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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
author devteam
date Fri, 06 Nov 2015 14:17:24 -0500
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8082f04de7ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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1 <tool id="hisat_index_builder_data_manager" name="HISAT index" tool_type="manage_data" version="1.0.0">
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2 <description>builder</description>
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3 <requirements>
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4 <requirement type="package" version="0.1.6">hisat</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range=":-1" />
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8 <exit_code range="1:" />
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9 </stdio>
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10 <command interpreter="python">hisat_index_builder.py "${out_file}" --fasta_filename "${all_fasta_source.fields.path}" --fasta_dbkey "${all_fasta_source.fields.dbkey}" --fasta_description "${all_fasta_source.fields.name}" --data_table_name "hisat_indexes"</command>
8082f04de7ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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11 <inputs>
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12 <param label="Source FASTA Sequence" name="all_fasta_source" type="select">
8082f04de7ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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13 <options from_data_table="all_fasta" />
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14 </param>
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15 <param label="Name of sequence" name="sequence_name" type="text" value="" />
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16 <param label="ID for sequence" name="sequence_id" type="text" value="" />
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17 </inputs>
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18 <outputs>
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19 <data format="data_manager_json" name="out_file" />
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20 </outputs>
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21 <help>
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22 <![CDATA[
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23 .. class:: infomark
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24
8082f04de7ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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25 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
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26
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27 What is HISAT?
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28 --------------
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29
8082f04de7ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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30 `HISAT <http://ccb.jhu.edu/software/hisat>`__ is a fast and sensitive
8082f04de7ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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31 spliced alignment program. As part of HISAT, we have developed a new
8082f04de7ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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32 indexing scheme based on the Burrows-Wheeler transform
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33 (`BWT <http://en.wikipedia.org/wiki/Burrows-Wheeler_transform>`__) and
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34 the `FM index <http://en.wikipedia.org/wiki/FM-index>`__, called
8082f04de7ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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35 hierarchical indexing, that employs two types of indexes: (1) one global
8082f04de7ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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36 FM index representing the whole genome, and (2) many separate local FM
8082f04de7ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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37 indexes for small regions collectively covering the genome. Our
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38 hierarchical index for the human genome (about 3 billion bp) includes
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39 ~48,000 local FM indexes, each representing a genomic region of
8082f04de7ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat_index_builder commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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40 ~64,000bp. As the basis for non-gapped alignment, the FM index is
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41 extremely fast with a low memory footprint, as demonstrated by
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42 `Bowtie <http://bowtie-bio.sf.net>`__. In addition, HISAT provides
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43 several alignment strategies specifically designed for mapping different
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44 types of RNA-seq reads. All these together, HISAT enables extremely fast
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45 and sensitive alignment of reads, in particular those spanning two exons
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46 or more. As a result, HISAT is much faster >50 times than
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47 `TopHat2 <http://ccb.jhu.edu/software/tophat>`__ with better alignment
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48 quality. Although it uses a large number of indexes, the memory
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49 requirement of HISAT is still modest, approximately 4.3 GB for human.
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50 HISAT uses the `Bowtie2 <http://bowtie-bio.sf.net/bowtie2>`__
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51 implementation to handle most of the operations on the FM index. In
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52 addition to spliced alignment, HISAT handles reads involving indels and
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53 supports a paired-end alignment mode. Multiple processors can be used
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54 simultaneously to achieve greater alignment speed. HISAT outputs
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55 alignments in `SAM <http://samtools.sourceforge.net/SAM1.pdf>`__ format,
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56 enabling interoperation with a large number of other tools (e.g.
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57 `SAMtools <http://samtools.sourceforge.net>`__,
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58 `GATK <http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit>`__)
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59 that use SAM. HISAT is distributed under the `GPLv3
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60 license <http://www.gnu.org/licenses/gpl-3.0.html>`__, and it runs on
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61 the command line under Linux, Mac OS X and Windows.
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62 ]]>
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63 </help>
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64 <citations>
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65 <citation type="doi">10.1038/nmeth.3317</citation>
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66 </citations>
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67 </tool>