--- a/fsd_beforevsafter.xml	Mon Oct 08 05:55:14 2018 -0400
+++ b/fsd_beforevsafter.xml	Mon Nov 26 04:26:20 2018 -0500
@@ -1,6 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <tool id="fsd_beforevsafter" name="FSD Before/After" version="1.0.0">
     <description>: Family Size Distribution of duplex sequecning tags during DuNovo analysis</description>
+    <macros>
+        <import>fsd_reg_macros.xml</import>
+    </macros>
     <requirements>
 		<!-- galaxy version 16.04 -->
         <requirement type="package" version="2.7">python</requirement>
@@ -8,13 +11,13 @@
         <requirement type="package" version="1.71">biopython</requirement>
     </requirements>
     <command>
-        python2 '$__tool_directory__/fsd_beforevsafter.py' --inputFile_SSCS '$file1' --inputName1 '$file1.name' --makeDCS '$makeDCS' --afterTrimming '$afterTrimming' --alignedTags '$alignedTags' --output_pdf $output_pdf --output_tabular $output_tabular
+        python2 '$__tool_directory__/fsd_beforevsafter.py' --inputFile_SSCS '$file1' --inputName1 '$file1.name' --makeDCS '$makeDCS' --afterTrimming '$afterTrimming' --bamFile '$bamFile' --output_pdf $output_pdf --output_tabular $output_tabular
     </command>
     <inputs>
         <param name="file1" type="data" format="tabular" label="Dataset 1: input tags of whole dataset" optional="false" help="Input in tabular format with the family size, tags and the direction of the strand ('ab' or 'ba') for each family."/>
         <param name="makeDCS" type="data" format="fasta" label="Dataset 2: tags after making DCSs" help="Input in fasta format with the tags of the reads, which were aligned to DCSs, and their family sizes of both strands (reverse and forward) in the header, as well as the read itself in the next line."/>
         <param name="afterTrimming" type="data" format="fasta" optional="true" label="Dataset 3: tags after trimming" help="Input in fasta format with the tags of the reads, which were not filtered out after trimming, and their family sizes of both strands (reverse and forward) in the header, as well as the read itself in the next following line."/>
-        <param name="alignedTags" type="data" format="txt" optional="true" label="Dataset 4: input tags aligned to the reference genome" help="Input in txt format with the regions of the reference genome and the tags, which were aligned to the reference genome."/>
+        <param name="bamFile" type="data" format="bam" optional="true" label="Dataset 4: input tags aligned to the reference genome" help="Input in BAM format with the reads that were aligned to the reference genome."/>
     </inputs>
     <outputs>
         <data name="output_pdf" format="pdf" />
@@ -22,12 +25,12 @@
     </outputs>
     <tests>
         <test>
-            <param name="file1" value="Test_data.tabular"/>
-            <param name="makeDCS" value="Test_data_DCS.fasta"/>
-            <param name="afterTrimming" value="Test_data_trimming.fasta"/>
-            <param name="alignedTags" value="Test_data_regions.txt"/>
-            <output name="output_pdf" file="output_file.pdf" lines_diff="183"/>
-            <output name="output_tabular" file="output_file.tabular"/>
+            <param name="file1" value="fsd_ba_data.tab"/>
+            <param name="makeDCS" value="fsd_ba_DCS.fna"/>
+            <param name="afterTrimming" value="fsd_ba_trimmed.fna"/>
+            <param name="bamFile" value="fsd_ba.bam"/>
+            <output name="output_pdf" file="fsd_ba_output.pdf" lines_diff="183"/>
+            <output name="output_tabular" file="fsd_ba_output.tab"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -56,32 +59,15 @@
   >AAAAAAAAGGCAGAAGATATACGC 11-3
   CNCNGGCCCCCCGCTCCGTGCACAGACGNNGCNACTGACAA
 	
-**Dataset 4 (optional):** Finally, a TXT file with the regions and all tags that were aligned to the reference genome can be given as input. This file can be obtained by the tool "Duplex Sequencing Analysis: range2tag"::
-
- 87_636   AAATCAAAGTATGAATGAAGTTGCCT
- 87_636   AAATTCATAGCATTAATTTCAACGGG
- 656_1143 GGGGCAGCCATATTGGCAATTATCAT
+**Dataset 4 (optional):** BAM file of the aligned reads. This file can be obtained by the tool "Map with BWA-MEM".	
 
 **Output**
         
 The output is a PDF file with the plot and a tabular file with the data of the plot.
          
-**About Author**
-        
-Author: Monika Heinzl
-Department: Institute of Bioinformatics, Johannes Kepler University Linz, Austria
-Contact: monika.heinzl@edumail.at
+@author@
         
 ]]> 
-
     </help>
-    <citations>
-        <citation type="bibtex">
-            @misc{duplex,
-            author = {Heinzl, Monika},
-            year = {2018},
-            title = {Development of algorithms for the analysis of duplex sequencing data}
-         }
-        </citation>
-    </citations>
+    <expand macro="@citation@" />
 </tool>