Mercurial > repos > iuc > data_manager_hisat2_index_builder
annotate data_manager/hisat2_index_builder.xml @ 4:d210e1f185bd draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
author | iuc |
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date | Tue, 04 Apr 2017 18:09:40 -0400 |
parents | 4014cb2c17db |
children | 8eac26f44d29 |
rev | line source |
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4
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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1 <tool id="hisat2_index_builder_data_manager" name="HISAT2 index" tool_type="manage_data" version="2.0.5"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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2 <description>builder</description> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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3 <requirements> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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4 <requirement type="package" version="2.0.5">hisat2</requirement> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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5 </requirements> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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6 <command detect_errors="exit_code"><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 4a5952b2404c0821cf9895cb2a5036da62b14d6e-dirty
iuc
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7 #if $advanced.adv_param_select == 'yes' and $advanced.gtf_input: |
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d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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8 ln -s '${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
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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
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10 hisat2_extract_exons.py gtf_file.gtf > exon.txt && |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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11 #end if |
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4014cb2c17db
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 4a5952b2404c0821cf9895cb2a5036da62b14d6e-dirty
iuc
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12 #if $advanced.adv_param_select == 'yes' and $advanced.snps: |
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d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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13 ln -s '${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
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14 #if $advanced.snps.is_of_type('vcf') |
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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15 hisat2_extract_snps_haplotypes_VCF.py '${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
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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
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17 hisat2_extract_snps_haplotypes_UCSC.py '${all_fasta_source.fields.path}' snps.tabular extracted && |
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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18 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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19 #end if |
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d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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20 python '$__tool_directory__/hisat2_index_builder.py' --output '${out_file}' |
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
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21 --fasta_filename '${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
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22 --fasta_dbkey '${all_fasta_source.fields.dbkey}' |
d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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23 --fasta_description '${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
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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
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25 --indexer_options "-p \${GALAXY_SLOTS:-1} |
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d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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26 #if $advanced.adv_param_select == 'yes': |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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27 --noauto |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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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
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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
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30 --haplotype "`pwd`/extracted.haplotype" |
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d3eb4d51b285
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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31 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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32 #if $advanced.gtf_input: |
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d210e1f185bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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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
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34 --exon "`pwd`/exon.txt" |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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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
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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
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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
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38 --dcv $advanced.dcv |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
iuc
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39 --offrate $advanced.offrate |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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40 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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41 " |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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42 ]]> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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43 </command> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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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
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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
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46 <options from_data_table="all_fasta" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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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
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48 <conditional name="advanced" label="Advanced parameters"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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49 <param name="adv_param_select" type="select" label="Advanced parameters"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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50 <option value="no">Use defaults</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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51 <option value="yes">Fine-tune indexing parameters</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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52 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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53 <when value="no" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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54 <when value="yes"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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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
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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
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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
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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
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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
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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" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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61 </when> |
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62 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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63 <param name="sequence_name" type="text" value="" label="Name of sequence" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
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64 <param name="sequence_id" type="text" value="" label="ID for sequence" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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65 </inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty
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66 <outputs> |
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67 <data name="out_file" format="data_manager_json" /> |
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68 </outputs> |
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69 <help> |
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70 <![CDATA[ |
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71 .. class:: infomark |
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72 |
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73 **Notice:** If you leave name, description, or id blank, it will be generated automatically. |
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74 |
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75 What is HISAT2? |
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76 --------------- |
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77 |
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78 `HISAT <http://ccb.jhu.edu/software/hisat>`__ is a fast and sensitive alignment |
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79 program for mapping next-generation sequencing reads (both DNA and RNA) against |
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80 the general human population (as well as against a single reference genome). |
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81 Based on an extension of BWT for graphs (`BWT <http://dl.acm.org/citation.cfm?id=2674828>`__) |
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82 we designed and implemented a graph FM index (GFM), an original approach and |
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83 its first implementation to the best of our knowledge. In addition to using one |
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84 global GFM index that represents the general population, HISAT2 uses a large set |
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85 of small GFM indexes that collectively cover the whole genome (each index |
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86 representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover |
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87 the human population). These small indexes (called local indexes), combined |
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88 with several alignment strategies, enable rapid and accurate alignment of |
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89 sequencing reads. This new indexing scheme is called a Hierarchical Graph |
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90 FM index (HGFM). In addition to spliced alignment, HISAT handles reads |
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91 involving indels and supports a paired-end alignment mode. Multiple processors |
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92 can be used simultaneously to achieve greater alignment speed. HISAT outputs |
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93 alignments in `SAM <http://samtools.sourceforge.net/SAM1.pdf>`__ format, enabling |
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94 interoperation with a large number of other tools (e.g. `SAMtools <http://samtools.sourceforge.net>`__, |
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95 `GATK <http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit>`__) |
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96 that use SAM. HISAT is distributed under the `GPLv3 license <http://www.gnu.org/licenses/gpl-3.0.html>`__, |
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97 and it runs on the command line under Linux, Mac OS X and Windows. |
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98 ]]> |
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99 </help> |
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100 <citations> |
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101 <citation type="doi">10.1038/nmeth.3317</citation> |
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102 </citations> |
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103 </tool> |