Mercurial > repos > iuc > data_manager_salmon_index_builder
annotate data_manager/salmon_index_builder.xml @ 0:7d4fd734b078 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
author | iuc |
---|---|
date | Wed, 24 Jul 2019 07:17:00 -0400 |
parents | |
children | 6b0f2bdcc1b7 |
rev | line source |
---|---|
0
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
1 <tool id="salmon_index_builder_data_manager" name="Salmon" tool_type="manage_data" version="0.11.3" profile_version="19.01"> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
2 <description>index builder</description> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
3 <requirements> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
4 <requirement type="package" version="0.11.3">salmon</requirement> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
5 <requirement type="package" version="3.7">python</requirement> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
6 </requirements> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
7 <macros> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
8 <token name="@IDX_VERSION@">q5</token> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
9 </macros> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
10 <command detect_errors="exit_code"><![CDATA[ |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
11 python '$__tool_directory__/salmon_index_builder.py' --output '${out_file}' |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
12 --fasta_filename '${all_fasta_source.fields.path}' |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
13 --fasta_dbkey '${all_fasta_source.fields.dbkey}' |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
14 --fasta_description '${all_fasta_source.fields.name}' |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
15 --kmer_size "${kmer_size}" |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
16 --data_table_name salmon_indexes_versioned |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
17 --index_version @IDX_VERSION@ |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
18 ]]> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
19 </command> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
20 <inputs> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
21 <param label="Source FASTA Sequence" name="all_fasta_source" type="select"> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
22 <options from_data_table="all_fasta" /> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
23 </param> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
24 <param name="sequence_name" type="text" value="" label="Name of sequence" /> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
25 <param name="sequence_id" type="text" value="" label="ID for sequence" /> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
26 <param name="kmer_size" type="integer" optional='true' value="21" max="32" label="The size of the k-mer on which the index is built" |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
27 help="There is a tradeoff here between the distinctiveness of the k-mers and their robustness to errors. The shorter the k-mers, the more robust they will be to errors in the reads, but the longer the k-mers, the more distinct they will be. We generally recommend using a k-mer size of at least 20. MUST BE AN ODD VALUE "/> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
28 </inputs> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
29 <outputs> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
30 <data name="out_file" format="data_manager_json" /> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
31 </outputs> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
32 <tests> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
33 <test> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
34 <param name="all_fasta_source" value="phiX174"/> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
35 <param name="sequence_name" value="sequence_name"/> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
36 <param name="sequence_id" value="sequence_id"/> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
37 <output name="out_file" file="salmon_phiX174.data_manager_json"/> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
38 </test> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
39 </tests> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
40 <help> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
41 <![CDATA[ |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
42 .. class:: infomark |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
43 |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
44 **Notice:** If you leave name, description, or id blank, it will be generated automatically. |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
45 ]]> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
46 </help> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
47 <citations> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
48 <citation type="doi">https://doi.org/10.1038/nmeth.4197</citation> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
49 </citations> |
7d4fd734b078
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff
changeset
|
50 </tool> |