--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/classify.xml	Fri Jan 22 14:33:05 2021 +0000
@@ -0,0 +1,229 @@
+<?xml version="1.0"?>
+<tool id="delly_classify" name="Delly classify" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
+    <description>somatic or germline copy-number variants</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+## initialize
+#if $input.is_of_type('vcf')
+    bcftools view -Ob '$input' > 'input.bcf.gz' &&
+    bcftools index 'input.bcf.gz' &&
+#else
+    ln -s '${input}' 'input.bcf.gz' &&
+    ln -s '${input.metadata.bcf_index}' 'input.bcf.gz.csi' &&
+#end if
+
+## run
+delly classify
+## generic options
+--filter $sv.mode_cond.mode_sel
+--outfile 'result.bcf'
+--minsize $generic.minsize
+--maxsize $generic.maxsize
+$generic.pass
+## somatic options
+#if $sv.mode_cond.mode_sel == 'somatic'
+    --samples '$sv.mode_cond.samples'
+    --pgerm $sv.mode_cond.pgerm
+    --cn-offset $sv.mode_cond.cnoffset
+## germline options
+#else if $sv.mode_cond.mode_sel == 'germline'
+    --ploidy $sv.mode_cond.ploidy
+    --qual $sv.mode_cond.qual
+    --maxsd $sv.mode_cond.maxsd
+#end if
+## input
+'input.bcf.gz'
+
+## postprocessing
+@LOG@
+@VCF@
+    ]]></command>
+    <inputs>
+        <expand macro="input" format="bcf,vcf" label="Select input file"/>
+        <section name="generic" title="Generic options" expanded="true">
+            <expand macro="minsize" default="1000" label="Set minimum CNV size"/>
+            <expand macro="maxsize" default="500000000" label="Set maximum CNV size"/>
+            <expand macro="pass"/>
+        </section>
+        <section name="sv" title="SV calling options" expanded="true">
+            <conditional name="mode_cond">
+                <param name="mode_sel" type="select" label="Select filter mode" help="(--filter)">
+                    <option value="somatic" selected="true">Somatic</option>
+                    <option value="germline">Germline</option>
+                </param>
+                <when value="somatic">
+                    <expand macro="samples"/>
+                    <param argument="--pgerm" type="float" value="0.05" label="Set probability germline"/>
+                    <expand macro="cnoffset" default="0.2"/>
+                </when>
+                <when value="germline">
+                    <expand macro="ploidy"/>
+                    <param argument="--qual" type="integer" value="50" label="Set minimum site quality"/>
+                    <param argument="--maxsd" type="float" value="0.15" label="Set maximum population SD"/>
+                </when>
+            </conditional>
+        </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 somatic, default -->
+        <test expect_num_outputs="3">
+            <param name="input" value="call_1.bcf.gz"/>
+            <section name="sv">
+                <conditional name="mode_cond">
+                    <param name="mode_sel" value="somatic"/>
+                    <param name="samples" value="samples.tsv"/>
+                </conditional>
+            </section>
+            <section name="oo">
+                <param name="out" value="bcf,vcf,log"/>
+            </section>
+            <output name="out_bcf">
+                <assert_contents>
+                    <has_size value="2322"/>
+                </assert_contents>
+            </output>
+            <output name="out_log">
+                <assert_contents>
+                    <has_text_matching expression=".+Done.+"/>
+                </assert_contents>
+            </output>
+            <output name="out_vcf">
+                <assert_contents>
+                    <has_size value="7762"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #2 somatic -->
+        <test expect_num_outputs="3">
+            <param name="input" value="call_1.bcf.gz"/>
+            <section name="generic">
+                <param name="minsize" value="1001"/>
+                <param name="maxsize" value="500000001"/>
+                <param name="pass" value="true"/>
+            </section>
+            <section name="sv">
+                <conditional name="mode_cond">
+                    <param name="mode_sel" value="somatic"/>
+                    <param name="samples" value="samples.tsv"/>
+                    <param name="pgerm" value="0.04"/>
+                    <param name="cnoffset" value="0.19"/>
+                </conditional>
+            </section>
+            <section name="oo">
+                <param name="out" value="bcf,vcf,log"/>
+            </section>
+            <output name="out_bcf">
+                <assert_contents>
+                    <has_size value="2322"/>
+                </assert_contents>
+            </output>
+            <output name="out_log">
+                <assert_contents>
+                    <has_text_matching expression=".+Done.+"/>
+                </assert_contents>
+            </output>
+            <output name="out_vcf">
+                <assert_contents>
+                    <has_size value="7762"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #3 germline, default -->
+        <test expect_num_outputs="3">
+            <param name="input" value="call_1.bcf.gz"/>
+            <section name="sv">
+                <conditional name="mode_cond">
+                    <param name="mode_sel" value="germline"/>
+                </conditional>
+            </section>
+            <section name="oo">
+                <param name="out" value="bcf,vcf,log"/>
+            </section>
+            <output name="out_bcf">
+                <assert_contents>
+                    <has_size value="2270"/>
+                </assert_contents>
+            </output>
+            <output name="out_log">
+                <assert_contents>
+                    <has_text_matching expression=".+Done.+"/>
+                </assert_contents>
+            </output>
+            <output name="out_vcf">
+                <assert_contents>
+                    <has_size value="7665"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #4 germline -->
+        <test expect_num_outputs="3">
+            <param name="input" value="call_1.bcf.gz"/>
+            <section name="sv">
+                <conditional name="mode_cond">
+                    <param name="mode_sel" value="germline"/>
+                    <param name="ploidy" value="1"/>
+                    <param name="qual" value="51"/>
+                    <param name="maxsd" value="0.16"/>
+                </conditional>
+            </section>
+            <section name="oo">
+                <param name="out" value="bcf,vcf,log"/>
+            </section>
+            <output name="out_bcf">
+                <assert_contents>
+                    <has_size value="2270"/>
+                </assert_contents>
+            </output>
+            <output name="out_log">
+                <assert_contents>
+                    <has_text_matching expression=".+Done.+"/>
+                </assert_contents>
+            </output>
+            <output name="out_vcf">
+                <assert_contents>
+                    <has_size value="7665"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+@WID@
+
+Delly *classify* for somatic or germline copy-number variants.
+
+**Input**
+
+Delly *classify* requires an input file in BCF format that can be generated with e.g. Delly *merge*. Additionally a tab-delimited sample description file is required where the first column is the sample id (as in the VCF/BCF file) and the second column is either tumor or control.
+
+**Output**
+
+The output is available in BCF and VCF format. Additionally a log file is provided.
+
+.. class:: infomark
+
+**References**
+
+@REFERENCES@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
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