Mercurial > repos > devteam > data_manager_build_kraken_database

annotate data_manager/kraken_database_builder.xml @ 6:4e6e90f31ffe draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 942704250204d57911949c0129f4a984dc0dc551
author iuc
date Tue, 17 Jul 2018 09:46:10 -0400
parents 6f0294046f41
children 5b0724200665
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d5d803e654dd Uploaded
devteam
parents:
diff changeset
1 <?xml version="1.0"?>
6
4e6e90f31ffe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 942704250204d57911949c0129f4a984dc0dc551
iuc
parents: 5
diff changeset
2 <tool id="kraken_database_builder" name="Kraken" tool_type="manage_data" version="1.1">
0
d5d803e654dd Uploaded
devteam
parents:
diff changeset
3 <description>database builder</description>
d5d803e654dd Uploaded
devteam
parents:
diff changeset
4 <requirements>
6
4e6e90f31ffe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 942704250204d57911949c0129f4a984dc0dc551
iuc
parents: 5
diff changeset
5 <requirement type="package" version="1.1">kraken</requirement>
0
d5d803e654dd Uploaded
devteam
parents:
diff changeset
6 </requirements>
d5d803e654dd Uploaded
devteam
parents:
diff changeset
7 <version_command>kraken -version | awk '{print $NF}'</version_command>
5
6f0294046f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 4
diff changeset
8 <command detect_errors="exit_code">
0
d5d803e654dd Uploaded
devteam
parents:
diff changeset
9 <![CDATA[
d5d803e654dd Uploaded
devteam
parents:
diff changeset
10 #set $library_list = str($libraries).split(',')
d5d803e654dd Uploaded
devteam
parents:
diff changeset
11 mkdir kraken-database && cd kraken-database &&
5
6f0294046f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 4
diff changeset
12 kraken-build --threads \${GALAXY_SLOTS:-1} --download-taxonomy --db '${database_name}' &&
0
d5d803e654dd Uploaded
devteam
parents:
diff changeset
13 #for $library in $library_list:
2
cdef63d8a141 Uploaded
devteam
parents: 1
diff changeset
14 #if str($library) != 'None':
5
6f0294046f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 4
diff changeset
15 kraken-build --threads \${GALAXY_SLOTS:-1} --download-library $library --db '${database_name}' &&
2
cdef63d8a141 Uploaded
devteam
parents: 1
diff changeset
16 #end if
0
d5d803e654dd Uploaded
devteam
parents:
diff changeset
17 #end for
d5d803e654dd Uploaded
devteam
parents:
diff changeset
18 #for $fasta in $input_fasta:
3
404ba485ec01 Uploaded
devteam
parents: 2
diff changeset
19 #if str($fasta) != 'None':
5
6f0294046f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 4
diff changeset
20 kraken-build --threads \${GALAXY_SLOTS:-1} --db '${database_name}' --add-to-library '$fasta' &&
3
404ba485ec01 Uploaded
devteam
parents: 2
diff changeset
21 #end if
0
d5d803e654dd Uploaded
devteam
parents:
diff changeset
22 #end for
5
6f0294046f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 4
diff changeset
23 kraken-build --threads \${GALAXY_SLOTS:-1} --db '${database_name}' --build --kmer-len ${kmer_len} --minimizer-len ${minimizer_len} &&
6f0294046f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 4
diff changeset
24 cd .. &&
6f0294046f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 4
diff changeset
25 python '$__tool_directory__/make_json.py' --db '${database_name}' --out '${out_file}'
0
d5d803e654dd Uploaded
devteam
parents:
diff changeset
26 ]]>
d5d803e654dd Uploaded
devteam
parents:
diff changeset
27 </command>
d5d803e654dd Uploaded
devteam
parents:
diff changeset
28 <inputs>
5
6f0294046f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 4
diff changeset
29 <param name="database_name" type="text" label="Name for this database" />
6f0294046f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 4
diff changeset
30 <param name="libraries" type="select" multiple="true" label="Select partial library to download">
0
d5d803e654dd Uploaded
devteam
parents:
diff changeset
31 <option value="bacteria">Bacteria</option>
d5d803e654dd Uploaded
devteam
parents:
diff changeset
32 <option value="plasmids">Plasmids</option>
d5d803e654dd Uploaded
devteam
parents:
diff changeset
33 <option value="viruses">Viruses</option>
d5d803e654dd Uploaded
devteam
parents:
diff changeset
34 <option value="human">Human</option>
d5d803e654dd Uploaded
devteam
parents:
diff changeset
35 </param>
5
6f0294046f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 4
diff changeset
36 <param name="input_fasta" type="data" format="fasta" multiple="True" optional="true" label="Select history item" />
6f0294046f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 4
diff changeset
37 <param name="kmer_len" type="integer" value="31" label="K-mer length in BP" />
6f0294046f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 4
diff changeset
38 <param name="minimizer_len" type="integer" value="15" label="Minimizer length" />
0
d5d803e654dd Uploaded
devteam
parents:
diff changeset
39 </inputs>
d5d803e654dd Uploaded
devteam
parents:
diff changeset
40 <outputs>
5
6f0294046f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 4
diff changeset
41 <data name="out_file" format="data_manager_json" />
0
d5d803e654dd Uploaded
devteam
parents:
diff changeset
42 </outputs>
5
6f0294046f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 4
diff changeset
43 <help>
6f0294046f41 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 4
diff changeset
44 </help>
0
d5d803e654dd Uploaded
devteam
parents:
diff changeset
45 <citations>
d5d803e654dd Uploaded
devteam
parents:
diff changeset
46 <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
d5d803e654dd Uploaded
devteam
parents:
diff changeset
47 </citations>
3
404ba485ec01 Uploaded
devteam
parents: 2
diff changeset
48 </tool>