--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cnv.xml	Fri Jan 22 14:28:01 2021 +0000
@@ -0,0 +1,201 @@
+<?xml version="1.0"?>
+<tool id="delly_cnv" name="Delly cnv" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
+    <description>discover and genotype copy-number variants</description>
+    <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