Mercurial > repos > vipints > deseq_hts
comparison deseq-hts_1.0/galaxy/deseq.xml @ 0:94a108763d9e draft
deseq-hts version 1.0 wraps the DESeq 1.6.0
author | vipints |
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date | Wed, 09 May 2012 20:43:47 -0400 |
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children | 8ab01cc29c4b |
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1 <tool id="deseq-hts" name="DESeq" version="1.6.0"> | |
2 <description>Determines differentially expressed transcripts from read alignments</description> | |
3 <command> | |
4 deseq-hts/src/deseq-hts.sh $anno_input_selected $deseq_out $deseq_out.extra_files_path/gene_map.mat | |
5 #for $i in $replicate_groups | |
6 #for $j in $i.replicates | |
7 $j.bam_alignment:#slurp | |
8 #end for | |
9 #end for | |
10 >> $Log_File </command> | |
11 <inputs> | |
12 <param format="gff3" name="anno_input_selected" type="data" label="Genome annotation in GFF3 file" help="A tab delimited format for storing sequence features and annotations"/> | |
13 <repeat name="replicate_groups" title="Replicate group" min="2"> | |
14 <repeat name="replicates" title="Replicate"> | |
15 <param format="bam" name="bam_alignment" type="data" label="BAM alignment file" help="BAM alignment file. Can be generated from SAM files using the SAM Tools."/> | |
16 </repeat> | |
17 </repeat> | |
18 </inputs> | |
19 | |
20 <outputs> | |
21 <data format="txt" name="deseq_out" label="DESeq result"/> | |
22 <data format="txt" name="Log_File" label="DESeq log file"/> | |
23 </outputs> | |
24 | |
25 <tests> | |
26 <test> | |
27 command: | |
28 ./deseq-hts.sh ../test_data/deseq_c_elegans_WS200-I-regions.gff3 ../test_data/deseq_c_elegans_WS200-I-regions_deseq.txt ../test_data/genes.mat ../test_data/deseq_c_elegans_WS200-I-regions-SRX001872.bam ../test_data/deseq_c_elegans_WS200-I-regions-SRX001875.bam | |
29 | |
30 <param name="anno_input_selected" value="deseq_c_elegans_WS200-I-regions.gff3" ftype="gff3" /> | |
31 <param name="bam_alignments1" value="deseq_c_elegans_WS200-I-regions-SRX001872.bam" ftype="bam" /> | |
32 <param name="bam_alignments2" value="deseq_c_elegans_WS200-I-regions-SRX001875.bam" ftype="bam" /> | |
33 <output name="deseq_out" file="deseq_c_elegans_WS200-I-regions_deseq.txt" /> | |
34 </test> | |
35 </tests> | |
36 | |
37 <help> | |
38 | |
39 .. class:: infomark | |
40 | |
41 **What it does** | |
42 | |
43 `DESeq` is a tool for differential expression testing of RNA-Seq data. | |
44 | |
45 | |
46 **Inputs** | |
47 | |
48 `DESeq` requires three input files to run: | |
49 | |
50 1. Annotation file in GFF3, containing the necessary information about the transcripts that are to be quantified. | |
51 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.) | |
52 | |
53 **Output** | |
54 | |
55 `DESeq` generates a text file containing the gene name and the p-value. | |
56 | |
57 ------ | |
58 | |
59 **Licenses** | |
60 | |
61 If **DESeq** is used to obtain results for scientific publications it | |
62 should be cited as [1]_. | |
63 | |
64 **References** | |
65 | |
66 .. [1] Anders, S and Huber, W (2010): `Differential expression analysis for sequence count data`_. | |
67 | |
68 .. _Differential expression analysis for sequence count data: http://dx.doi.org/10.1186/gb-2010-11-10-r106 | |
69 | |
70 ------ | |
71 | |
72 .. class:: infomark | |
73 | |
74 **About formats** | |
75 | |
76 | |
77 **GFF3 format** General Feature Format is a format for describing genes | |
78 and other features associated with DNA, RNA and protein | |
79 sequences. GFF3 lines have nine tab-separated fields: | |
80 | |
81 1. seqid - The name of a chromosome or scaffold. | |
82 2. source - The program that generated this feature. | |
83 3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon". | |
84 4. start - The starting position of the feature in the sequence. The first base is numbered 1. | |
85 5. stop - The ending position of the feature (inclusive). | |
86 6. score - A score between 0 and 1000. If there is no score value, enter ".". | |
87 7. strand - Valid entries include '+', '-', or '.' (for don't know/care). | |
88 8. phase - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be '.'. | |
89 9. attributes - All lines with the same group are linked together into a single item. | |
90 | |
91 For more information see http://www.sequenceontology.org/gff3.shtml | |
92 | |
93 **SAM/BAM format** The Sequence Alignment/Map (SAM) format is a | |
94 tab-limited text format that stores large nucleotide sequence | |
95 alignments. BAM is the binary version of a SAM file that allows for | |
96 fast and intensive data processing. The format specification and the | |
97 description of SAMtools can be found on | |
98 http://samtools.sourceforge.net/. | |
99 | |
100 ------ | |
101 | |
102 DESeq-hts Wrapper Version 0.3 (Feb 2012) | |
103 | |
104 </help> | |
105 </tool> |