--- a/fsd_beforevsafter.xml	Wed May 23 15:04:39 2018 -0400
+++ b/fsd_beforevsafter.xml	Mon Oct 08 05:55:14 2018 -0400
@@ -1,90 +1,78 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="fsd_beforevsafter" name="Duplex Sequencing Analysis: fsd_beforevsafter" version="0.0.9">
+<tool id="fsd_beforevsafter" name="FSD Before/After" version="1.0.0">
+    <description>: Family Size Distribution of duplex sequecning tags during DuNovo analysis</description>
     <requirements>
 		<!-- galaxy version 16.04 -->
         <requirement type="package" version="2.7">python</requirement>
         <requirement type="package" version="1.4">matplotlib</requirement>
         <requirement type="package" version="1.71">biopython</requirement>
-        
     </requirements>
-    <description>Family size distribution (FSD) of tags from various steps of the Du Novo pipeline</description>
     <command>
-        python2 $__tool_directory__/fsd_beforevsafter.py --inputFile_SSCS "$file1" --inputName1 "$file1.name" --makeDCS "$makeDCS" --afterTrimming "$afterTrimming" --alignedTags "$alignedTags" --sep $separator --output_pdf $output_pdf --output_csv $output_csv 
+        python2 '$__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
     </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 and the tags, which were aligned to the reference genome."/>
-        <param name="separator" type="text" label="Separator of the CSV file." help="can be a single character" value=","/>
+        <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."/>
     </inputs>
     <outputs>
         <data name="output_pdf" format="pdf" />
-        <data name="output_csv" format="csv"/>
+        <data name="output_tabular" format="tabular"/>
     </outputs>
-    <help> <![CDATA[
+    <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"/>
+        </test>
+    </tests>
+    <help><![CDATA[
 
 **What it does**
         
-    This tool will create a distribution of family sizes of various datasets obtained from different steps of the Du Novo pipeline. 
+This tool will create a distribution of family sizes of various datasets obtained from different steps of the Du Novo pipeline. 
+
+-----
                
 **Input**
         
-    **Dataset 1:** This tools expects a tabular file with the tags of all families, their sizes and information about forward (ab) and reverse (ba) strands. 
-    
-    +-----+----------------------------+----+
-    | 1   | AAAAAAAAAAAATGTTGGAATCTT   | ba |
-    +-----+----------------------------+----+
-    | 10  | AAAAAAAAAAAGGCGGTCCACCCC   | ab |
-    +-----+----------------------------+----+
-    | 28  | AAAAAAAAAAATGGTATGGACCGA   | ab |
-    +-----+----------------------------+----+
-    
-    
-    
-    **Dataset 2:** And a fasta file with all tags and their family sizes of both strands (forward and reverse) in the header and the read itself in the next line is required. This input file can be obtained by Du Novo: make consensus reads. 
-    
-    
-    **Dataset 3 (optional):** In addition, the fasta file with all tags, which were not filtered out after trimming, can be given.
-    For both input files, only one file from both tools are necessary (these tools give for both forward and reverse strands an output file), since both files have the same tags and family sizes, but different reads, which are not required in this tool.
+**Dataset 1:** This tools expects a tabular file with the tags of all families, their sizes and information about forward (ab) and reverse (ba) strands.:: 
+
+      1  AAAAAAAAAAAATGTTGGAATCTT ba
+     10  AAAAAAAAAAAGGCGGTCCACCCC ab
+     28  AAAAAAAAAAATGGTATGGACCGA ab
+          
+**Dataset 2:** A fasta file with all tags and their family sizes of both strands (forward and reverse) in the header and the read itself in the next line is required. This input file can be obtained by the tool "Du Novo: make consensus reads". 
     
-    +-------------------------------------------+
-    | >AAAAAAAAATAGATCATAGACTCT 7-10            |
-    |                                           |
-    | CTAGACTCACTGGCGTTACTGACTGCGAGACCCTCCACGTG |
-    +-------------------------------------------+
-    | >AAAAAAAAGGCAGAAGATATACGC 11-3            |
-    |                                           |
-    | CNCNGGCCCCCCGCTCCGTGCACAGACGNNGCNACTGACAA |
-    +-------------------------------------------+
-    
-    
-    
+**Dataset 3 (optional):** In addition, the fasta file with all tags, which were not filtered out after trimming, can be given. This file can be obtained by the tool "Sequence Content Trimmer".
+For both input files, only one file from both tools are necessary (these tools give for both forward and reverse strands an output file), since both files have the same tags and family sizes, but different reads, which are not required in this tool::
+ 
+  >AAAAAAAAATAGATCATAGACTCT 7-10
+  CTAGACTCACTGGCGTTACTGACTGCGAGACCCTCCACGTG
+  >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 obtained from "Duplex Sequencing Analysis: range2tag"
+**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   |
-    +-----------+------------------------------+
-   
+ 87_636   AAATCAAAGTATGAATGAAGTTGCCT
+ 87_636   AAATTCATAGCATTAATTTCAACGGG
+ 656_1143 GGGGCAGCCATATTGGCAATTATCAT
+
 **Output**
         
-    The output is a PDF file with the plot and a CSV with the data of the plot.
-        
-        
+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: Monika Heinzl
+Department: Institute of Bioinformatics, Johannes Kepler University Linz, Austria
+Contact: monika.heinzl@edumail.at
         
-        ]]> 
+]]> 
 
     </help>
     <citations>