diff control_freec.xml @ 1:2c6349fb175c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec commit a8b671c0a0d277296751dd2ae403603bea1c58dd"

--- a/control_freec.xml	Thu Aug 13 09:50:35 2020 -0400
+++ b/control_freec.xml	Tue Aug 18 08:52:45 2020 -0400
@@ -13,11 +13,15 @@
             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 +46,7 @@
         #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' '$WGS_WES.advanced_settings.ploidy'
         #end if
     ]]></command>
     <configfiles>
@@ -159,7 +160,10 @@
         <data name="out_gc_profile" format="tabular" label="${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>