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comparison deseq-hts_1.0/galaxy/deseq.xml @ 9:e27b4f7811c2 draft

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Updated DESeq version 1.12
author vipints <vipin@cbio.mskcc.org>
date Tue, 08 Oct 2013 08:09:28 -0400
parents 8ab01cc29c4b
children
comparison
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8:2b3bb3348076 9:e27b4f7811c2
1 <tool id="deseq-hts" name="DESeq" version="1.6.1"> 1 <tool id="deseq-hts" name="DESeq" version="1.12.1">
2 <description>Determines differentially expressed transcripts from read alignments</description> 2 <description> Determines differentially expressed transcripts from read alignments</description>
3 <command> 3 <requirements>
4 deseq-hts/src/deseq-hts.sh $anno_input_selected $deseq_out $deseq_out.extra_files_path/gene_map.mat 4 <requirement type="package" version="0.1">oqtans</requirement>
5 </requirements>
6 <command interpreter="bash">
7 ./../src/deseq-hts.sh $anno_input_selected $deseq_out $deseq_out.extra_files_path/gene_map.mat
5 #for $i in $replicate_groups 8 #for $i in $replicate_groups
6 #for $j in $i.replicates 9 #for $j in $i.replicates
7 $j.bam_alignment:#slurp 10 $j.bam_alignment:#slurp
8 #end for 11 #end for
9 12
17 </repeat> 20 </repeat>
18 </repeat> 21 </repeat>
19 </inputs> 22 </inputs>
20 23
21 <outputs> 24 <outputs>
22 <data format="txt" name="deseq_out" label="DESeq result"/> 25 <data format="txt" name="deseq_out" label="${tool.name} on ${on_string}: Differential Expression"/>
23 <data format="txt" name="Log_File" label="DESeq log file"/> 26 <data format="txt" name="Log_File" label="${tool.name} on ${on_string}: log"/>
24 </outputs> 27 </outputs>
25 28
26 <tests> 29 <tests>
27 <test> 30 <test>
28 command: 31 command:
39 42
40 .. class:: infomark 43 .. class:: infomark
41 44
42 **What it does** 45 **What it does**
43 46
44 `DESeq` is a tool for differential expression testing of RNA-Seq data. 47 DESeq_ is a tool for differential expression testing of RNA-Seq data.
45 48
49 .. _DESeq: http://bioconductor.org/packages/release/bioc/html/DESeq.html
46 50
47 **Inputs** 51 `DESeq` requires:
48 52
49 `DESeq` requires three input files to run: 53 Genome annotation file in GFF3, containing the necessary information about the transcripts that are to be quantified.
50 54
51 1. Annotation file in GFF3, containing the necessary information about the transcripts that are to be quantified. 55 The BAM alignment files grouped into replicate groups, each containing several replicates. BAM files store the read alignments, The program will also work with only two groups containing only a single replicate each. However, this analysis has less statistical power and is therefore not recommended!
52 2. The BAM alignment files grouped into replicate groups, each containing several replicates. BAM files store the read alignments in a compressed format. They can be generated using the `SAM-to-BAM` tool in the NGS: SAM Tools section. (The script will also work with only two groups containing only a single replicate each. However, this analysis has less statistical power and is therefor not recommended.)
53
54 **Output**
55
56 `DESeq` generates a text file containing the gene name and the p-value.
57 56
58 ------ 57 ------
59 58
60 **Licenses** 59 **Licenses**
61 60
98 description of SAMtools can be found on 97 description of SAMtools can be found on
99 http://samtools.sourceforge.net/. 98 http://samtools.sourceforge.net/.
100 99
101 ------ 100 ------
102 101
103 DESeq-hts Wrapper Version 0.3 (Feb 2012) 102 DESeq-hts Wrapper Version 0.5 (Aug 2013)
104 103
105 </help> 104 </help>
106 </tool> 105 </tool>