Mercurial > repos > devteam > kraken
annotate kraken.xml @ 6:2fdac3e78553 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
author | iuc |
---|---|
date | Mon, 07 Aug 2017 17:29:06 -0400 |
parents | b2392a9dfb01 |
children | 658d47fd33e3 |
rev | line source |
---|---|
0
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
1 <?xml version="1.0"?> |
6
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
2 <tool id="kraken" name="Kraken" version="@WRAPPER_VERSION@"> |
0
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
3 <description> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
4 assign taxonomic labels to sequencing reads |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
5 </description> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
6 <macros> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
7 <import>macros.xml</import> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
8 </macros> |
3
7c41dbaa9875
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 0d8d0e2d94ac0cb08a56d020af26ffcbc33d250d
devteam
parents:
2
diff
changeset
|
9 <expand macro="requirements" /> |
7c41dbaa9875
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 0d8d0e2d94ac0cb08a56d020af26ffcbc33d250d
devteam
parents:
2
diff
changeset
|
10 <expand macro="version_command" /> |
6
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
11 <command detect_errors="exit_code"> |
0
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
12 <![CDATA[ |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
13 @SET_DATABASE_PATH@ && |
6
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
14 |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
15 kraken |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
16 --threads \${GALAXY_SLOTS:-1} |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
17 @INPUT_DATABASE@ |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
18 ${only_classified_output} |
0
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
19 |
6
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
20 #if str( $quick_operation.quick ) == "yes": |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
21 --quick |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
22 --min-hits ${quick_operation.min_hits} |
0
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
23 |
6
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
24 #end if |
0
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
25 |
6
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
26 #if $single_paired.single_paired_selector == 'yes' |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
27 #if $forward_input.is_of_type( 'fastq' ): |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
28 --fastq-input |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
29 #else: |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
30 --fasta-input |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
31 #end if |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
32 '${single_paired.forward_input}' '${single_paired.reverse_input}' |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
33 ${single_paired.check_names} |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
34 #elif $single_paired.single_paired_selector == "collection": |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
35 #if $single_paired.input_pair.forward.is_of_type( 'fastq' ): |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
36 --fastq-input |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
37 #else: |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
38 --fasta-input |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
39 #end if |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
40 "${single_paired.input_pair.forward}" "${single_paired.input_pair.reverse}" |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
41 ${single_paired.check_names} |
2
642f30185af2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
1
diff
changeset
|
42 #else: |
6
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
43 #if $single_paired.input_sequences.is_of_type('fastq') |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
44 --fastq-input |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
45 #else: |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
46 --fasta-input |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
47 #end if |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
48 '${single_paired.input_sequences}' |
1
7b3ef9b4af80
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 8fdf574819623961b1595461e906dd5a34e01add
devteam
parents:
0
diff
changeset
|
49 #end if |
0
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
50 |
6
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
51 #if $split_reads: |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
52 --classified-out "${classified_out}" --unclassified-out "${unclassified_out}" |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
53 #end if |
3
7c41dbaa9875
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 0d8d0e2d94ac0cb08a56d020af26ffcbc33d250d
devteam
parents:
2
diff
changeset
|
54 |
6
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
55 ## The --output option was changed to redirect as it does not work properly is some situations. For example, on test database the tool classifies 4 reads but does not write them into a file if --output is specified. It does however print correct output into STDOUT. This behavior can be re-created with test database provided in test-data/test_db/ folder. This is the reason for incrementing version number from 1.1.2 to 1.1.3 |
3
7c41dbaa9875
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 0d8d0e2d94ac0cb08a56d020af26ffcbc33d250d
devteam
parents:
2
diff
changeset
|
56 |
6
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
57 > "${output}" |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
58 ##kraken-translate --db ${kraken_database.fields.name} "${output}" > "${translated}" |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
59 ]]></command> |
0
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
60 <inputs> |
1
7b3ef9b4af80
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 8fdf574819623961b1595461e906dd5a34e01add
devteam
parents:
0
diff
changeset
|
61 <conditional name="single_paired"> |
2
642f30185af2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
1
diff
changeset
|
62 <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired"> |
642f30185af2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
1
diff
changeset
|
63 <option value="collection">Collection</option> |
3
7c41dbaa9875
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 0d8d0e2d94ac0cb08a56d020af26ffcbc33d250d
devteam
parents:
2
diff
changeset
|
64 <option value="yes">Paired</option> |
7c41dbaa9875
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 0d8d0e2d94ac0cb08a56d020af26ffcbc33d250d
devteam
parents:
2
diff
changeset
|
65 <option selected="True" value="no">Single</option> |
1
7b3ef9b4af80
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 8fdf574819623961b1595461e906dd5a34e01add
devteam
parents:
0
diff
changeset
|
66 </param> |
2
642f30185af2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
1
diff
changeset
|
67 <when value="collection"> |
6
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
68 <param format="fasta,fastq" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTA or FASTQ datasets" /> |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
69 <param name="check_names" argument="--check-names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match"/> |
2
642f30185af2
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
1
diff
changeset
|
70 </when> |
1
7b3ef9b4af80
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 8fdf574819623961b1595461e906dd5a34e01add
devteam
parents:
0
diff
changeset
|
71 <when value="yes"> |
6
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
72 <param format="fasta,fastq" name="forward_input" type="data" label="Forward strand" help="FASTA or FASTQ dataset"/> |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
73 <param format="fasta,fastq" name="reverse_input" type="data" label="Reverse strand" help="FASTA or FASTQ dataset"/> |
1
7b3ef9b4af80
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 8fdf574819623961b1595461e906dd5a34e01add
devteam
parents:
0
diff
changeset
|
74 <param name="check_names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match" help="--check-names" /> |
7b3ef9b4af80
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 8fdf574819623961b1595461e906dd5a34e01add
devteam
parents:
0
diff
changeset
|
75 </when> |
7b3ef9b4af80
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 8fdf574819623961b1595461e906dd5a34e01add
devteam
parents:
0
diff
changeset
|
76 <when value="no"> |
7b3ef9b4af80
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 8fdf574819623961b1595461e906dd5a34e01add
devteam
parents:
0
diff
changeset
|
77 <param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/> |
7b3ef9b4af80
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 8fdf574819623961b1595461e906dd5a34e01add
devteam
parents:
0
diff
changeset
|
78 </when> |
7b3ef9b4af80
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 8fdf574819623961b1595461e906dd5a34e01add
devteam
parents:
0
diff
changeset
|
79 |
7b3ef9b4af80
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 8fdf574819623961b1595461e906dd5a34e01add
devteam
parents:
0
diff
changeset
|
80 </conditional> |
6
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
81 <param name="split_reads" type="boolean" label="Output classified and unclassified reads?" help="Sets --unclassified-out and --classified-out"/> |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
82 |
0
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
83 <conditional name="quick_operation"> |
6
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
84 <param argument="--quick" type="select" label="Enable quick operation" |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
85 help="Quick mode: rather than searching all k-mers in a sequence, stop classification after a specified number of database hit"> |
0
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
86 <option value="yes">Yes</option> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
87 <option selected="True" value="no">No</option> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
88 </param> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
89 <when value="yes"> |
6
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
90 <param name="min_hits" argument="--min-hits" type="integer" value="1" label="Number of hits required for classification" |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
91 help="min-hits will allow you to require multiple hits before declaring a sequence classified, which can be especially useful with custom databases when testing to see if sequences either do or do not belong to a particular genome; default=1"/> |
0
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
92 </when> |
6
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
93 <when value="no"/><!-- Do absolutely nothing --> |
0
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
94 </conditional> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
95 |
6
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
96 <param name="only_classified_output" argument="--only-classified-output" type="boolean" checked="False" truevalue="--only-classified-output" falsevalue="" |
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
97 label="Print no Kraken output for unclassified sequences"/> |
0
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
98 |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
99 <expand macro="input_database" /> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
100 </inputs> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
101 <outputs> |
6
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
102 <data name="classified_out" format_source="input_sequences" label="${tool.name} on ${on_string}: Classified reads"> |
0
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
103 <filter>(split_reads)</filter> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
104 </data> |
6
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
105 <data name="unclassified_out" format_source="input_sequences" label="${tool.name} on ${on_string}: Unclassified reads"> |
0
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
106 <filter>(split_reads)</filter> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
107 </data> |
6
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
108 <data name="output" format="tabular" label="${tool.name} on ${on_string}: Classification"/> |
0
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
109 <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />--> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
110 </outputs> |
3
7c41dbaa9875
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 0d8d0e2d94ac0cb08a56d020af26ffcbc33d250d
devteam
parents:
2
diff
changeset
|
111 |
7c41dbaa9875
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 0d8d0e2d94ac0cb08a56d020af26ffcbc33d250d
devteam
parents:
2
diff
changeset
|
112 <tests> |
7c41dbaa9875
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 0d8d0e2d94ac0cb08a56d020af26ffcbc33d250d
devteam
parents:
2
diff
changeset
|
113 <test> |
7c41dbaa9875
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 0d8d0e2d94ac0cb08a56d020af26ffcbc33d250d
devteam
parents:
2
diff
changeset
|
114 <param name="single_paired_selector" value="no"/> |
7c41dbaa9875
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 0d8d0e2d94ac0cb08a56d020af26ffcbc33d250d
devteam
parents:
2
diff
changeset
|
115 <param name="input_sequences" value="kraken_test1.fa" ftype="fasta"/> |
7c41dbaa9875
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 0d8d0e2d94ac0cb08a56d020af26ffcbc33d250d
devteam
parents:
2
diff
changeset
|
116 <param name="split_reads" value="false"/> |
7c41dbaa9875
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 0d8d0e2d94ac0cb08a56d020af26ffcbc33d250d
devteam
parents:
2
diff
changeset
|
117 <param name="quick" value="no"/> |
7c41dbaa9875
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 0d8d0e2d94ac0cb08a56d020af26ffcbc33d250d
devteam
parents:
2
diff
changeset
|
118 <param name="only-classified-output" value="false"/> |
7c41dbaa9875
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 0d8d0e2d94ac0cb08a56d020af26ffcbc33d250d
devteam
parents:
2
diff
changeset
|
119 <param name="kraken_database" value="test_db"/> |
6
2fdac3e78553
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
iuc
parents:
5
diff
changeset
|
120 |
3
7c41dbaa9875
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 0d8d0e2d94ac0cb08a56d020af26ffcbc33d250d
devteam
parents:
2
diff
changeset
|
121 <output name="output" file="kraken_test1_output.tab" ftype="tabular"/> |
7c41dbaa9875
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 0d8d0e2d94ac0cb08a56d020af26ffcbc33d250d
devteam
parents:
2
diff
changeset
|
122 </test> |
7c41dbaa9875
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 0d8d0e2d94ac0cb08a56d020af26ffcbc33d250d
devteam
parents:
2
diff
changeset
|
123 </tests> |
0
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
124 <help> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
125 <![CDATA[ |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
126 **What it does** |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
127 |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
128 Kraken is a taxonomic sequence classifier that assigns taxonomic labels to short DNA reads. It does this by examining the k-mers within a read and querying a database with those k-mers. This database contains a mapping of every k-mer in Kraken's genomic library to the lowest common ancestor (LCA) in a taxonomic tree of all genomes that contain that k-mer. The set of LCA taxa that correspond to the k-mers in a read are then analyzed to create a single taxonomic label for the read; this label can be any of the nodes in the taxonomic tree. Kraken is designed to be rapid, sensitive, and highly precise. |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
129 |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
130 ----- |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
131 |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
132 **Output Format** |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
133 |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
134 Each sequence classified by Kraken results in a single line of output. Output lines contain five tab-delimited fields; from left to right, they are:: |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
135 |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
136 1. "C"/"U": one letter code indicating that the sequence was either classified or unclassified. |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
137 2. The sequence ID, obtained from the FASTA/FASTQ header. |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
138 3. The taxonomy ID Kraken used to label the sequence; this is 0 if the sequence is unclassified. |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
139 4. The length of the sequence in bp. |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
140 5. A space-delimited list indicating the LCA mapping of each k-mer in the sequence. For example, "562:13 561:4 A:31 0:1 562:3" would indicate that: |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
141 a) the first 13 k-mers mapped to taxonomy ID #562 |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
142 b) the next 4 k-mers mapped to taxonomy ID #561 |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
143 c) the next 31 k-mers contained an ambiguous nucleotide |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
144 d) the next k-mer was not in the database |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
145 e) the last 3 k-mers mapped to taxonomy ID #562 |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
146 ]]> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
147 </help> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
148 <expand macro="citations" /> |
0f17a8816b28
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
diff
changeset
|
149 </tool> |