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comparison 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
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5:c8467246b57e 6:53db9cb721f1
2 <description>using coordinates from assembled/unassembled genomes</description> 2 <description>using coordinates from assembled/unassembled genomes</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.7.1">bx-python</requirement> 4 <requirement type="package" version="0.7.1">bx-python</requirement>
5 <requirement type="package" version="324">ucsc-fatotwobit</requirement> 5 <requirement type="package" version="324">ucsc-fatotwobit</requirement>
6 </requirements> 6 </requirements>
7 <command> 7 <command detect_errors="exit_code"><![CDATA[
8 <![CDATA[ 8 #set genome = $input.metadata.dbkey
9 #set genome = $input.metadata.dbkey 9 #set datatype = $input.datatype
10 #set datatype = $input.datatype 10 mkdir -p output_dir &&
11 mkdir -p output_dir && 11 python '$__tool_directory__/extract_genomic_dna.py'
12 python $__tool_directory__/extract_genomic_dna.py 12 --input '$input'
13 --input "$input" 13 --genome '$genome'
14 --genome "$genome" 14 #if $input.is_of_type("gff"):
15 #if $input.is_of_type("gff"): 15 --input_format gff
16 --input_format "gff" 16 --columns '1,4,5,7'
17 --columns "1,4,5,7" 17 --interpret_features $interpret_features
18 --interpret_features $interpret_features 18 #else:
19 #else: 19 --input_format interval
20 --input_format "interval" 20 --columns '${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol},${input.metadata.nameCol}'
21 --columns "${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol},${input.metadata.nameCol}" 21 #end if
22 #end if 22 --reference_genome_source $reference_genome_cond.reference_genome_source
23 --reference_genome_source $reference_genome_cond.reference_genome_source 23 #if str($reference_genome_cond.reference_genome_source) == "cached"
24 #if str($reference_genome_cond.reference_genome_source) == "cached" 24 --reference_genome '$reference_genome_cond.reference_genome.fields.path'
25 --reference_genome $reference_genome_cond.reference_genome.fields.path 25 #else:
26 #else: 26 --reference_genome '$reference_genome_cond.reference_genome'
27 --reference_genome $reference_genome_cond.reference_genome 27 #end if
28 #end if 28 --output_format $output_format_cond.output_format
29 --output_format $output_format_cond.output_format 29 #if str($output_format_cond.output_format) == "fasta":
30 #if str($output_format_cond.output_format) == "fasta": 30 --fasta_header_type $output_format_cond.fasta_header_type_cond.fasta_header_type
31 --fasta_header_type $output_format_cond.fasta_header_type_cond.fasta_header_type 31 #if str($output_format_cond.fasta_header_type_cond.fasta_header_type) == "char_delimited":
32 #if str($output_format_cond.fasta_header_type_cond.fasta_header_type) == "char_delimited": 32 --fasta_header_delimiter $output_format_cond.fasta_header_type_cond.fasta_header_delimiter
33 --fasta_header_delimiter $output_format_cond.fasta_header_type_cond.fasta_header_delimiter 33 #end if
34 #end if 34 #end if
35 #end if 35 --output '$output'
36 --output $output
37 ]]> 36 ]]>
38 </command> 37 </command>
39 <inputs> 38 <inputs>
40 <param name="input" type="data" format="gff,interval" label="Fetch sequences for intervals in"> 39 <param name="input" type="data" format="gff,interval" label="Fetch sequences for intervals in">
41 <validator type="unspecified_build" /> 40 <validator type="unspecified_build" />