diff fsd_regions.xml @ 4:b202c97deabe draft

planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd_regions commit dfaab79252a858e8df16bbea3607ebf1b6962e5a

--- a/fsd_regions.xml	Wed May 23 15:06:27 2018 -0400
+++ b/fsd_regions.xml	Mon Oct 08 05:53:50 2018 -0400
@@ -1,22 +1,29 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="fsd_regions" name="Duplex Sequencing Analysis: fsd_regions" version="0.0.4">
+<tool id="fsd_regions" name="Duplex Sequencing Analysis: fsd_regions" version="1.0.0">
+    <description>Family size distribution (FSD) of user-specified regions in the reference genome</description>
     <requirements>
         <requirement type="package" version="2.7">python</requirement>
-        <requirement type="package" version="1.4">matplotlib</requirement>
+        <requirement type="package" version="1.4.0">matplotlib</requirement>
     </requirements>
-    <description>Family size distribution (FSD) of user-specified regions</description>
     <command>
-        python2 $__tool_directory__/fsd_regions.py --inputFile "$file1" --inputName1 "$file1.name" --ref_genome "$file2" --sep $separator --output_pdf $output_pdf --output_csv $output_csv 
+        python2 '$__tool_directory__/fsd_regions.py' --inputFile '$file1' --inputName1 '$file1.name' --ref_genome '$file2' --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="file2" type="data" format="txt" label="Dataset 2: 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="file2" type="data" format="txt" label="Dataset 2: input tags aligned to the reference genome" help="Input in txt format with the regions in 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>
+    <tests>
+        <test>
+            <param name="file1" value="Test_data.tabular"/>
+            <param name="file2" value="Test_data_regions.txt"/>
+            <output name="output_pdf" file="output_file.pdf" lines_diff="136"/>
+            <output name="output_tabular" file="output_file.tabular"/>
+        </test>
+    </tests>
     <help> <![CDATA[
 
 **What it does**
@@ -49,7 +56,7 @@
     
 **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**