# HG changeset patch
# User bebatut
# Date 1461846890 14400
# Node ID d7747e6f329ffd36aa9bde15f52c46fe39d3a946
# Parent  b4cf778be846767f16642b6a43bca4d7a2c58ae9
planemo upload commit 0a1bbb0870f6b776175151d4bc818c5546731ca8-dirty

diff -r b4cf778be846 -r d7747e6f329f convert_extract_sequence_file.py
--- a/convert_extract_sequence_file.py	Tue Apr 26 08:17:42 2016 -0400
+++ b/convert_extract_sequence_file.py	Thu Apr 28 08:34:50 2016 -0400
@@ -42,7 +42,7 @@
         return None
     split_line = id_line[1:].split(' ')
     seq_id = split_line[0]
-    description = ' '.join(split_line[1:])
+    description = id_line[1:]
     new_line = get_new_line(input_file, generate_error = False)
     seq = ''
     while new_line != None:
@@ -265,7 +265,7 @@
         if args.custom_extraction_type == 'True':
             to_extract = args.to_extract[1:-1].split(',')
             with open(args.output_information, 'w') as output_information_file:
-                output_information_file.write('\t'.join(to_extract) + '\n')
+                #output_information_file.write('\t'.join(to_extract) + '\n')
                 for record in self.conserved_records:
                     extracted_info = record.extract_information(to_extract)
                     string_info = [str(info) for info in extracted_info]
diff -r b4cf778be846 -r d7747e6f329f convert_extract_sequence_file.xml
--- a/convert_extract_sequence_file.xml	Tue Apr 26 08:17:42 2016 -0400
+++ b/convert_extract_sequence_file.xml	Thu Apr 28 08:34:50 2016 -0400
@@ -7,6 +7,7 @@
             <param name="to_extract" type="select" display="checkboxes" multiple="true" label="Information to extract" help="">
                 <option value="id">Identifiant</option>
                 <option value="length">Length</option>
+                <option value="description">Description</option>
                 <validator type="no_options" message="Select at least one information to extract"/>
             </param>
         </xml>
@@ -179,7 +180,7 @@
   	</inputs>
 
   	<outputs>
-        <data format="txt" name="information_file" 
+        <data format="tabular" name="information_file" 
             label="${tool.name} on ${on_string}: Information">
             <filter>((sequence_file_format['extraction']['specific_extraction'] == "True" ))</filter>
         </data>
diff -r b4cf778be846 -r d7747e6f329f test-data/information_lenght_fasta_output.txt
--- a/test-data/information_lenght_fasta_output.txt	Tue Apr 26 08:17:42 2016 -0400
+++ b/test-data/information_lenght_fasta_output.txt	Thu Apr 28 08:34:50 2016 -0400
@@ -1,4 +1,3 @@
-length
 86
 141
 300