diff extract_genomic_dna.xml @ 11:80414c33a59a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 6db2d98b513e4980788fcba49d809c91e5750296

--- a/extract_genomic_dna.xml	Fri Dec 06 15:24:00 2019 -0500
+++ b/extract_genomic_dna.xml	Thu Nov 21 07:20:29 2024 +0000
@@ -1,10 +1,13 @@
-<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="3.0.3+galaxy2">
+<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="3.0.3+galaxy3">
     <description>using coordinates from assembled/unassembled genomes</description>
     <requirements>
         <requirement type="package" version="0.7.1">bx-python</requirement>
         <requirement type="package" version="1.13.0">six</requirement>
         <requirement type="package" version="377">ucsc-fatotwobit</requirement>
     </requirements>
+    <required_files>
+        <include path="extract_genomic_dna_utils.py" />
+    </required_files>
     <command detect_errors="exit_code"><![CDATA[
 #set genome = $input.metadata.dbkey
 #set datatype = $input.datatype
@@ -104,7 +107,7 @@
             <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="reference_genome" value="mm9.fasta" dbkey="mm9" ftype="fasta"/>
             <param name="output_format" value="fasta"/>
             <param name="fasta_header_type" value="char_delimited"/>
             <param name="fasta_header_delimiter" value="tilde"/>
@@ -114,7 +117,7 @@
             <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
             <param name="interpret_features" value="yes"/>
             <param name="reference_genome_source" value="history"/>
-            <param name="reference_genome" value="mm9.fasta"/>
+            <param name="reference_genome" value="mm9.fasta" dbkey="mm9"/>
             <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" />
@@ -123,7 +126,7 @@
             <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="reference_genome" value="mm9.fasta" dbkey="mm9"/>
             <param name="output_format" value="interval"/>
             <output name="output" file="extract_genomic_dna_out3.gff" compare="contains" />
         </test>
@@ -131,7 +134,7 @@
             <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
             <param name="interpret_features" value="yes"/>
             <param name="reference_genome_source" value="history"/>
-            <param name="reference_genome" value="mm9.fasta"/>
+            <param name="reference_genome" value="mm9.fasta" dbkey="mm9"/>
             <param name="output_format" value="interval"/>
             <output name="output" file="extract_genomic_dna_out4.gff" compare="contains" />
         </test>