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