--- a/control_freec.xml	Thu Aug 13 13:49:44 2020 +0000
+++ b/control_freec.xml	Tue Aug 31 08:10:37 2021 +0000
@@ -1,5 +1,8 @@
 <tool id="control_freec" name="Control-FREEC" version="@WRAPPER_VERSION@">
     <description>detects copy-number changes and allelic imbalances</description>
+    <xrefs>
+        <xref type="bio.tools">freec</xref>
+    </xrefs>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -13,11 +16,15 @@
             samtools faidx ./genome.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for control-freec' >&2 &&
         #else
             ln -s '$reference_source.ref.fields.path' ./genome.fa &&
-            ln -s '${reference_source.ref.fields.path}.fai' ./genome.fa.fai &&
+            cp '${reference_source.ref.fields.path}.fai' ./genome.fa.fai &&
         #end if
 
         #if int($WGS_WES.advanced_settings.window_section.window) == 0
             ln -s '$WGS_WES.input_capture_file' ./capture.bed &&
+
+            cat ./capture.bed | cut -f 1 | sort | uniq > ./capture.bed_tmp &&
+            cp ./genome.fa.fai ./genome.fa.fai_tmp &&
+            awk 'NR==FNR{A[$1];next}($1 in A)' ./capture.bed_tmp ./genome.fa.fai_tmp > ./genome.fa.fai &&
         #end if
 
         mkdir ./chromosomes &&
@@ -42,10 +49,7 @@
         #end if
 
         #if $output_section.circos_data
-            && python '$__tool_directory__/ratio2circos.py'
-               -i ./output/sample.bam_ratio.BedGraph
-               -p '$WGS_WES.advanced_settings.ploidy'
-               -o sample.bam_ratio_log2_circos.txt
+            && python '$__tool_directory__/ratio2circos.py' '$WGS_WES.advanced_settings.ploidy'
         #end if
     ]]></command>
     <configfiles>
@@ -159,7 +163,10 @@
         <data name="out_gc_profile" format="tabular" label="${tool.name} on ${on_string}: GC-content profile" from_work_dir="output/GC_profile.targetedRegions.cnp">
             <filter>int(WGS_WES['advanced_settings']['window_section']['window']) == 0</filter>
         </data>
-        <data name="out_ratio_log2_circos" format="tabular" label="${tool.name} on ${on_string}: Circos 2D-track data" from_work_dir="output/sample.bam_ratio_log2_circos.txt">
+        <data name="out_ratio_log2_circos" format="tabular" label="${tool.name} on ${on_string}: Circos Log2 Ratio (2D Data Track)" from_work_dir="output/sample.bam_ratio_log2_circos.txt">
+            <filter>output_section['circos_data']</filter>
+        </data>
+        <data name="out_chr_sorted_circos" format="tabular" label="${tool.name} on ${on_string}: Circos Karyotype" from_work_dir="output/karyotype_circos.txt">
             <filter>output_section['circos_data']</filter>
         </data>
     </outputs>