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1 <tool id="deseq-hts" name="DESeq" version="1.12.1">
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2 <description> Determines differentially expressed transcripts from read alignments</description>
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3 <requirements>
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4 <requirement type="package" version="0.1">oqtans</requirement>
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5 </requirements>
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6 <command interpreter="bash">
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7 ./../src/deseq-hts.sh $anno_input_selected $deseq_out $deseq_out.extra_files_path/gene_map.mat
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8 #for $i in $replicate_groups
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9 #for $j in $i.replicates
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10 $j.bam_alignment:#slurp
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11 #end for
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12
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13 #end for
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14 >> $Log_File </command>
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15 <inputs>
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16 <param format="gff3" name="anno_input_selected" type="data" label="Genome annotation in GFF3 file" help="A tab delimited format for storing sequence features and annotations"/>
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17 <repeat name="replicate_groups" title="Replicate group" min="2">
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18 <repeat name="replicates" title="Replicate">
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19 <param format="bam" name="bam_alignment" type="data" label="BAM alignment file" help="BAM alignment file. Can be generated from SAM files using the SAM Tools."/>
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20 </repeat>
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21 </repeat>
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22 </inputs>
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23
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24 <outputs>
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25 <data format="txt" name="deseq_out" label="${tool.name} on ${on_string}: Differential Expression"/>
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26 <data format="txt" name="Log_File" label="${tool.name} on ${on_string}: log"/>
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27 </outputs>
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28
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29 <tests>
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30 <test>
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31 command:
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32 ./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
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33
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34 <param name="anno_input_selected" value="deseq_c_elegans_WS200-I-regions.gff3" ftype="gff3" />
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35 <param name="bam_alignments1" value="deseq_c_elegans_WS200-I-regions-SRX001872.bam" ftype="bam" />
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36 <param name="bam_alignments2" value="deseq_c_elegans_WS200-I-regions-SRX001875.bam" ftype="bam" />
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37 <output name="deseq_out" file="deseq_c_elegans_WS200-I-regions_deseq.txt" />
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38 </test>
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39 </tests>
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40
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41 <help>
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42
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43 .. class:: infomark
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44
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45 **What it does**
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46
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47 DESeq_ is a tool for differential expression testing of RNA-Seq data.
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48
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49 .. _DESeq: http://bioconductor.org/packages/release/bioc/html/DESeq.html
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50
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51 `DESeq` requires:
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52
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53 Genome annotation file in GFF3, containing the necessary information about the transcripts that are to be quantified.
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54
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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!
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56
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57 ------
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58
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59 **Licenses**
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60
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61 If **DESeq** is used to obtain results for scientific publications it
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62 should be cited as [1]_.
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63
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64 **References**
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65
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66 .. [1] Anders, S and Huber, W (2010): `Differential expression analysis for sequence count data`_.
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67
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68 .. _Differential expression analysis for sequence count data: http://dx.doi.org/10.1186/gb-2010-11-10-r106
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69
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70 ------
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71
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72 .. class:: infomark
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73
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74 **About formats**
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75
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76
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77 **GFF3 format** General Feature Format is a format for describing genes
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78 and other features associated with DNA, RNA and protein
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79 sequences. GFF3 lines have nine tab-separated fields:
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80
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81 1. seqid - The name of a chromosome or scaffold.
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82 2. source - The program that generated this feature.
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83 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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84 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
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85 5. stop - The ending position of the feature (inclusive).
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86 6. score - A score between 0 and 1000. If there is no score value, enter ".".
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87 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
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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 '.'.
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89 9. attributes - All lines with the same group are linked together into a single item.
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90
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91 For more information see http://www.sequenceontology.org/gff3.shtml
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92
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93 **SAM/BAM format** The Sequence Alignment/Map (SAM) format is a
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94 tab-limited text format that stores large nucleotide sequence
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95 alignments. BAM is the binary version of a SAM file that allows for
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96 fast and intensive data processing. The format specification and the
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97 description of SAMtools can be found on
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98 http://samtools.sourceforge.net/.
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99
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100 ------
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101
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102 DESeq-hts Wrapper Version 0.5 (Aug 2013)
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103
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104 </help>
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105 </tool>
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