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changeset 5:69f47e0b804e draft

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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/fsd commit 9829d657c07703b117bed2f259ddba432b244312
author mheinzl
date Wed, 09 May 2018 09:13:46 -0400
parents 5bae51dc7fa1
children c4b8222dce29
files fsd.py fsd.xml
diffstat 2 files changed, 7 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/fsd.py	Wed May 09 09:09:26 2018 -0400
+++ b/fsd.py	Wed May 09 09:13:46 2018 -0400
@@ -29,8 +29,8 @@
 
 def make_argparser():
     parser = argparse.ArgumentParser(description='Family Size Distribution of duplex sequencing data')
-    parser.add_argument('inputFile',
-                        help='Tabular File with three columns: ab or ba, tag and family size.')
+  #  parser.add_argument('inputFile',
+   #                     help='Tabular File with three columns: ab or ba, tag and family size.')
     parser.add_argument('--inputName1')
     parser.add_argument('--inputFile2',default=None,
                         help='Tabular File with three columns: ab or ba, tag and family size.')
@@ -53,8 +53,10 @@
     parser = make_argparser()
     args=parser.parse_args(argv[1:])
 
-    firstFile = args.inputFile
+    #firstFile = args.inputFile
     name1 = args.inputName1
+    firstFile = args.inputName1
+    
     secondFile = args.inputFile2
     name2 = args.inputName2
     thirdFile = args.inputFile3
--- a/fsd.xml	Wed May 09 09:09:26 2018 -0400
+++ b/fsd.xml	Wed May 09 09:13:46 2018 -0400
@@ -1,13 +1,13 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!-- galaxy version 16.04 -->
-<tool id="fsd" name="Duplex Sequencing Analysis:" version="0.0.5">
+<tool id="fsd" name="Duplex Sequencing Analysis:" version="0.0.6">
     <description>Family size distribution (FSD) of tags</description>
     <requirements>
         <requirement type="package" version="1.4">matplotlib</requirement>
     </requirements>
     
     <command>
-        python $__tool_directory__/fsd.py $file1.name --inputName1 $file1.name --inputFile2 $file2.name --inputName2 $file2.name --inputFile3 $file3.name --inputName3 $file3.name --inputFile4 $file4.name --inputName4 $file4.name --sep $separator --output_csv $output_csv --output_pdf $output_pdf
+        python $__tool_directory__/fsd.py --inputName1 $file1.name --inputFile2 $file2.name --inputName2 $file2.name --inputFile3 $file3.name --inputName3 $file3.name --inputFile4 $file4.name --inputName4 $file4.name --sep $separator --output_csv $output_csv --output_pdf $output_pdf
     </command>
     <inputs>
         <param name="file1" type="data" format="tabular" label="Dataset 1: input tags" optional="false"/>