Mercurial > repos > greg > extract_genomic_dna

comparison extract_genomic_dna.xml @ 12:9886ad53474a draft

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author greg
date Tue, 19 Jan 2016 21:48:00 -0500
parents 59bb87024183
children fe88f4eeaddc
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11:b9c52a655249 12:9886ad53474a
10 #set datatype = $input.datatype 10 #set datatype = $input.datatype
11 mkdir -p output_dir && 11 mkdir -p output_dir &&
12 python $__tool_directory__/extract_genomic_dna.py 12 python $__tool_directory__/extract_genomic_dna.py
13 --input "$input" 13 --input "$input"
14 --genome "$genome" 14 --genome "$genome"
15 #if isinstance($datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__): 15 #if $input.is_of_type("gff"):
16 --input_format "gff" 16 --input_format "gff"
17 --columns "1,4,5,7" 17 --columns "1,4,5,7"
18 --interpret_features $interpret_features 18 --interpret_features $interpret_features
19 #else: 19 #else:
20 --input_format "interval" 20 --input_format "interval"
60 </param> 60 </param>
61 </when> 61 </when>
62 </conditional> 62 </conditional>
63 <param name="output_format" type="select" label="Select output format"> 63 <param name="output_format" type="select" label="Select output format">
64 <option value="fasta" selected="True">fasta</option> 64 <option value="fasta" selected="True">fasta</option>
65 <option value="gff">gff</option>
65 <option value="interval">interval</option> 66 <option value="interval">interval</option>
66 </param> 67 </param>
67 </inputs> 68 </inputs>
68 <outputs> 69 <outputs>
69 <data name="output" format="gff"> 70 <data name="output" format="fasta">
70 <change_format> 71 <change_format>
71 <when output_format="interval" format="interval" /> 72 <when input="output_format" value="gff" format="gff" />
73 <when input="output_format" value="interval" format="interval" />
72 </change_format> 74 </change_format>
73 </data> 75 </data>
74 </outputs> 76 </outputs>
75 <tests> 77 <tests>
76 <test> 78 <test>