&
+    ln -s '${current.metadata.bam_index}' 'input_${i}.bam.bai' &&
+#end for
+    ]]></token>
+    <token name="@DUMP@"><![CDATA[
+#if 'dump' in $oo.out
+    && test -f 'dump.tsv.gz' && bgzip -d 'dump.tsv.gz' || echo 'No dump file.'
+#end if
+    ]]></token>
+    <token name="@LOG@"><![CDATA[
+#if 'log' in $oo.out
+    |& tee '$out_log'
+#end if
+    ]]></token>
+    <token name="@VCF@"><![CDATA[
+#if 'vcf' in $oo.out
+    && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.'
+#end if
+    ]]></token>
+
+    <!-- input -->
+
+    <xml name="cnoffset" token_default="">
+        <param name="cnoffset" type="float" min="0.0" max="1.0" value="@DEFAULT@" label="Set minimum CN offset" help="(--cn-offset)"/>
+    </xml>
+    <xml name="coverage" token_label="">
+        <param argument="--coverage" type="integer" value="10" label="@LABEL@"/>
+    </xml>
+    <xml name="exclude">
+        <param argument="--exclude" type="data" format="tabular" optional="true" label="Select file with regions to exclude"/>
+    </xml>
+    <xml name="genome">
+        <param argument="--genome" type="data" format="fasta" label="Select genome file"/>
+    </xml>
+    <xml name="genoqual">
+        <param name="genoqual" type="integer" value="5" label="Set minimum mapping quality for genotyping" help="(--geno-qual)"/>
+    </xml>
+    <xml name="input" token_format="" token_multiple="false" token_label="">
+        <param name="input" type="data" format="@FORMAT@" multiple="@MULTIPLE@" label="@LABEL@"/>
+    </xml>
+    <xml name="maxreadsep" token_default="">
+        <param argument="--maxreadsep" type="integer" value="@DEFAULT@" label="Set maximum read separation"/>
+    </xml>
+    <xml name="maxsize" token_default="" token_label="">
+        <param argument="--maxsize" type="integer" value="@DEFAULT@" label="@LABEL@"/>
+    </xml>
+    <xml name="minclip">
+        <param argument="--minclip" type="integer" value="25" label="Set minimum clipping length"/>
+    </xml>
+    <xml name="mincliquesize">
+        <param name="mincliquesize" type="integer" value="2" label="Set minimum paired-end/single-read clique size" help="(--min-clique-size)"/>
+    </xml>
+    <xml name="minrefsep" token_default="">
+        <param argument="--minrefsep" type="integer" value="@DEFAULT@" label="Set minimum reference separation"/>
+    </xml>
+    <xml name="minsize" token_default="" token_label="">
+        <param argument="--minsize" type="integer" value="@DEFAULT@" label="@LABEL@"/>
+    </xml>
+    <xml name="pass">
+        <param argument="--pass" type="boolean" truevalue="--pass" falsevalue="" label="Filter sites for PASS?"/>
+    </xml>
+    <xml name="ploidy">
+        <param argument="--ploidy" type="integer" value="2" label="Set baseline ploidy"/>
+    </xml>
+    <xml name="samples">
+        <param argument="--samples" type="data" format="tabular" label="Select sample file" help="Two-column sample file listing sample name and tumor or control."/>
+    </xml>
+    <xml name="svtype">
+        <param argument="--svtype" type="select" label="Select type(s) of structural variants to detect">
+            <option value="ALL" selected="true">All types (ALL)</option>
+            <option value="DEL">Deletion (DEL)</option>
+            <option value="DUP">Duplication (DUP)</option>
+            <option value="INS">Insertion (INS)</option>
+            <option value="INV">Inversion (INV)</option>
+            <option value="BND">Translocation (BND)</option>
+        </param>
+    </xml>
+    <xml name="vcffile">
+        <param argument="--vcffile" type="data" format="bcf,vcf" optional="true" label="Select genotyping file"/>
+    </xml>
+
+    <!-- output -->
+
+    <xml name="bcf">
+        <data name="out_bcf" format="bcf" from_work_dir="result.bcf" label="${tool.name} on ${on_string}: Result (BCF)">
+            <filter>'bcf' in oo['out']</filter>
+        </data>
+    </xml>
+    <xml name="vcf">
+        <data name="out_vcf" format="vcf" from_work_dir="result.vcf" label="${tool.name} on ${on_string}: Result (VCF)">
+            <filter>'vcf' in oo['out']</filter>
+        </data>
+    </xml>
+    <xml name="dump">
+        <data name="out_dump" format="tabular" from_work_dir="dump.tsv" label="${tool.name} on ${on_string}: SV-reads">
+            <filter>'dump' in oo['out']</filter>
+        </data>
+    </xml>
+    <xml name="log">
+        <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
+            <filter>'log' in oo['out']</filter>
+        </data>
+    </xml>
+
+    <!-- help -->
+
+    <token name="@WID@"><![CDATA[
+Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.
+
+Short-read SV calling
+
+- *call* to discover and genotype structural variants
+- *merge* structural variants across VCF/BCF files and within a single VCF/BCF file
+- *filter* somatic or germline structural variants
+
+Long-read SV calling
+
+- *lr* for long-read SV discovery
+
+Copy-number variant calling
+
+- *cnv* to discover and genotype copy-number variants
+- *classify* somatic or germline copy-number variants
+    ]]></token>
+    <token name="@REFERENCES@"><![CDATA[
+More information are available on `GitHub <https://github.com/dellytools/delly>`_.
+    ]]></token>
+</macros>
\ No newline at end of file
diff -r eb4284f666b1 -r 0e56998aebc6 merge.xml.orig
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/merge.xml.orig	Tue Aug 31 07:58:59 2021 +0000
@@ -0,0 +1,179 @@
+<?xml version="1.0"?>
+<tool id="delly_merge" name="Delly merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
+<<<<<<< HEAD
+    <description>structural variants across/within BCF/VCF file(s)</description>
+=======
+    <description>structural variants across/within VCF/BCF file(s)</description>
+    <expand macro="bio_tools"/>
+>>>>>>> 20ed9dd6f (add bio.tools ID)
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+## initialize
+#for $i, $current in enumerate($input)
+    #if $current.is_of_type('vcf')
+        bcftools view -Ob '$current' > 'input_${i}.bcf.gz' &&
+        bcftools index 'input_${i}.bcf.gz' &&
+    #else
+        ln -s '${current}' 'input_${i}.bcf.gz' &&
+        ln -s '${current.metadata.bcf_index}' 'input_${i}.bcf.gz.csi' &&
+    #end if
+#end for
+
+## run
+delly merge
+## generic options
+--outfile 'result.bcf'
+--chunks $generic.chunks
+--vaf $generic.vaf
+--coverage $generic.coverage
+--minsize $generic.minsize
+--maxsize $generic.maxsize
+$generic.cnvmode
+$generic.precise
+$generic.pass
+## overlap options
+--bp-offset $overlap.bpoffset
+--rec-overlap $overlap.recoverlap
+## input
+#for $i, $current in enumerate($input)
+    'input_${i}.bcf.gz'
+#end for
+
+## postprocessing
+@LOG@
+@VCF@
+    ]]></command>
+    <inputs>
+        <expand macro="input" format="bcf,vcf" multiple="true" label="Select input files"/>
+        <section name="generic" title="Generic options" expanded="true">
+            <param argument="--chunks" type="integer" value="500" label="Set maximum chunk size to merge groups of BCF files"/>
+            <param argument="--vaf" type="float" value="0.15" min="0.0" max="1.0" label="Set minimum fractional ALT support"/>
+            <expand macro="coverage" label="Set minimum coverage"/>
+            <expand macro="minsize" default="0" label="Set minimum SV size"/>
+            <expand macro="maxsize" default="1000000" label="Set maximum SV size"/>
+            <param argument="--cnvmode" type="boolean" truevalue="--cnvmode" falsevalue="" label="Merge Delly CNV files?"/>
+            <param argument="--precise" type="boolean" truevalue="--precise" falsevalue="" label="Filter sites for PRECISE?"/>
+            <expand macro="pass"/>
+        </section>
+        <section name="overlap" title="Overlap options" expanded="true">
+            <param name="bpoffset" type="integer" value="1000" label="Set maximum breakpoint offset" help="(--bp-offset)"/>
+            <param name="recoverlap" type="float" value="0.8" label="Set minimum reciprocal overlap" help="(--rec-overlap)"/>
+        </section>
+        <section name="oo" title="Output options" expanded="true">
+            <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">
+                <option value="bcf" selected="true">BCF</option>
+                <option value="log">Log</option>
+                <option value="vcf">VCF</option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <expand macro="bcf"/>
+        <expand macro="log"/>
+        <expand macro="vcf"/>
+    </outputs>
+    <tests>
+        <!-- #1 bcf, default -->
+        <test expect_num_outputs="2">
+            <param name="input" value="call_1.bcf.gz,call_2.bcf.gz"/>
+            <section name="oo">
+                <param name="out" value="vcf,bcf"/>
+            </section>
+            <output name="out_bcf">
+                <assert_contents>
+                    <has_size value="1851" delta="10"/>
+                </assert_contents>
+            </output>
+            <output name="out_vcf">
+                <assert_contents>
+                    <has_n_lines n="128"/>
+                    <has_line line="##fileformat=VCFv4.2"/>
+                    <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #2 bcf -->
+        <test expect_num_outputs="3">
+            <param name="input" value="call_1.bcf.gz,call_2.bcf.gz"/>
+            <section name="generic">
+                <param name="chunks" value="500"/>
+                <param name="vaf" value="0.16"/>
+                <param name="coverage" value="10"/>
+                <param name="minsize" value="0"/>
+                <param name="maxsize" value="1000000"/>
+                <param name="cnvmode" value="true"/>
+                <param name="precise" value="true"/>
+                <param name="pass" value="true"/>
+            </section>
+            <section name="overlap">
+                <param name="bp-offset" value="1000"/>
+                <param name="rec-overlap" value="0.79"/>
+            </section>
+            <section name="oo">
+                <param name="out" value="vcf,bcf,log"/>
+            </section>
+            <output name="out_bcf">
+                <assert_contents>
+                    <has_size value="1021" delta="10"/>
+                </assert_contents>
+            </output>
+            <output name="out_log">
+                <assert_contents>
+                    <has_text_matching expression=".+Done\."/>
+                </assert_contents>
+            </output>
+            <output name="out_vcf">
+                <assert_contents>
+                    <has_n_lines n="108"/>
+                    <has_line line="##fileformat=VCFv4.2"/>
+                    <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #3 vcf, default -->
+        <test expect_num_outputs="2">
+            <param name="input" value="call_1.vcf.gz,call_2.vcf.gz"/>
+            <section name="oo">
+                <param name="out" value="vcf,bcf"/>
+            </section>
+            <output name="out_bcf">
+                <assert_contents>
+                    <has_size value="1851" delta="10"/>
+                </assert_contents>
+            </output>
+            <output name="out_vcf">
+                <assert_contents>
+                    <has_n_lines n="128"/>
+                    <has_line line="##fileformat=VCFv4.2"/>
+                    <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+@WID@
+
+**Input**
+
+Delly *merge* requires BCF or VCF files.
+
+**Output**
+
+A single file in BCF/VCF format.  Additionally a log file is provided.
+
+.. class:: infomark
+
+**References**
+
+@REFERENCES@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
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