Mercurial > repos > dfornika > mentalist

annotate data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml @ 1:c6a98b93e569 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 83ebe793451a5ccbfeff873eda359f699e14ae1e
author dfornika
date Sat, 24 Mar 2018 23:12:21 -0400
parents 1d9e3950ce61
children 4ea71c8e2db0
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
1 <?xml version="1.0"?>
1
c6a98b93e569 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 83ebe793451a5ccbfeff873eda359f699e14ae1e
dfornika
parents: 0
diff changeset
2 <tool id="mentalist_build_db" name="MentaLiST Build DB" tool_type="manage_data" version="0.2.2">
0
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
3 <requirements>
1
c6a98b93e569 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 83ebe793451a5ccbfeff873eda359f699e14ae1e
dfornika
parents: 0
diff changeset
4 <requirement type="package" version="0.2.2">mentalist</requirement>
0
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
5 </requirements>
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
6 <command detect_errors="exit_code">
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
7 <![CDATA[
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
8 python '$__tool_directory__/mentalist_build_db.py'
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
9 '${out_file}'
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
10 --db '$database_name'
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
11 -k '$kmer_size'
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
12 #if $profile
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
13 --profile '$profile'
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
14 #end if
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
15 --fasta_files ${" ".join(map(str, $input_fastas))}
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
16 ]]>
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
17 </command>
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
18 <inputs>
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
19 <param name="database_name" type="text"
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
20 label="Database Name" help="Database Name" />
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
21 <param name="kmer_size" type="integer"
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
22 label="Kmer size" help="Kmer size"
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
23 value="31" min="1" max="32" />
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
24 <param name="input_fastas" type="data_collection" collection_type="list" format="fasta" multiple="true"
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
25 label="Input Fasta" help="Fasta input files" />
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
26 <param name="profile" type="data" format="tsv" optional="true"
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
27 label="Profile" help="Profile for known genotypes" />
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
28 </inputs>
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
29 <outputs>
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
30 <data name="out_file" format="data_manager_json" />
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
31 </outputs>
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
32 <citations>
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
33 <citation type="doi">10.1101/172858</citation>
1
c6a98b93e569 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 83ebe793451a5ccbfeff873eda359f699e14ae1e
dfornika
parents: 0
diff changeset
34 <citation type="doi">10.1099/mgen.0.000146</citation>
0
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
35 </citations>
1d9e3950ce61 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
dfornika
parents:
diff changeset
36 </tool>