Mercurial > repos > fubar > data_manager_rnasta

comparison data_manager/rnastar_index_builder.xml @ 4:102bdfdda10b draft

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author fubar
date Thu, 08 Jan 2015 17:53:14 -0500
parents 8a2d16bfdae2
children 503097df1670
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3:2468ef56337a 4:102bdfdda10b
2 <description>builder</description> 2 <description>builder</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.4.0d">rnastar</requirement> 4 <requirement type="package" version="2.4.0d">rnastar</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="python"> 6 <command interpreter="python">
7 rnastar_index_builder.py --out_file "${out_file}" --fasta_filename "${all_fasta_source.fields.path}" 7 rnastar_index_builder.py "${out_file}" --fasta_filename "${all_fasta_source.fields.path}"
8 --fasta_dbkey "${all_fasta_source.fields.dbkey}" --fasta_description "${all_fasta_source.fields.name}" 8 --fasta_dbkey "${all_fasta_source.fields.dbkey}" --fasta_description "${all_fasta_source.fields.name}"
9 --data_table_name "rnastar_indexes" --out_index_path "${out_file.extra_files_path}" --runThreadN 1 9 --runThreadN 1
10 #if $genemodel.modelformat=="gff3": 10 #if $genemodel.modelformat=="gff3":
11 --sjdbGTFchrPrefix "${genemodel.sjdbGTFchrPrefix}"
11 --sjdbOverhang "${genemodel.sjdbOverhang}" 12 --sjdbOverhang "${genemodel.sjdbOverhang}"
12 --sjdbGTFfile "${genemodel.sjdbGTFfile}" 13 --sjdbGTFfile "${genemodel.sjdbGTFfile}"
13 --sjdbGTFtagExonParentTranscript "${genemodel.sjdbGTFtagExonParentTranscript}" 14 --sjdbGTFtagExonParentTranscript "${genemodel.sjdbGTFtagExonParentTranscript}"
14 --sjdbGTFfeatureExon "${genemodel.sjdbGTFfeatureExon}" 15 --sjdbGTFfeatureExon "${genemodel.sjdbGTFfeatureExon}"
15 #end if 16 #end if
18 --sjdbOverhang "${genemodel.sjdbOverhang}" 19 --sjdbOverhang "${genemodel.sjdbOverhang}"
19 #end if 20 #end if
20 #if $genemodel.modelformat=="None": 21 #if $genemodel.modelformat=="None":
21 --sjdbOverhang 0 22 --sjdbOverhang 0
22 #end if 23 #end if
24 --data_table_name "rnastar_index"
23 </command> 25 </command>
26
24 <stdio> 27 <stdio>
25 <regex match=".*" source="both" level="warning" description="stdout/err chatter:"/> 28 <regex match=".*" source="both" level="warning" description="stdout/err chatter:"/>
26 </stdio> 29 </stdio>
27 <inputs> 30 <inputs>
28 <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> 31 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
48 help='GTF prefix for chromosome names (e.g. "chr" to use ENSMEBL annotations with UCSC geneomes)' > 51 help='GTF prefix for chromosome names (e.g. "chr" to use ENSMEBL annotations with UCSC geneomes)' >
49 <sanitizer invalid_char=""> 52 <sanitizer invalid_char="">
50 <valid initial="string.printable"/> 53 <valid initial="string.printable"/>
51 </sanitizer> 54 </sanitizer>
52 </param> 55 </param>
53 <param type="text" name="sjdbGTFfeatureExon" value="exon_id" label="GTF feature to use as exon marker" 56 <param type="text" name="sjdbGTFfeatureExon" value="exon" label="GTF feature to use as exon marker"
54 help="GTF feature type in GTF file to be used as exons for building transcripts - use what's in your GTF"> 57 help="GTF feature type in GTF file to be used as exons for building transcripts - use what's in your GTF">
55 <sanitizer invalid_char=""> 58 <sanitizer invalid_char="">
56 <valid initial="string.printable"/> 59 <valid initial="string.printable"/>
57 </sanitizer> 60 </sanitizer>
58 </param> 61 </param>
59 62
60 <param type="text" name="sjdbGTFtagExonParentTranscript" value="transcript_id" label="GTF feature to define for each exon's parents" 63 <param type="text" name="sjdbGTFtagExonParentTranscript" value="transcript_id" label="GTF feature to define for each exon's parents"
61 help="GTF tag name to be used as exons' parents for building transcripts - use what's in your GTF"> 64 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">
62 <sanitizer invalid_char=""> 65 <sanitizer invalid_char="">
63 <valid initial="string.printable"/> 66 <valid initial="string.printable"/>
64 </sanitizer> 67 </sanitizer>
65 </param> 68 </param>
66 69