Mercurial > repos > vipints > deseq_hts
diff 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 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/deseq-hts_2.0/galaxy/deseq2.xml Tue Oct 08 08:15:34 2013 -0400 @@ -0,0 +1,106 @@ +<tool id="deseq2-hts" name="DESeq2" version="1.0.19"> + <description> Differential gene expression analysis based on the negative binomial distribution</description> + <command interpreter="bash"> +./../src/deseq2-hts.sh $anno_input_selected $deseq_out $deseq_out.extra_files_path/gene_map.mat +$distype +#for $i in $replicate_groups +#for $j in $i.replicates +$j.bam_alignment:#slurp +#end for + +#end for + >> $Log_File </command> + <inputs> + <param format="gff,gtf,gff3" name="anno_input_selected" type="data" label="Genome annotation in GFF file" help="A tab delimited format for storing sequence features and annotations"/> + <repeat name="replicate_groups" title="Replicate group" min="2"> + <repeat name="replicates" title="Replicate"> + <param format="bam" name="bam_alignment" type="data" label="BAM alignment file" help="BAM alignment file. Can be generated from SAM files using the SAMTools."/> + </repeat> + </repeat> + + <param name="distype" type="select" label="Select fitting of dispersions to the mean intensity"> + <option value="parametric">Parametric</option> + <option value="local">Local</option> + <option value="mean" selected="true">Mean</option> + </param> + + </inputs> + + <outputs> + <data format="txt" name="deseq_out" label="${tool.name} on ${on_string}: Differential Expression"/> + <data format="txt" name="Log_File" label="${tool.name} on ${on_string}: log"/> + </outputs> + + <tests> + <test> + ./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 + + <param name="anno_input_selected" value="deseq_c_elegans_WS200-I-regions.gff3" ftype="gff3" /> + <param name="bam_alignments1" value="deseq_c_elegans_WS200-I-regions-SRX001872.bam" ftype="bam" /> + <param name="bam_alignments2" value="deseq_c_elegans_WS200-I-regions-SRX001875.bam" ftype="bam" /> + <output name="deseq_out" file="deseq_c_elegans_WS200-I-regions_deseq.txt" /> + </test> + </tests> + + <help> + +.. class:: infomark + +**What it does** + +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. + +.. _DESeq2: http://bioconductor.org/packages/2.12/bioc/html/DESeq2.html + +`DESeq2` requires: + +Genome annotation in GFF file type, containing the necessary information about the transcripts that are to be quantified. + +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! + +------ + +**Licenses** + +If **DESeq2** is used to obtain results for scientific publications it +should be cited as [1]_. + +**References** + +.. [1] Anders, S and Huber, W (2010): `Differential expression analysis for sequence count data`_. + +.. _Differential expression analysis for sequence count data: http://dx.doi.org/10.1186/gb-2010-11-10-r106 + +------ + +.. class:: infomark + +**About formats** + +**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: + +1. seqid - The name of a chromosome or scaffold. +2. source - The program that generated this feature. +3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon". +4. start - The starting position of the feature in the sequence. The first base is numbered 1. +5. stop - The ending position of the feature (inclusive). +6. score - A score between 0 and 1000. If there is no score value, enter ".". +7. strand - Valid entries include '+', '-', or '.' (for don't know/care). +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 '.'. +9. attributes - All lines with the same group are linked together into a single item. + +For more information see http://www.sequenceontology.org/gff3.shtml + +**BAM format** The Sequence Alignment/Map (SAM) format is a +tab-limited text format that stores large nucleotide sequence +alignments. BAM is the binary version of a SAM file that allows for +fast and intensive data processing. The format specification and the +description of SAMtools can be found on +http://samtools.sourceforge.net/. + +------ + +DESeq2-hts Wrapper Version 0.2 (Aug 2013) + +</help> +</tool>