--- a/macros.xml	Thu Oct 29 20:50:39 2020 +0000
+++ b/macros.xml	Fri Jan 22 14:31:44 2021 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">0.8.5</token>
+    <token name="@TOOL_VERSION@">0.8.7</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
@@ -17,14 +17,12 @@
         </citations>
     </xml>
 	
-    <!--
-        command 
-    -->
+    <!-- command -->
 
     <token name="@BAM@"><![CDATA[
-#for $i, $current in enumerate($samples)
-    ln -s '${current}' 'sample_${i}.bam' &&
-    ln -s '${current.metadata.bam_index}' 'sample_${i}.bam.bai' &&
+#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[
@@ -43,68 +41,79 @@
 #end if
     ]]></token>
 
-    <!--
-        input 
-    -->
+    <!-- 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"/>
+        <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="maxreadsep" token_default="40">
-        <param argument="--maxreadsep" type="integer" value="@DEFAULT@" label="Set maximum read separation"/>
+    <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="maxsize" token_default="1000000">
-        <param argument="--maxsize" type="integer" value="@DEFAULT@" label="Set maximum SV size"/>
-    </xml>
-    <xml name="mincliquesize">
-        <param name="mincliquesize" type="integer" value="2" label="Set minimum min. PE/SR clique size" help="(--min-clique-size)"/>
-    </xml>
-    <xml name="minrefsep" token_default="25">
+    <xml name="minrefsep" token_default="">
         <param argument="--minrefsep" type="integer" value="@DEFAULT@" label="Set minimum reference separation"/>
     </xml>
-    <xml name="minsize">
-        <param argument="--minsize" type="integer" value="0" label="Set minimum SV size"/>
+    <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="samples" token_format="bam" token_multiple="true" token_label="Select sample file(s)">
-        <param name="samples" type="data" format="@FORMAT@" multiple="@MULTIPLE@" label="@LABEL@"/>
+    <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="DUP">Duplication (DUP)</option>
             <option value="INV">Inversion (INV)</option>
             <option value="BND">Translocation (BND)</option>
         </param>
     </xml>
     <xml name="vcffile">
-        <param argument="--vcffile" type="data" format="vcf,bcf" optional="true" label="Select genotyping file"/>
+        <param argument="--vcffile" type="data" format="bcf,vcf" optional="true" label="Select genotyping file"/>
     </xml>
 
-    <!--
-        output 
-    -->
+    <!-- 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 ${on_string}: Result (VCF)">
             <filter>'vcf' in oo['out']</filter>
         </data>
     </xml>
-     <xml name="bcf">
-        <data name="out_bcf" format="bcf" from_work_dir="result.bcf" label="${tool.name} on ${on_string}: Result (BCF)">
-            <filter>'bcf' in oo['out']</filter>
-        </data>
-    </xml>
     <xml name="dump">
         <data name="out_dump" format="tabular" from_work_dir="dump.tsv" label="${tool.name} on ${on_string}: SV-reads">
             <filter>'dump' in oo['out']</filter>
@@ -116,12 +125,25 @@
         </data>
     </xml>
 
-    <!--
-        Help
-    -->
+    <!-- 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>`_.