Mercurial > repos > iuc > data_manager_hisat2_index_builder
annotate data_manager/hisat2_index_builder.xml @ 5:8eac26f44d29 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
author | iuc |
---|---|
date | Mon, 18 Nov 2019 17:22:30 -0500 |
parents | d210e1f185bd |
children |
rev | line source |
---|---|
5
8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
4
diff
changeset
|
1 <tool id="hisat2_index_builder_data_manager" name="HISAT2 index" tool_type="manage_data" version="2.1.0" profile="19.05"> |
0
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
2 <description>builder</description> |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
3 <requirements> |
5
8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
4
diff
changeset
|
4 <requirement type="package" version="2.1.0">hisat2</requirement> |
0
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
5 </requirements> |
4
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
6 <command detect_errors="exit_code"><![CDATA[ |
2
4014cb2c17db
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 4a5952b2404c0821cf9895cb2a5036da62b14d6e-dirty
iuc
parents:
1
diff
changeset
|
7 #if $advanced.adv_param_select == 'yes' and $advanced.gtf_input: |
4
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
8 ln -s '${advanced.gtf_input}' gtf_file.gtf && |
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
9 hisat2_extract_splice_sites.py gtf_file.gtf > splice_sites.txt && |
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
10 hisat2_extract_exons.py gtf_file.gtf > exon.txt && |
0
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
11 #end if |
2
4014cb2c17db
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 4a5952b2404c0821cf9895cb2a5036da62b14d6e-dirty
iuc
parents:
1
diff
changeset
|
12 #if $advanced.adv_param_select == 'yes' and $advanced.snps: |
4
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
13 ln -s '${advanced.snps}' snps.tabular && |
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
14 #if $advanced.snps.is_of_type('vcf') |
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
15 hisat2_extract_snps_haplotypes_VCF.py '${all_fasta_source.fields.path}' snps.tabular extracted && |
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
16 #else |
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
17 hisat2_extract_snps_haplotypes_UCSC.py '${all_fasta_source.fields.path}' snps.tabular extracted && |
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
18 #end if |
0
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
19 #end if |
4
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
20 python '$__tool_directory__/hisat2_index_builder.py' --output '${out_file}' |
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
21 --fasta_filename '${all_fasta_source.fields.path}' |
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
22 --fasta_dbkey '${all_fasta_source.fields.dbkey}' |
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
23 --fasta_description '${all_fasta_source.fields.name}' |
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
24 --data_table_name hisat2_indexes |
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
25 --indexer_options "-p \${GALAXY_SLOTS:-1} |
0
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
26 #if $advanced.adv_param_select == 'yes': |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
27 --noauto |
4
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
28 #if $advanced.snps: |
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
29 --snps "`pwd`/extracted.snp" |
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
30 --haplotype "`pwd`/extracted.haplotype" |
0
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
31 #end if |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
32 #if $advanced.gtf_input: |
4
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
33 --ss "`pwd`/splice_sites.txt" |
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
34 --exon "`pwd`/exon.txt" |
0
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
35 #end if |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
36 --bmax $advanced.bmax |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
37 --bmaxdivn $advanced.bmaxdivn |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
38 --dcv $advanced.dcv |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
39 --offrate $advanced.offrate |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
40 #end if |
4
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
41 " |
0
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
42 ]]> |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
43 </command> |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
44 <inputs> |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
45 <param label="Source FASTA Sequence" name="all_fasta_source" type="select"> |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
46 <options from_data_table="all_fasta" /> |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
47 </param> |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
48 <conditional name="advanced" label="Advanced parameters"> |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
49 <param name="adv_param_select" type="select" label="Advanced parameters"> |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
50 <option value="no">Use defaults</option> |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
51 <option value="yes">Fine-tune indexing parameters</option> |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
52 </param> |
4
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
53 <when value="no" /> |
0
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
54 <when value="yes"> |
4
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
55 <param argument="--bmax" type="integer" value="4" label="Maximum number of suffixes allowed in a block" /> |
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
56 <param argument="--bmaxdivn" type="integer" value="4" label="Maximum number of suffixes allowed in a block, expressed as a fraction of the length of the reference" /> |
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
57 <param argument="--dcv" type="integer" min="2" max="4096" value="1024" label="Period for the difference-cover sample" help="A larger period yields less memory overhead, but may make suffix sorting slower, especially if repeats are present. Must be a power of 2 no greater than 4096" /> |
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
58 <param argument="--offrate" type="integer" value="4" label="Mark rows in the Burrows-Wheeler transform" help="To map alignments back to positions on the reference sequences, it's necessary to annotate ("mark") some or all of the Burrows-Wheeler rows with their corresponding location on the genome. This parameter governs how many rows get marked: the indexer will mark every 2^<int> rows. Marking more rows makes reference-position lookups faster, but requires more memory to hold the annotations at runtime. The default is 4 (every 16th row is marked; for human genome, annotations occupy about 680 megabytes)" /> |
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
59 <param name="snps" type="data" format="tabular,vcf" optional="true" label="Provide a list of SNPs in the UCSC dbSNP or VCF format" help="If you include SNPs or splice sites and exons, building an index on the human genome will consume up to 200GB RAM as index building involves a graph construction" /> |
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
60 <param name="gtf_input" type="data" format="gtf" optional="true" label="Provide a GTF file for HISAT2 to extract splice sites from" help="If you include SNPs or splice sites and exons, building an index on the human genome will consume up to 200GB RAM as index building involves a graph construction" /> |
0
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
61 </when> |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
62 </conditional> |
4
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
63 <param name="sequence_name" type="text" value="" label="Name of sequence" /> |
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
64 <param name="sequence_id" type="text" value="" label="ID for sequence" /> |
0
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
65 </inputs> |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
66 <outputs> |
4
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
2
diff
changeset
|
67 <data name="out_file" format="data_manager_json" /> |
0
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
68 </outputs> |
5
8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
4
diff
changeset
|
69 <tests> |
8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
4
diff
changeset
|
70 <test> |
8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
4
diff
changeset
|
71 <param name="all_fasta_source" value="phiX174"/> |
8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
4
diff
changeset
|
72 <output name="out_file" file="hisat2_data_manager.json"/> |
8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
4
diff
changeset
|
73 </test> |
8eac26f44d29
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 05c191c21eba39e75a8c8d6e6a00d8db63552695"
iuc
parents:
4
diff
changeset
|
74 </tests> |
0
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
75 <help> |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
76 <![CDATA[ |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
77 .. class:: infomark |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
78 |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
79 **Notice:** If you leave name, description, or id blank, it will be generated automatically. |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
80 |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
81 What is HISAT2? |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
82 --------------- |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
83 |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
84 `HISAT <http://ccb.jhu.edu/software/hisat>`__ is a fast and sensitive alignment |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
85 program for mapping next-generation sequencing reads (both DNA and RNA) against |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
86 the general human population (as well as against a single reference genome). |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
87 Based on an extension of BWT for graphs (`BWT <http://dl.acm.org/citation.cfm?id=2674828>`__) |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
88 we designed and implemented a graph FM index (GFM), an original approach and |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
89 its first implementation to the best of our knowledge. In addition to using one |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
90 global GFM index that represents the general population, HISAT2 uses a large set |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
91 of small GFM indexes that collectively cover the whole genome (each index |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
92 representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
93 the human population). These small indexes (called local indexes), combined |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
94 with several alignment strategies, enable rapid and accurate alignment of |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
95 sequencing reads. This new indexing scheme is called a Hierarchical Graph |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
96 FM index (HGFM). In addition to spliced alignment, HISAT handles reads |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
97 involving indels and supports a paired-end alignment mode. Multiple processors |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
98 can be used simultaneously to achieve greater alignment speed. HISAT outputs |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
99 alignments in `SAM <http://samtools.sourceforge.net/SAM1.pdf>`__ format, enabling |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
100 interoperation with a large number of other tools (e.g. `SAMtools <http://samtools.sourceforge.net>`__, |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
101 `GATK <http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit>`__) |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
102 that use SAM. HISAT is distributed under the `GPLv3 license <http://www.gnu.org/licenses/gpl-3.0.html>`__, |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
103 and it runs on the command line under Linux, Mac OS X and Windows. |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
104 ]]> |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
105 </help> |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
106 <citations> |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
107 <citation type="doi">10.1038/nmeth.3317</citation> |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
108 </citations> |
d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
parents:
diff
changeset
|
109 </tool> |