data_manager_rnasta: data_manager/rnastar_index

annotate data_manager/rnastar_index_builder.xml @ 8:363d6797d366 draft default tip

Uploaded

author	fubar
date	Fri, 09 Jan 2015 23:40:09 -0500
parents	f9d8dc8c2152
children

rev	line source
5 503097df1670 Uploaded fubar parents: 4 diff changeset	1 <tool id="rnastar_index_builder_data_manager" name="rnastar index" tool_type="manage_data" version="0.0.2">
0 84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	2 <description>builder</description>
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	3 <requirements>
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	4 <requirement type="package" version="2.4.0d">rnastar</requirement>
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	5 </requirements>
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	6 <command interpreter="python">
4 102bdfdda10b Uploaded fubar parents: 2 diff changeset	7 rnastar_index_builder.py "${out_file}" --fasta_filename "${all_fasta_source.fields.path}"
0 84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	8 --fasta_dbkey "${all_fasta_source.fields.dbkey}" --fasta_description "${all_fasta_source.fields.name}"
4 102bdfdda10b Uploaded fubar parents: 2 diff changeset	9 --runThreadN 1
0 84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	10 #if $genemodel.modelformat=="gff3":
4 102bdfdda10b Uploaded fubar parents: 2 diff changeset	11 --sjdbGTFchrPrefix "${genemodel.sjdbGTFchrPrefix}"
0 84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	12 --sjdbOverhang "${genemodel.sjdbOverhang}"
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	13 --sjdbGTFfile "${genemodel.sjdbGTFfile}"
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	14 --sjdbGTFtagExonParentTranscript "${genemodel.sjdbGTFtagExonParentTranscript}"
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	15 --sjdbGTFfeatureExon "${genemodel.sjdbGTFfeatureExon}"
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	16 #end if
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	17 #if $genemodel.modelformat=="bed":
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	18 --sjdbFileChrStartEnd "${genemodel.sjdbFileChrStartEnd}"
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	19 --sjdbOverhang "${genemodel.sjdbOverhang}"
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	20 #end if
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	21 #if $genemodel.modelformat=="None":
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	22 --sjdbOverhang 0
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	23 #end if
4 102bdfdda10b Uploaded fubar parents: 2 diff changeset	24 --data_table_name "rnastar_index"
6 f9d8dc8c2152 Uploaded fubar parents: 5 diff changeset	25 </command>
0 84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	26 <inputs>
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	27 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	28 <options from_data_table="all_fasta"/>
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	29 </param>
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	30 <param type="text" name="sequence_name" value="" label="Informative name for sequence index" />
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	31 <param type="text" name="sequence_id" value="" label="ID for sequence index" />
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	32 <conditional name="genemodel">
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	33 <param name="modelformat" type="select"
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	34 label="Choose the format of gene model data from your history - bed or gff3"
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	35 help="This will be the source of splice junction indexing if required">
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	36 <option value="gff3" selected="true">gff3,gtf</option>
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	37 <option value="bed">BED - tabular chr,start,end,strand</option>
6 f9d8dc8c2152 Uploaded fubar parents: 5 diff changeset	38 <option value="None">None - no splice junction index</option>
0 84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	39 </param>
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	40 <when value="gff3">
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	41 <param type="data" format="gff3,gff" name="sjdbGTFfile" value="" label="Gene model - must be gff3 or compatible and must match the input genome"
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	42 help="Required if you want to index splice junctions during index generation." />
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	43
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	44 <param type="text" name="sjdbGTFchrPrefix" value="chr" label="String prefix for GTF chromosomes"
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	45 help='GTF prefix for chromosome names (e.g. "chr" to use ENSMEBL annotations with UCSC geneomes)' >
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	46 <sanitizer invalid_char="">
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	47 <valid initial="string.printable"/>
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	48 </sanitizer>
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	49 </param>
4 102bdfdda10b Uploaded fubar parents: 2 diff changeset	50 <param type="text" name="sjdbGTFfeatureExon" value="exon" label="GTF feature to use as exon marker"
0 84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	51 help="GTF feature type in GTF file to be used as exons for building transcripts - use what's in your GTF">
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	52 <sanitizer invalid_char="">
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	53 <valid initial="string.printable"/>
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	54 </sanitizer>
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	55 </param>
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	56
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	57 <param type="text" name="sjdbGTFtagExonParentTranscript" value="transcript_id" label="GTF feature to define for each exon's parents"
4 102bdfdda10b Uploaded fubar parents: 2 diff changeset	58 help="GTF tag name to be used as exons' parents for building transcripts - use what's in your gene model file eg parent for gff3">
0 84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	59 <sanitizer invalid_char="">
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	60 <valid initial="string.printable"/>
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	61 </sanitizer>
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	62 </param>
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	63
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	64 <param type="integer" name="sjdbOverhang" value="100" label="Splice junction overhang. If=0, splice junction database NOT used"
5 503097df1670 Uploaded fubar parents: 4 diff changeset	65 help="integer length of the donor/acceptor sequence on each side, (mate_length - 1)" />
0 84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	66
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	67 </when>
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	68 <when value='bed'>
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	69 <param type="data" format="bed" name="sjdbFileChrStartEnd" value="" label="Introns as a tabular bed (chr,start,end,strand) file matching the input genome"
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	70 help="Required if you want to index splice junctions during index generation." />
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	71 <param type="integer" name="sjdbOverhang" value="100" label="Splice junction overhang. If=0, splice junction database NOT used"
5 503097df1670 Uploaded fubar parents: 4 diff changeset	72 help="integer length of the donor/acceptor sequence on each side, (mate_length - 1)" />
0 84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	73 </when>
6 f9d8dc8c2152 Uploaded fubar parents: 5 diff changeset	74 <when value='None'>
f9d8dc8c2152 Uploaded fubar parents: 5 diff changeset	75 </when>
0 84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	76 </conditional>
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	77 </inputs>
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	78 <outputs>
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	79 <data name="out_file" format="data_manager_json"/>
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	80 </outputs>
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	81 <help>
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	82
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	83 .. class:: infomark
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	84
6 f9d8dc8c2152 Uploaded fubar parents: 5 diff changeset	85 <![CDATA[
0 84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	86 What it does
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	87
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	88 This is a Galaxy datamanager for the rna STAR gap-aware RNA aligner.
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	89
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	90 Please read the fine manual - that and the google group are the places to learn about the options above.
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	91
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	92 Note on sjdbOverhang
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	93
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	94 From https://groups.google.com/forum/#!topic/rna-star/h9oh10UlvhI::
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	95
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	96 James is right, using large enough --sjdbOverhang is safer and should not generally cause any problems with reads of varying length. If your reads are very short, <50b, then I would strongly recommend using optimum --sjdbOverhang=mateLength-1
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	97 By mate length I mean the length of one of the ends of the read, i.e. it's 100 for 2x100b PE or 1x100b SE. For longer reads you can simply use generic --sjdbOverhang 100.
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	98 It is a bit confusing because of the way I named this parameter. --sjdbOverhang Noverhang is only used at the genome generation step for constructing the reference sequence out of the annotations.
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	99 Basically, the Noverhang exonic bases from the donor site and Noverhang exonic bases from the acceptor site are spliced together for each of the junctions, and these spliced sequences are added to the genome sequence.
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	100
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	101 At the mapping stage, the reads are aligned to both genomic and splice sequences simultaneously. If a read maps to one of spliced sequences and crosses the "junction" in the middle of it, the coordinates of two pspliced pieces are translated back to genomic space and added to the collection of mapped pieces, which are then all "stitched" together to form the final alignment. Since in the process of "maximal mapped length" search the read is split into pieces of no longer than --seedSearchStartLmax (=50 by default) bases, even if the read (mate) is longer than --sjdbOverhang, it can still be mapped to the spliced reference, as long as --sjdbOverhang > --seedSearchStartLmax.
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	102
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	103 Cheers
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	104 Alex
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	105
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	106 Note on gene model requirements for splice junctions
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	107
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	108 From https://groups.google.com/forum/#!msg/rna-star/3Y_aaTuzBrE/lUylTB8h5vMJ::
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	109
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	110 When you generate a genome with annotations, you need to specify --sjdbOverhang value, which ideally should be equal to (oneMateLength-1), or you could use a generic value of ~100.
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	111
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	112 Your gtf lines look fine to me. STAR needs 3 features from a GTF file:
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	113 1. Chromosome names in col.1 that agree with chromosome names in genome .fasta files. If you have "chr2L" names in the genome .fasta files, and "2L" in the .gtf file, then you need to use --sjdbGTFchrPrefix chr option.
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	114 2. 'exon' in col.3 for the exons of all transcripts (this name can be changed with --sjdbGTFfeatureExon)
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	115 3. 'transcript_id' attribute that assigns each exon to a transcript (--this name can be changed with --sjdbGTFtagExonParentTranscript)
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	116
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	117 Cheers
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	118 Alex
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	119
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	120 Notice: If you leave name, description, or id blank, it will be generated automatically.
6 f9d8dc8c2152 Uploaded fubar parents: 5 diff changeset	121 ]]>
0 84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	122 </help>
84f6e67cbae5 Initial commit - problems testing on my ram starved laptop - need to test on a bigger ram machine fubar parents: diff changeset	123 </tool>

Mercurial > repos > fubar > data_manager_rnasta

annotate data_manager/rnastar_index_builder.xml @ 8:363d6797d366 draft default tip