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comparison data_manager/rnastar_index_builder.xml @ 6:f9d8dc8c2152 draft

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author fubar
date Fri, 09 Jan 2015 23:16:54 -0500
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5:503097df1670 6:f9d8dc8c2152
20 #end if 20 #end if
21 #if $genemodel.modelformat=="None": 21 #if $genemodel.modelformat=="None":
22 --sjdbOverhang 0 22 --sjdbOverhang 0
23 #end if 23 #end if
24 --data_table_name "rnastar_index" 24 --data_table_name "rnastar_index"
25 </command> 25 </command>
26 <inputs> 26 <inputs>
27 <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> 27 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
28 <options from_data_table="all_fasta"/> 28 <options from_data_table="all_fasta"/>
29 </param> 29 </param>
30 <param type="text" name="sequence_name" value="" label="Informative name for sequence index" /> 30 <param type="text" name="sequence_name" value="" label="Informative name for sequence index" />
33 <param name="modelformat" type="select" 33 <param name="modelformat" type="select"
34 label="Choose the format of gene model data from your history - bed or gff3" 34 label="Choose the format of gene model data from your history - bed or gff3"
35 help="This will be the source of splice junction indexing if required"> 35 help="This will be the source of splice junction indexing if required">
36 <option value="gff3" selected="true">gff3,gtf</option> 36 <option value="gff3" selected="true">gff3,gtf</option>
37 <option value="bed">BED - tabular chr,start,end,strand</option> 37 <option value="bed">BED - tabular chr,start,end,strand</option>
38 <option value="None" >None - no splice junction index</option> 38 <option value="None">None - no splice junction index</option>
39 </param> 39 </param>
40 <when value="gff3"> 40 <when value="gff3">
41 <param type="data" format="gff3,gff" name="sjdbGTFfile" value="" label="Gene model - must be gff3 or compatible and must match the input genome" 41 <param type="data" format="gff3,gff" name="sjdbGTFfile" value="" label="Gene model - must be gff3 or compatible and must match the input genome"
42 help="Required if you want to index splice junctions during index generation." /> 42 help="Required if you want to index splice junctions during index generation." />
43 43
69 <param type="data" format="bed" name="sjdbFileChrStartEnd" value="" label="Introns as a tabular bed (chr,start,end,strand) file matching the input genome" 69 <param type="data" format="bed" name="sjdbFileChrStartEnd" value="" label="Introns as a tabular bed (chr,start,end,strand) file matching the input genome"
70 help="Required if you want to index splice junctions during index generation." /> 70 help="Required if you want to index splice junctions during index generation." />
71 <param type="integer" name="sjdbOverhang" value="100" label="Splice junction overhang. If=0, splice junction database NOT used" 71 <param type="integer" name="sjdbOverhang" value="100" label="Splice junction overhang. If=0, splice junction database NOT used"
72 help="integer length of the donor/acceptor sequence on each side, (mate_length - 1)" /> 72 help="integer length of the donor/acceptor sequence on each side, (mate_length - 1)" />
73 </when> 73 </when>
74 <when value='None'> 74 <when value='None'>
75 </when> 75 </when>
76 </conditional> 76 </conditional>
77 </inputs> 77 </inputs>
78 <outputs> 78 <outputs>
79 <data name="out_file" format="data_manager_json"/> 79 <data name="out_file" format="data_manager_json"/>
80 </outputs> 80 </outputs>
81 <help> 81 <help>
82 82
83 .. class:: infomark 83 .. class:: infomark
84 84
85 <![CDATA[
85 *What it does* 86 *What it does*
86 87
87 This is a Galaxy datamanager for the rna STAR gap-aware RNA aligner. 88 This is a Galaxy datamanager for the rna STAR gap-aware RNA aligner.
88 89
89 Please read the fine manual - that and the google group are the places to learn about the options above. 90 Please read the fine manual - that and the google group are the places to learn about the options above.
115 116
116 Cheers 117 Cheers
117 Alex 118 Alex
118 119
119 **Notice:** If you leave name, description, or id blank, it will be generated automatically. 120 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
120 121 ]]>
121 </help> 122 </help>
122 </tool> 123 </tool>