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1 <tool id="deseq2" name="DESeq2" version="2.0.1">
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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="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
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13 #if $pdf:
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14 -p "$plots"
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15 #end if
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16
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17 -i "$input_matrix"
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18
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19 #if $filter_sel.filter_sel_opts == 'all_vs_all':
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20 -s 'all_vs_all'
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21 #else:
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22 -s ## build a string like '1,2 5,6'
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23 "${filter_sel.control_cols} ${filter_sel.experiement_cols}"
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24
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25 #set $temp_factor_list = list()
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26 #set $is_multi_factor_analysis = False
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27 #for $factor in $filter_sel.factor:
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28 #set $is_multi_factor_analysis = True
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29 $temp_factor_list.append( '%s:%s' % ($factor.factor_name.replace(' ','_'), $factor.factor_index) )
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30 #end for
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31
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32 #if $is_multi_factor_analysis:
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33 -f "#echo ' '.join( $temp_factor_list )#"
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34 #end if
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35 #end if
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36
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37 </command>
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38 <stdio>
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39 <regex match="Execution halted"
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40 source="both"
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41 level="fatal"
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42 description="Execution halted." />
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43 <regex match="Input-Error 01"
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44 source="both"
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45 level="fatal"
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46 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
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47 <regex match="Error in"
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48 source="both"
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49 level="fatal"
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50 description="An undefined error occured, please check your intput carefully and contact your administrator." />
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51 </stdio>
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52 <inputs>
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53 <param format="tabular" name="input_matrix" type="data" label="Countmatrix" help="You can create a count matrix with the tool ..."/>
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54
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55 <conditional name="filter_sel">
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56 <param name="filter_sel_opts" type="select" label="Select properties to filter">
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57 <option value="all_vs_all">All against all</option>
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58 <option value="specific">specific</option>
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59 </param>
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60 <when value="specific">
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61
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62 <param name="control_cols" label="Select columns containing treatment." type="data_column" data_ref="input_matrix"
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63 numerical="True" multiple="true" use_header_names="true" size="120" display="checkboxes">
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64 <validator type="no_options" message="Please select at least one column."/>
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65 </param>
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66
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67 <param name="experiement_cols" label="Select columns containing treatment." type="data_column" data_ref="input_matrix"
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68 numerical="True" multiple="true" use_header_names="true" size="120" display="checkboxes">
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69 <validator type="no_options" message="Please select at least one column."/>
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70 </param>
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71
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72 <repeat name="factor" title="Include multi-factor analysis">
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73 <param name="factor_name" type="text" value="Factor Name" label="Specify a factor name" help=""/>
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74
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75 <param name="factor_index" label="Select columns that are associated with a factor." type="data_column" data_ref="input_matrix"
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76 numerical="True" multiple="true" use_header_names="true" size="120" display="checkboxes">
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77 <validator type="no_options" message="Please select at least one column."/>
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78 </param>
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79 </repeat>
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80
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81 </when>
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82 <when value="all_v_all" />
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83 </conditional>
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84
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85 <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true" label="Visualising the analysis results"
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86 help="output an additional PDF file" />
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87
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88 </inputs>
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89
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90 <outputs>
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91 <data format="tabular" name="deseq_out" label="DESeq2 result file on ${on_string}"/>
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92 <data format="pdf" name="plots" label="DESeq2 plots on ${on_string}">
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93 <filter>pdf == True</filter>
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94 </data>
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95 </outputs>
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96
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97 <help>
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98
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99 .. class:: infomark
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100
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101 **What it does**
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102
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103 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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104
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105
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106 **Inputs**
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107
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108 DESeq2_ requires one count matrix as input file. You can use the tool
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109
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110
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111
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112 **Output**
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113
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114 DESeq2_ generates a tabular file containing the different columns and optional visualized results as PDF.
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115
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116 ====== ==========================================================
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117 Column Description
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118 ------ ----------------------------------------------------------
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119 1 Sample ID (corresponds to the header in your count matrix)
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120 2 Gene Identifiers
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121 3 mean normalised counts, averaged over all samples from both conditions
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122 4 the logarithm (to basis 2) of the fold change
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123 5 standard error estimate for the log2 fold change estimate
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124 6 p value for the statistical significance of this change
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125 7 p value adjusted for multiple testing with the Benjamini-Hochberg procedure
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126 which controls false discovery rate (FDR)
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127 ====== ==========================================================
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128
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129
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130 ------
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131
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132 **References**
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133
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134 DESeq2_ Authors: Michael Love (MPIMG Berlin), Simon Anders, Wolfgang Huber (EMBL Heidelberg)
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135
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136 If _DESeq2_ is used to obtain results for scientific publications it
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137 should be cited as [1]_. A paper describing DESeq2_ is in preparation.
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138
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139
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140
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141 .. [1] Anders, S and Huber, W (2010): `Differential expression analysis for sequence count data`_.
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142
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143 .. _Differential expression analysis for sequence count data: http://dx.doi.org/10.1186/gb-2010-11-10-r106
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144 .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html
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145
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146
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147 </help>
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148 </tool>
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