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comparison data_manager/kallisto_index_builder.xml @ 0:6843a0db2da0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author iuc
date Sat, 05 Aug 2017 04:02:01 -0400
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1 <tool id="kallisto_index_builder_data_manager" name="Kallisto" tool_type="manage_data" version="0.43.1">
2 <description>index builder</description>
3 <requirements>
4 <requirement type="package" version="0.43.1">kallisto</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 python '$__tool_directory__/kallisto_index_builder.py' --output '${out_file}'
8 --fasta_filename '${all_fasta_source.fields.path}'
9 --fasta_dbkey '${all_fasta_source.fields.dbkey}'
10 --fasta_description '${all_fasta_source.fields.name}'
11 --data_table_name kallisto_indexes
12 ]]>
13 </command>
14 <inputs>
15 <param label="Source FASTA Sequence" name="all_fasta_source" type="select">
16 <options from_data_table="all_fasta" />
17 </param>
18 <param name="sequence_name" type="text" value="" label="Name of sequence" />
19 <param name="sequence_id" type="text" value="" label="ID for sequence" />
20 </inputs>
21 <outputs>
22 <data name="out_file" format="data_manager_json" />
23 </outputs>
24 <help>
25 <![CDATA[
26 .. class:: infomark
27
28 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
29
30 What is Kallisto?
31 ---------------
32
33 `kallisto <https://pachterlab.github.io/kallisto/about>`__ is a program for
34 quantifying abundances of transcripts from RNA-Seq data, or more generally of
35 target sequences using high-throughput sequencing reads. It is based on the
36 novel idea of pseudoalignment for rapidly determining the compatibility of
37 reads with targets, without the need for alignment. On benchmarks with standard
38 RNA-Seq data, kallisto can quantify 30 million human reads in less than 3
39 minutes on a Mac desktop computer using only the read sequences and a
40 transcriptome index that itself takes less than 10 minutes to build.
41 Pseudoalignment of reads preserves the key information needed for
42 quantification, and kallisto is therefore not only fast, but also as accurate
43 as existing quantification tools. In fact, because the pseudoalignment
44 procedure is robust to errors in the reads, in many benchmarks kallisto
45 significantly outperforms existing tools.
46 ]]>
47 </help>
48 <citations>
49 <citation type="doi">10.1038/nmeth.3317</citation>
50 </citations>
51 </tool>