Mercurial > repos > iuc > extract_genomic_dna

diff extract_genomic_dna.xml @ 6:53db9cb721f1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
author iuc
date Mon, 03 Jul 2017 07:19:41 -0400
parents 4822a36300fd
children 3088e7e70888
line wrap: on
line diff
--- a/extract_genomic_dna.xml	Sat Jan 21 14:41:27 2017 -0500
+++ b/extract_genomic_dna.xml	Mon Jul 03 07:19:41 2017 -0400
@@ -4,36 +4,35 @@
         <requirement type="package" version="0.7.1">bx-python</requirement>
         <requirement type="package" version="324">ucsc-fatotwobit</requirement>
     </requirements>
-    <command>
-        <![CDATA[
-            #set genome = $input.metadata.dbkey
-            #set datatype = $input.datatype
-            mkdir -p output_dir &&
-            python $__tool_directory__/extract_genomic_dna.py
-            --input "$input"
-            --genome "$genome"
-            #if $input.is_of_type("gff"):
-                --input_format "gff"
-                --columns "1,4,5,7"
-                --interpret_features $interpret_features
-            #else:
-                --input_format "interval"
-                --columns "${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol},${input.metadata.nameCol}"
-            #end if
-            --reference_genome_source $reference_genome_cond.reference_genome_source
-            #if str($reference_genome_cond.reference_genome_source) == "cached"
-                --reference_genome $reference_genome_cond.reference_genome.fields.path
-            #else:
-                --reference_genome $reference_genome_cond.reference_genome
-            #end if
-            --output_format $output_format_cond.output_format
-            #if str($output_format_cond.output_format) == "fasta":
-                --fasta_header_type $output_format_cond.fasta_header_type_cond.fasta_header_type
-                #if str($output_format_cond.fasta_header_type_cond.fasta_header_type) == "char_delimited":
-                    --fasta_header_delimiter $output_format_cond.fasta_header_type_cond.fasta_header_delimiter
-                #end if
-            #end if
-            --output $output
+    <command detect_errors="exit_code"><![CDATA[
+#set genome = $input.metadata.dbkey
+#set datatype = $input.datatype
+mkdir -p output_dir &&
+python '$__tool_directory__/extract_genomic_dna.py'
+--input '$input'
+--genome '$genome'
+#if $input.is_of_type("gff"):
+    --input_format gff
+    --columns '1,4,5,7'
+    --interpret_features $interpret_features
+#else:
+    --input_format interval
+    --columns '${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol},${input.metadata.nameCol}'
+#end if
+--reference_genome_source $reference_genome_cond.reference_genome_source
+#if str($reference_genome_cond.reference_genome_source) == "cached"
+    --reference_genome '$reference_genome_cond.reference_genome.fields.path'
+#else:
+    --reference_genome '$reference_genome_cond.reference_genome'
+#end if
+--output_format $output_format_cond.output_format
+#if str($output_format_cond.output_format) == "fasta":
+    --fasta_header_type $output_format_cond.fasta_header_type_cond.fasta_header_type
+    #if str($output_format_cond.fasta_header_type_cond.fasta_header_type) == "char_delimited":
+        --fasta_header_delimiter $output_format_cond.fasta_header_type_cond.fasta_header_delimiter
+    #end if
+#end if
+--output '$output'
         ]]>
     </command>
     <inputs>