# HG changeset patch
# User greg
# Date 1457096319 18000
# Node ID 2b565382e4697d1ebcb494d38f3e8f0d6b6fdff2
# Parent  2a80b722679c118afda92a3dc4fe412369de66f4
Uploaded

diff -r 2a80b722679c -r 2b565382e469 extract_genomic_dna.xml
--- a/extract_genomic_dna.xml	Fri Mar 04 07:58:19 2016 -0500
+++ b/extract_genomic_dna.xml	Fri Mar 04 07:58:39 2016 -0500
@@ -83,8 +83,8 @@
                             <option value="underscore" selected="True">underscore (_)</option>
                             <option value="semicolon">semicolon (;)</option>
                             <option value="comma">comma (,)</option>
-                            <option value="tilda">tilda (~)</option>
-                            <option value="vetical_bar">vertical bar (|)</option>
+                            <option value="tilde">tilde (~)</option>
+                            <option value="vertical_bar">vertical bar (|)</option>
                         </param>
                     </when>
                 </conditional>
@@ -104,7 +104,7 @@
             <param name="input" value="1.bed" dbkey="hg17" ftype="bed" />
             <param name="interpret_features" value="yes"/>
             <param name="index_source" value="cached"/>
-            <param name="out_format" value="fasta"/>
+            <param name="output_format" value="fasta"/>
             <param name="fasta_header_type" value="char_delimited"/>
             <param name="fasta_header_delimiter" value="underscore"/>
             <output name="out_file1" file="extract_genomic_dna_out1.fasta" compare="contains" />
@@ -113,7 +113,7 @@
             <param name="input" value="droPer1.bed" dbkey="droPer1" ftype="bed" />
             <param name="interpret_features" value="yes"/>
             <param name="index_source" value="cached"/>
-            <param name="out_format" value="fasta"/>
+            <param name="output_format" value="fasta"/>
             <param name="fasta_header_type" value="char_delimited"/>
             <param name="fasta_header_delimiter" value="underscore"/>
             <output name="out_file1" file="extract_genomic_dna_out2.fasta" compare="contains" />
@@ -122,7 +122,7 @@
             <param name="input" value="1.bed" dbkey="hg17" ftype="bed" />
             <param name="interpret_features" value="yes"/>
             <param name="index_source" value="cached"/>
-            <param name="out_format" value="interval"/>
+            <param name="output_format" value="interval"/>
             <output name="out_file1" file="extract_genomic_dna_out3.interval" compare="contains" />
         </test>
         <!-- Test GFF file support. -->
@@ -130,14 +130,14 @@
             <param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" />
             <param name="interpret_features" value="no"/>
             <param name="index_source" value="cached"/>
-            <param name="out_format" value="interval"/>
+            <param name="output_format" value="interval"/>
             <output name="out_file1" file="extract_genomic_dna_out4.gff" compare="contains" />
         </test>
         <test>
             <param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" />
             <param name="interpret_features" value="no"/>
             <param name="index_source" value="cached"/>
-            <param name="out_format" value="fasta"/>
+            <param name="output_format" value="fasta"/>
             <param name="fasta_header_type" value="char_delimited"/>
             <param name="fasta_header_delimiter" value="underscore"/>
             <output name="out_file1" file="extract_genomic_dna_out5.fasta" compare="contains" />
@@ -148,7 +148,7 @@
             <param name="interpret_features" value="no"/>
             <param name="index_source" value="history"/>
             <param name="ref_file" value="tophat_in1.fasta"/>
-            <param name="out_format" value="fasta"/>
+            <param name="output_format" value="fasta"/>
             <param name="fasta_header_type" value="char_delimited"/>
             <param name="fasta_header_delimiter" value="underscore"/>
             <output name="out_file1" file="extract_genomic_dna_out6.fasta" compare="contains" />
@@ -158,7 +158,7 @@
             <param name="interpret_features" value="yes"/>
             <param name="index_source" value="history"/>
             <param name="ref_file" value="tophat_in1.fasta"/>
-            <param name="out_format" value="fasta"/>
+            <param name="output_format" value="fasta"/>
             <param name="fasta_header_type" value="bedtools_getfasta_default"/>
             <output name="out_file1" file="extract_genomic_dna_out7.fasta" compare="contains" />
         </test>
@@ -220,7 +220,7 @@
     chr7  127485994  127486166  NM_000230  0  +
     chr7  127486011  127486166  D49487     0  +
 
-Extracting sequences with **FASTA** output data type  and **Description Field Delimiter** set to the underscore character returns::
+Extracting sequences with **FASTA** output data type, **character delimited field values** as header format and **header field delimiter** set to the underscore character returns::
 
     &gt;hg17_chr7_127475281_127475310_+ NM_000230
     GTAGGAATCGCAGCGCCAGCGGTTGCAAG
@@ -245,7 +245,7 @@
     <citations>
         <citation type="bibtex">
             @unpublished{None,
-            author = {Guru Ananda, Greg Von Kuster},
+            author = {Guru Ananda,Greg Von Kuster},
             title = {None},
             year = {None},
             eprint = {None},