--- a/fsd_beforevsafter.xml	Wed Dec 04 16:32:40 2019 -0500
+++ b/fsd_beforevsafter.xml	Fri Sep 10 06:59:00 2021 +0000
@@ -8,7 +8,11 @@
         <requirement type="package" version="1.71">biopython</requirement>
         <requirement type="package" version="0.15">pysam</requirement>
     </expand>
-    <command>
+    <command><![CDATA[
+#if $bamFile:
+    ln -s '$bamFile' 'reads.bam' &&
+    ln -s '$bamFile.metadata.bam_index' 'reads.bam.bai' &&
+#end if
 python '$__tool_directory__/fsd_beforevsafter.py'
 --inputFile_SSCS '$file'
 --inputName1 @ESCAPE_IDENTIFIER@
@@ -17,11 +21,11 @@
     --afterTrimming '$afterTrimming'
 #end if
 #if $bamFile:
---bamFile '$bamFile'
+    --bamFile 'reads.bam'
 #end if
 --output_pdf '$output_pdf'
 --output_tabular '$output_tabular'
-    </command>
+    ]]></command>
     <inputs>
         <param name="file" type="data" format="tabular" label="Input tags of SSCSs" optional="false" help="This dataset is generated by post-processing of the output from 'Make Families' or 'Correct Barcodes' tool by extracting the first two columns, sorting the tags (column 1) and adding the counts of unique occurencies of each tag. See Help section below for a detailed explanation."/>
         <param name="makeDCS" type="data" format="fasta" label="Input tags after making DCSs" help="Input in fasta format with the tags of the reads, which were aligned to DCSs. This file is produced by the 'Make consensus reads' tool."/>