# HG changeset patch
# User greg
# Date 1457208712 18000
# Node ID 23eaaaf7902e8293813af074da4585cf6183ce96
# Parent  2b565382e4697d1ebcb494d38f3e8f0d6b6fdff2
Uploaded

diff -r 2b565382e469 -r 23eaaaf7902e extract_genomic_dna.xml
--- a/extract_genomic_dna.xml	Fri Mar 04 07:58:39 2016 -0500
+++ b/extract_genomic_dna.xml	Sat Mar 05 15:11:52 2016 -0500
@@ -1,8 +1,10 @@
 <tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="3.0.2">
     <description>using coordinates from assembled/unassembled genomes</description>
     <requirements>
+        <requirement type="package" version="35x1">faToTwoBit</requirement>
         <requirement type="package" version="0.7.1">bx-python</requirement>
-        <requirement type="package" version="35x1">faToTwoBit</requirement>
+        <!-- conda dependencies -->
+        <requirement type="package" version="324">ucsc-fatotwobit</requirement>
     </requirements>
     <command>
         <![CDATA[
@@ -101,66 +103,39 @@
     </outputs>
     <tests>
         <test>
-            <param name="input" value="1.bed" dbkey="hg17" ftype="bed" />
-            <param name="interpret_features" value="yes"/>
-            <param name="index_source" value="cached"/>
+            <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
+            <param name="interpret_features" value="no"/>
+            <param name="reference_genome_source" value="history"/>
+            <param name="reference_genome" value="mm9.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" />
-        </test>
-        <test>
-            <param name="input" value="droPer1.bed" dbkey="droPer1" ftype="bed" />
-            <param name="interpret_features" value="yes"/>
-            <param name="index_source" value="cached"/>
-            <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" />
+            <param name="fasta_header_delimiter" value="tilde"/>
+            <output name="output" file="extract_genomic_dna_out1.fasta" compare="contains" />
         </test>
         <test>
-            <param name="input" value="1.bed" dbkey="hg17" ftype="bed" />
+            <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
             <param name="interpret_features" value="yes"/>
-            <param name="index_source" value="cached"/>
-            <param name="output_format" value="interval"/>
-            <output name="out_file1" file="extract_genomic_dna_out3.interval" compare="contains" />
-        </test>
-        <!-- Test GFF file support. -->
-        <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="output_format" value="interval"/>
-            <output name="out_file1" file="extract_genomic_dna_out4.gff" compare="contains" />
+            <param name="reference_genome_source" value="history"/>
+            <param name="reference_genome" value="mm9.fasta"/>
+            <param name="output_format" value="fasta"/>
+            <param name="fasta_header_type" value="bedtools_getfasta_default"/>
+            <output name="output" file="extract_genomic_dna_out2.fasta" compare="contains" />
         </test>
         <test>
-            <param name="input" value="gff_filter_by_attribute_out1.gff" dbkey="mm9" ftype="gff" />
+            <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
             <param name="interpret_features" value="no"/>
-            <param name="index_source" value="cached"/>
-            <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" />
-        </test>
-        <!-- Test custom sequences support and GFF feature interpretation. -->
-        <test>
-            <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" />
-            <param name="interpret_features" value="no"/>
-            <param name="index_source" value="history"/>
-            <param name="ref_file" value="tophat_in1.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" />
+            <param name="reference_genome_source" value="history"/>
+            <param name="reference_genome" value="mm9.fasta"/>
+            <param name="output_format" value="interval"/>
+            <output name="output" file="extract_genomic_dna_out3.gff" compare="contains" />
         </test>
         <test>
-            <param name="input" value="cufflinks_out1.gtf" dbkey="mm9" ftype="gff" />
+            <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
             <param name="interpret_features" value="yes"/>
-            <param name="index_source" value="history"/>
-            <param name="ref_file" value="tophat_in1.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" />
+            <param name="reference_genome_source" value="history"/>
+            <param name="reference_genome" value="mm9.fasta"/>
+            <param name="output_format" value="interval"/>
+            <output name="output" file="extract_genomic_dna_out4.gff" compare="contains" />
         </test>
     </tests>
     <help>