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1 <tool id="deseq2" name="DESeq2" version="2.0">
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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="binary">Rscript</requirement>
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5 <requirement type="R-module">DESeq2</requirement>
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6 <requirement type="package" version="3.0.1">R_3_0_1</requirement>
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7 <requirement type="set_environment">DESEQ2_SCRIPT_PATH</requirement>
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8 </requirements>
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9 <command interpreter="Rscript">
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10 deseq2.R
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11 -o "$deseq_out"
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12 -p "$plots"
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13 -i "$input_matrix"
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14
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15 #if $filter_sel.filter_sel_opts == 'all_vs_all':
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16 -s 'all_vs_all'
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17 #else:
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18 -s ## build a string like '1:2 5:6'
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19 "${filter_sel.control_cols} ${filter_sel.experiement_cols}"
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20 #end if
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21
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22 </command>
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23 <inputs>
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24 <param format="tabular" name="input_matrix" type="data" label="Countmatrix" help="You can create a count matrix with the tool ..."/>
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25
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26 <conditional name="filter_sel">
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27 <param name="filter_sel_opts" type="select" label="Select properties to filter">
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28 <option value="all_vs_all">All against all</option>
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29 <option value="specific">specific</option>
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30 </param>
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31 <when value="specific">
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32
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33 <param name="control_cols" label="Select columns containing treatment." type="data_column" data_ref="input_matrix"
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34 numerical="True" multiple="true" use_header_names="true" size="120" display="checkboxes">
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35 <validator type="no_options" message="Please select at least one column."/>
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36 </param>
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37
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38 <param name="experiement_cols" label="Select columns containing treatment." type="data_column" data_ref="input_matrix"
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39 numerical="True" multiple="true" use_header_names="true" size="120" display="checkboxes">
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40 <validator type="no_options" message="Please select at least one column."/>
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41 </param>
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42
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43 </when>
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44 <when value="all_v_all" />
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45 </conditional>
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46
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47 </inputs>
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48
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49 <outputs>
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50 <data format="txt" name="deseq_out" label="DESeq2 result file"/>
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51 <data format="pdf" name="plots" label="Plot collection"/>
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52 <data format="txt" name="log" label="DESeq2 log file"/>
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53 </outputs>
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54
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55 <help>
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56
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57 .. class:: infomark
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58
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59 **What it does**
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60
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61 `DESeq` is a tool for differential expression testing of RNA-Seq data.
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62
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63
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64 **Inputs**
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65
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66 `DESeq` requires three input files to run:
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67
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68 1. Annotation file in GFF3, containing the necessary information about the transcripts that are to be quantified.
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69 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.)
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70
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71 **Output**
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72
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73 `DESeq` generates a text file containing the gene name and the p-value.
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74
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75 ------
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76
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77 **Licenses**
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78
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79 If **DESeq** is used to obtain results for scientific publications it
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80 should be cited as [1]_.
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81
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82 **References**
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83
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84 .. [1] Anders, S and Huber, W (2010): `Differential expression analysis for sequence count data`_.
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85
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86 .. _Differential expression analysis for sequence count data: http://dx.doi.org/10.1186/gb-2010-11-10-r106
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87
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88 ------
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89
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90 For more information see http://www.sequenceontology.org/gff3.shtml
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91
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92 **SAM/BAM format** The Sequence Alignment/Map (SAM) format is a
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93 tab-limited text format that stores large nucleotide sequence
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94 alignments. BAM is the binary version of a SAM file that allows for
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95 fast and intensive data processing. The format specification and the
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96 description of SAMtools can be found on
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97 http://samtools.sourceforge.net/.
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98
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99 ------
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100
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101 DESeq-hts Wrapper Version 0.3 (Feb 2012)
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102
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103 </help>
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104 </tool>
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