Mercurial > repos > vipints > deseq_hts
comparison deseq-hts_2.0/galaxy/deseq2.xml @ 10:2fe512c7bfdf draft
DESeq2 version 1.0.19 added to the repo
author | vipints <vipin@cbio.mskcc.org> |
---|---|
date | Tue, 08 Oct 2013 08:15:34 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
9:e27b4f7811c2 | 10:2fe512c7bfdf |
---|---|
1 <tool id="deseq2-hts" name="DESeq2" version="1.0.19"> | |
2 <description> Differential gene expression analysis based on the negative binomial distribution</description> | |
3 <command interpreter="bash"> | |
4 ./../src/deseq2-hts.sh $anno_input_selected $deseq_out $deseq_out.extra_files_path/gene_map.mat | |
5 $distype | |
6 #for $i in $replicate_groups | |
7 #for $j in $i.replicates | |
8 $j.bam_alignment:#slurp | |
9 #end for | |
10 | |
11 #end for | |
12 >> $Log_File </command> | |
13 <inputs> | |
14 <param format="gff,gtf,gff3" name="anno_input_selected" type="data" label="Genome annotation in GFF file" help="A tab delimited format for storing sequence features and annotations"/> | |
15 <repeat name="replicate_groups" title="Replicate group" min="2"> | |
16 <repeat name="replicates" title="Replicate"> | |
17 <param format="bam" name="bam_alignment" type="data" label="BAM alignment file" help="BAM alignment file. Can be generated from SAM files using the SAMTools."/> | |
18 </repeat> | |
19 </repeat> | |
20 | |
21 <param name="distype" type="select" label="Select fitting of dispersions to the mean intensity"> | |
22 <option value="parametric">Parametric</option> | |
23 <option value="local">Local</option> | |
24 <option value="mean" selected="true">Mean</option> | |
25 </param> | |
26 | |
27 </inputs> | |
28 | |
29 <outputs> | |
30 <data format="txt" name="deseq_out" label="${tool.name} on ${on_string}: Differential Expression"/> | |
31 <data format="txt" name="Log_File" label="${tool.name} on ${on_string}: log"/> | |
32 </outputs> | |
33 | |
34 <tests> | |
35 <test> | |
36 ./deseq2-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 | |
37 | |
38 <param name="anno_input_selected" value="deseq_c_elegans_WS200-I-regions.gff3" ftype="gff3" /> | |
39 <param name="bam_alignments1" value="deseq_c_elegans_WS200-I-regions-SRX001872.bam" ftype="bam" /> | |
40 <param name="bam_alignments2" value="deseq_c_elegans_WS200-I-regions-SRX001875.bam" ftype="bam" /> | |
41 <output name="deseq_out" file="deseq_c_elegans_WS200-I-regions_deseq.txt" /> | |
42 </test> | |
43 </tests> | |
44 | |
45 <help> | |
46 | |
47 .. class:: infomark | |
48 | |
49 **What it does** | |
50 | |
51 DESeq2_ Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. | |
52 | |
53 .. _DESeq2: http://bioconductor.org/packages/2.12/bioc/html/DESeq2.html | |
54 | |
55 `DESeq2` requires: | |
56 | |
57 Genome annotation in GFF file type, containing the necessary information about the transcripts that are to be quantified. | |
58 | |
59 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! | |
60 | |
61 ------ | |
62 | |
63 **Licenses** | |
64 | |
65 If **DESeq2** is used to obtain results for scientific publications it | |
66 should be cited as [1]_. | |
67 | |
68 **References** | |
69 | |
70 .. [1] Anders, S and Huber, W (2010): `Differential expression analysis for sequence count data`_. | |
71 | |
72 .. _Differential expression analysis for sequence count data: http://dx.doi.org/10.1186/gb-2010-11-10-r106 | |
73 | |
74 ------ | |
75 | |
76 .. class:: infomark | |
77 | |
78 **About formats** | |
79 | |
80 **GFF/GTF format** General Feature Format/Gene Transfer Format is a format for describing genes and other features associated with DNA, RNA and protein sequences. GFF3 lines have nine tab-separated fields: | |
81 | |
82 1. seqid - The name of a chromosome or scaffold. | |
83 2. source - The program that generated this feature. | |
84 3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon". | |
85 4. start - The starting position of the feature in the sequence. The first base is numbered 1. | |
86 5. stop - The ending position of the feature (inclusive). | |
87 6. score - A score between 0 and 1000. If there is no score value, enter ".". | |
88 7. strand - Valid entries include '+', '-', or '.' (for don't know/care). | |
89 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 '.'. | |
90 9. attributes - All lines with the same group are linked together into a single item. | |
91 | |
92 For more information see http://www.sequenceontology.org/gff3.shtml | |
93 | |
94 **BAM format** The Sequence Alignment/Map (SAM) format is a | |
95 tab-limited text format that stores large nucleotide sequence | |
96 alignments. BAM is the binary version of a SAM file that allows for | |
97 fast and intensive data processing. The format specification and the | |
98 description of SAMtools can be found on | |
99 http://samtools.sourceforge.net/. | |
100 | |
101 ------ | |
102 | |
103 DESeq2-hts Wrapper Version 0.2 (Aug 2013) | |
104 | |
105 </help> | |
106 </tool> |