Mercurial > repos > matthias > data_manager_megan_tools

annotate data_manager/megan_tools_fetcher.xml @ 5:ba3aab283a68 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit c529846e9c5cf125d11dd8d4f843cfadf7da3cec-dirty
author matthias
date Thu, 01 Nov 2018 15:46:01 -0400
parents 24c02af5fd77
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
1 <?xml version="1.0"?>
5
ba3aab283a68 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit c529846e9c5cf125d11dd8d4f843cfadf7da3cec-dirty
matthias
parents: 2
diff changeset
2 <tool id="megan_tools_fetcher" name="megan tools" tool_type="manage_data" version="0.0.3">
0
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
3 <description>Mapping files downloader</description>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
4 <command detect_errors="exit_code">
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
5 <![CDATA[
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
6 python '$__tool_directory__/data_manager.py'
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
7 --out '${out_file}'
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
8 --file '$type_cond.database_name'
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
9 ]]>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
10 </command>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
11 <inputs>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
12 <conditional name="type_cond">
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
13 <param name="type_select" type="select" label="mapping type">
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
14 <option value="ncbi_current">Mapping files for current NCBI-nr protein database (not containing GI numbers)</option>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
15 <option value="silva">Mapping file for working with the SILVA SSU database</option>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
16 <option value="ncbi_deprecated">Deprecated mapping files for NCBI-nr protein database (releases until August 2016, containing GI numbers):</option>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
17 </param>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
18 <when value="ncbi_current">
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
19 <param name="database_name" type="select" label="mapping data">
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
20 <option value="prot_acc2tax-June2018X1.abin.zip">Protein accession to NCBI-taxonomy (June2018X1)</option>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
21 <option value="nucl_acc2tax-June2018.abin.zip">Nucleotide accession to NCBI-taxonomy (June2018)</option>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
22 <option value="acc2interpro-June2018X.abin.zip">Protein accession to InterPro (June2018X)</option>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
23 <option value="acc2eggnog-Oct2016X.abin.zip">Protein accession to eggNOG (Oct2016X)</option>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
24 <option value="acc2seed-May2015XX.abin.zip">Protein accession to SEED (May2015XX)</option>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
25 <option value="acc2kegg-Dec2017X1-ue.abin.zip">Protein accession to KEGG (Dec2017X1). Only for use with the Ultimate Edition of MEGAN.</option>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
26 </param>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
27 </when>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
28 <when value="silva">
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
29 <param name="database_name" type="select" label="mapping data">
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
30 <option value="SSURef_Nr99_132_tax_silva_to_NCBI_synonyms.map.gz">SSURef_Nr99_132_tax_silva_to_NCBI_synonyms.map.gz</option>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
31 <option value="SSURef_NR99_128_tax_silva_to_NCBI_synonyms.map.gz">SSURef_NR99_128_tax_silva_to_NCBI_synonyms.map.gz</option>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
32 </param>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
33 </when>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
34 <when value="ncbi_deprecated">
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
35 <param name="database_name" type="select" label="mapping data">
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
36 <option value="prot_gi2tax-Aug2016X.bin.zip">Protein accession to NCBI-taxonomy (Aug2016X)</option>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
37 <option value="nucl_gi2tax-Aug2016.bin.zip">Nucleotide accession to NCBI-taxonomy (Aug2016)</option>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
38 <option value="gi2eggnog-June2016X.bin.zip">Protein accession to InterPro (June2016X)</option>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
39 <option value="gi2interpro-June2016X.bin.zip">Protein accession to eggNOG (June2016X)</option>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
40 <option value="gi2seed-May2015X.bin.zip">Protein accession to SEED (May2015X)</option>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
41 <option value="gi2kegg-Aug2016X-ue.bin.zip">Protein accession to KEGG (Aug2016X). Only for use with the Ultimate Edition of MEGAN.</option>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
42 </param>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
43 </when>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
44 </conditional>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
45 </inputs>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
46 <outputs>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
47 <data name="out_file" format="data_manager_json" />
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
48 </outputs>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
49 <tests>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
50 <test>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
51 <conditional name="type_cond">
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
52 <param name="type_select" value="silva"/>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
53 <param name="database_name" value="SSURef_Nr99_132_tax_silva_to_NCBI_synonyms.map.gz"/>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
54 </conditional>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
55 <output name="out_file" file="SSURef_Nr99_132_tax_silva_to_NCBI_synonyms_json"/>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
56 </test>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
57 </tests>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
58 <help>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
59 TODO
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
60 </help>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
61 </tool>
1f839ba466da planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_megan_tools commit d7a7a198e8f8c9b95491f1520d478e7400a1f59c-dirty
matthias
parents:
diff changeset
62