Mercurial > repos > iuc > data_manager_salmon_index_builder
comparison 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 |
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date | Wed, 24 Jul 2019 07:17:00 -0400 |
parents | |
children | 6b0f2bdcc1b7 |
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1 <tool id="salmon_index_builder_data_manager" name="Salmon" tool_type="manage_data" version="0.11.3" profile_version="19.01"> | |
2 <description>index builder</description> | |
3 <requirements> | |
4 <requirement type="package" version="0.11.3">salmon</requirement> | |
5 <requirement type="package" version="3.7">python</requirement> | |
6 </requirements> | |
7 <macros> | |
8 <token name="@IDX_VERSION@">q5</token> | |
9 </macros> | |
10 <command detect_errors="exit_code"><![CDATA[ | |
11 python '$__tool_directory__/salmon_index_builder.py' --output '${out_file}' | |
12 --fasta_filename '${all_fasta_source.fields.path}' | |
13 --fasta_dbkey '${all_fasta_source.fields.dbkey}' | |
14 --fasta_description '${all_fasta_source.fields.name}' | |
15 --kmer_size "${kmer_size}" | |
16 --data_table_name salmon_indexes_versioned | |
17 --index_version @IDX_VERSION@ | |
18 ]]> | |
19 </command> | |
20 <inputs> | |
21 <param label="Source FASTA Sequence" name="all_fasta_source" type="select"> | |
22 <options from_data_table="all_fasta" /> | |
23 </param> | |
24 <param name="sequence_name" type="text" value="" label="Name of sequence" /> | |
25 <param name="sequence_id" type="text" value="" label="ID for sequence" /> | |
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" | |
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 "/> | |
28 </inputs> | |
29 <outputs> | |
30 <data name="out_file" format="data_manager_json" /> | |
31 </outputs> | |
32 <tests> | |
33 <test> | |
34 <param name="all_fasta_source" value="phiX174"/> | |
35 <param name="sequence_name" value="sequence_name"/> | |
36 <param name="sequence_id" value="sequence_id"/> | |
37 <output name="out_file" file="salmon_phiX174.data_manager_json"/> | |
38 </test> | |
39 </tests> | |
40 <help> | |
41 <![CDATA[ | |
42 .. class:: infomark | |
43 | |
44 **Notice:** If you leave name, description, or id blank, it will be generated automatically. | |
45 ]]> | |
46 </help> | |
47 <citations> | |
48 <citation type="doi">https://doi.org/10.1038/nmeth.4197</citation> | |
49 </citations> | |
50 </tool> |