annotate extract_genomic_dna.xml @ 9:e1f5bdd8279c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
author iuc
date Thu, 17 Oct 2019 03:00:47 -0400
parents 3088e7e70888
children 5cc8e93ee98f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
4822a36300fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 1f61dbad440e0589e73a3bc0c304b00e9fbf2606
iuc
parents: 2
diff changeset
1 <tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="3.0.3">
0
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
2 <description>using coordinates from assembled/unassembled genomes</description>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
3 <requirements>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
4 <requirement type="package" version="0.7.1">bx-python</requirement>
7
3088e7e70888 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 4a3c9f195ba5d899b1a1ce5e80281cdf230f456a
iuc
parents: 6
diff changeset
5 <requirement type="package" version="1.10.0">six</requirement>
2
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
6 <requirement type="package" version="324">ucsc-fatotwobit</requirement>
0
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
7 </requirements>
6
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
9 #set genome = $input.metadata.dbkey
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
10 #set datatype = $input.datatype
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
11 mkdir -p output_dir &&
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
12 python '$__tool_directory__/extract_genomic_dna.py'
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
13 --input '$input'
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
14 --genome '$genome'
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
15 #if $input.is_of_type("gff"):
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
16 --input_format gff
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
17 --columns '1,4,5,7'
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
18 --interpret_features $interpret_features
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
19 #else:
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
20 --input_format interval
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
21 --columns '${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol},${input.metadata.nameCol}'
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
22 #end if
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
23 --reference_genome_source $reference_genome_cond.reference_genome_source
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
24 #if str($reference_genome_cond.reference_genome_source) == "cached"
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
25 --reference_genome '$reference_genome_cond.reference_genome.fields.path'
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
26 #else:
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
27 --reference_genome '$reference_genome_cond.reference_genome'
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
28 #end if
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
29 --output_format $output_format_cond.output_format
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
30 #if str($output_format_cond.output_format) == "fasta":
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
31 --fasta_header_type $output_format_cond.fasta_header_type_cond.fasta_header_type
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
32 #if str($output_format_cond.fasta_header_type_cond.fasta_header_type) == "char_delimited":
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
33 --fasta_header_delimiter $output_format_cond.fasta_header_type_cond.fasta_header_delimiter
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
34 #end if
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
35 #end if
53db9cb721f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 01b3157ca9272d2f9f0e850a0de8f8a1cf085dab
iuc
parents: 4
diff changeset
36 --output '$output'
0
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
37 ]]>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
38 </command>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
39 <inputs>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
40 <param name="input" type="data" format="gff,interval" label="Fetch sequences for intervals in">
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
41 <validator type="unspecified_build" />
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
42 </param>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
43 <param name="interpret_features" type="select" label="Interpret features when possible" help="Applicable only when input dataset format is in the gff family">
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
44 <option value="yes">Yes</option>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
45 <option value="no">No</option>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
46 </param>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
47 <conditional name="reference_genome_cond">
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
48 <param name="reference_genome_source" type="select" label="Choose the source for the reference genome">
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
49 <option value="cached">locally cached</option>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
50 <option value="history">from history</option>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
51 </param>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
52 <when value="cached">
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
53 <param name="reference_genome" type="select" label="Using reference genome">
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
54 <options from_data_table="twobit">
9
e1f5bdd8279c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
iuc
parents: 7
diff changeset
55 <filter type="data_meta" key="dbkey" ref="input" column="dbkey"/>
0
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
56 </options>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
57 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
58 </param>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
59 </when>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
60 <when value="history">
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
61 <param name="reference_genome" type="data" format="fasta" label="Using reference genome">
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
62 <options>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
63 <filter type="data_meta" key="dbkey" ref="input"/>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
64 </options>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
65 <validator type="no_options" message="The current history does not include a fasta dataset with the build associated with the selected input file"/>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
66 </param>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
67 </when>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
68 </conditional>
2
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
69 <conditional name="output_format_cond">
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
70 <param name="output_format" type="select" label="Select output format">
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
71 <option value="fasta" selected="True">fasta</option>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
72 <option value="interval">interval</option>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
73 </param>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
74 <when value="fasta">
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
75 <conditional name="fasta_header_type_cond">
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
76 <param name="fasta_header_type" type="select" label="Select fasta header format">
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
77 <option value="bedtools_getfasta_default" selected="True">bedtools getfasta default</option>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
78 <option value="char_delimited">character delimited field values</option>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
79 </param>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
80 <when value="bedtools_getfasta_default"/>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
81 <when value="char_delimited">
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
82 <param name="fasta_header_delimiter" type="select" label="Select fasta header field delimiter">
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
83 <option value="underscore" selected="True">underscore (_)</option>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
84 <option value="semicolon">semicolon (;)</option>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
85 <option value="comma">comma (,)</option>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
86 <option value="tilde">tilde (~)</option>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
87 <option value="vertical_bar">vertical bar (|)</option>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
88 </param>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
89 </when>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
90 </conditional>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
91 </when>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
92 <when value="interval"/>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
93 </conditional>
0
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
94 </inputs>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
95 <outputs>
1
9af3f57e50b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'f42aabcc7ec5afe35588fd6471fa9ca0a86d7e98'
iuc
parents: 0
diff changeset
96 <data format_source="input" name="output" metadata_source="input">
0
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
97 <change_format>
2
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
98 <when input="output_format_cond.output_format" value="fasta" format="fasta" />
0
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
99 </change_format>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
100 </data>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
101 </outputs>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
102 <tests>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
103 <test>
2
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
104 <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
105 <param name="interpret_features" value="no"/>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
106 <param name="reference_genome_source" value="history"/>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
107 <param name="reference_genome" value="mm9.fasta"/>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
108 <param name="output_format" value="fasta"/>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
109 <param name="fasta_header_type" value="char_delimited"/>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
110 <param name="fasta_header_delimiter" value="tilde"/>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
111 <output name="output" file="extract_genomic_dna_out1.fasta" compare="contains" />
0
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
112 </test>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
113 <test>
2
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
114 <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
0
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
115 <param name="interpret_features" value="yes"/>
2
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
116 <param name="reference_genome_source" value="history"/>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
117 <param name="reference_genome" value="mm9.fasta"/>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
118 <param name="output_format" value="fasta"/>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
119 <param name="fasta_header_type" value="bedtools_getfasta_default"/>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
120 <output name="output" file="extract_genomic_dna_out2.fasta" compare="contains" />
0
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
121 </test>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
122 <test>
2
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
123 <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
0
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
124 <param name="interpret_features" value="no"/>
2
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
125 <param name="reference_genome_source" value="history"/>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
126 <param name="reference_genome" value="mm9.fasta"/>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
127 <param name="output_format" value="interval"/>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
128 <output name="output" file="extract_genomic_dna_out3.gff" compare="contains" />
0
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
129 </test>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
130 <test>
2
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
131 <param name="input" value="mm9_input1.gff" dbkey="mm9" ftype="gff" />
0
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
132 <param name="interpret_features" value="yes"/>
2
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
133 <param name="reference_genome_source" value="history"/>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
134 <param name="reference_genome" value="mm9.fasta"/>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
135 <param name="output_format" value="interval"/>
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
136 <output name="output" file="extract_genomic_dna_out4.gff" compare="contains" />
0
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
137 </test>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
138 </tests>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
139 <help>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
140
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
141 .. class:: warningmark
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
142
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
143 This tool requires interval or gff (special tabular formatted data). If your data is not TAB delimited, first use *Text Manipulation-&gt;Convert*.
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
144
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
145 .. class:: warningmark
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
146
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
147 Make sure that the genome build is specified for the dataset from which you are extracting sequences (click the pencil icon in the history item if it is not specified).
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
148
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
149 .. class:: warningmark
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
150
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
151 All of the following will cause a line from the input dataset to be skipped and a warning generated. The number of warnings and skipped lines is documented in the resulting history item.
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
152 - Any lines that do not contain at least 3 columns, a chromosome and numerical start and end coordinates.
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
153 - Sequences that fall outside of the range of a line's start and end coordinates.
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
154 - Chromosome, start or end coordinates that are invalid for the specified build.
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
155 - Any lines whose data columns are not separated by a **TAB** character ( other white-space characters are invalid ).
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
156
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
157 -----
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
158
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
159 **What it does**
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
160
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
161 This tool uses coordinate, strand, and build information to fetch genomic DNAs in FASTA or interval format.
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
162
2
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
163 If the output format is FASTA, the header format can be specified. Selecting the **bedtools getfasta default**
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
164 option produces a FASTA header formatted like the default header produced the the bedtools getfasta tool, and
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
165 the "force strandedness" option is assumed. If the input data includes a strand column and the strand is '+'
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
166 or '-', it is included in the header. If the input data includes a strand column and the value is anything but
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
167 '+' or '-', a '.' is included in the header. If the input data does not include a strand column, a '.' is included
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
168 in the header.
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
169
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
170 An example FASTA header produced by selecting this option is:
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
171
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
172 &gt;chr7:127475281-127475310(+)
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
173
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
174 Selecing the **character delimited field values** option allows selection of a character delimiter that is used
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
175 when generating the FASTA header with fields genome, chrom, start, end, strand (name) delimited by the
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
176 selected character. For example, selecting an underscore will produce a FASTA header like this:
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
177
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
178 &gt;mm9_53_550_+ test_chromosome
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
179
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
180 while selecting a vertical bar will produce a FASTA header like this:
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
181
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
182 &gt;mm9|53|550|+ test_chromosome
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
183
0
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
184 If strand is not defined, the default value is "+".
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
185
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
186 -----
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
187
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
188 **Example**
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
189
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
190 If the input dataset is::
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
191
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
192 chr7 127475281 127475310 NM_000230 0 +
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
193 chr7 127485994 127486166 NM_000230 0 +
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
194 chr7 127486011 127486166 D49487 0 +
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
195
2
702970e4a134 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit 9192c1e90e2fd5017e6044884bcc6f2e80ba8b31
iuc
parents: 1
diff changeset
196 Extracting sequences with **FASTA** output data type, **character delimited field values** as header format and **header field delimiter** set to the underscore character returns::
0
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
197
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
198 &gt;hg17_chr7_127475281_127475310_+ NM_000230
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
199 GTAGGAATCGCAGCGCCAGCGGTTGCAAG
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
200 &gt;hg17_chr7_127485994_127486166_+ NM_000230
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
201 GCCCAAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCG
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
202 GATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATC
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
203 CAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAG
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
204 GATCAATGACATTTCACACACG
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
205 &gt;hg17_chr7_127486011_127486166_+ D49487
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
206 TGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGG
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
207 CCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGA
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
208 CACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCAC
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
209 ACACG
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
210
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
211 Extracting sequences with **Interval** output data type returns::
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
212
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
213 chr7 127475281 127475310 NM_000230 0 + GTAGGAATCGCAGCGCCAGCGGTTGCAAG
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
214 chr7 127485994 127486166 NM_000230 0 + GCCCAAGAAGCCCATCCTGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCACACACG
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
215 chr7 127486011 127486166 D49487 0 + TGGGAAGGAAAATGCATTGGGGAACCCTGTGCGGATTCTTGTGGCTTTGGCCCTATCTTTTCTATGTCCAAGCTGTGCCCATCCAAAAAGTCCAAGATGACACCAAAACCCTCATCAAGACAATTGTCACCAGGATCAATGACATTTCACACACG
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
216
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
217 </help>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
218 <citations>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
219 <citation type="bibtex">
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
220 @unpublished{None,
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
221 author = {Guru Ananda,Greg Von Kuster},
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
222 title = {None},
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
223 year = {None},
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
224 eprint = {None},
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
225 url = {http://www.bx.psu.edu/~anton/labSite/}
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
226 }</citation>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
227 </citations>
8dd8e89c0603 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
parents:
diff changeset
228 </tool>