Mercurial > repos > iuc > deseq2

annotate deseq2.xml @ 42:6ef2cba4e35a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
author iuc
date Fri, 26 Aug 2022 11:15:32 +0000
parents 0a0a3388e3f2
children 621ddf5967d2
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1 <tool id="deseq2" name="DESeq2" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@">
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2 <description>Determines differentially expressed features from count tables</description>
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3 <macros>
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4 <import>deseq2_macros.xml</import>
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5 </macros>
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6 <expand macro='requirements'/>
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7 <expand macro='edam_ontology' />
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8 <expand macro='xrefs'/>
6
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9 <stdio>
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10 <regex match="Execution halted"
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11 source="both"
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12 level="fatal"
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13 description="Execution halted." />
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14 <regex match="Error in"
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15 source="both"
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16 level="fatal"
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17 description="An undefined error occurred, please check your input carefully and contact your administrator." />
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18 <regex match="Fatal error"
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19 source="both"
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20 level="fatal"
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21 description="An undefined error occurred, please check your input carefully and contact your administrator." />
6
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22 </stdio>
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23 <version_command><![CDATA[
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24 echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
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25 ]]></version_command>
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26 <command><![CDATA[
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27 #if $tximport.tximport_selector == 'tximport':
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28 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
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29 ln -s '$tximport.mapping_format.gtf_file' mapping.gff &&
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30 #else:
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31 ln -s '$tximport.mapping_format.tabular_file' mapping.txt &&
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32 #end if
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33 #end if
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34
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35 ## This is needed for Pulsar to transfer the file
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36 cat '$__tool_directory__/get_deseq_dataset.R' > /dev/null &&
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37
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38 #import json
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39 #import os
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40 Rscript '${__tool_directory__}/deseq2.R'
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41 --cores \${GALAXY_SLOTS:-1}
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42 -o '$deseq_out'
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43 #if 'pdf' in $output_options.output_selector:
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44 -p '$plots'
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45 #end if
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46 -A $output_options.alpha_ma
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47 #if 'normCounts' in $output_options.output_selector:
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48 -n '$counts_out'
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49 #end if
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50 #if 'sizefactors' in $output_options.output_selector:
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51 -F '$sizefactors_out'
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52 #end if
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53 #if 'normRLog' in $output_options.output_selector:
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54 -r '$rlog_out'
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55 #end if
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56 #if 'normVST' in $output_options.output_selector:
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57 -v '$vst_out'
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58 #end if
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59 #set $filename_to_element_identifiers = {}
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60 #set $temp_factor_names = list()
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61 #for $factor in $select_data.rep_factorName:
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62 #set $temp_factor = list()
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63 #for $level in $factor.rep_factorLevel:
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64 #set $count_files = list()
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65 #if $select_data.how == 'group_tags':
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66 #for $group in $level.groups.value:
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67 #for $file in $select_data.countsFile.get_datasets_for_group($group):
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68 $count_files.append(str($file))
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69 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier)
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70 #end for
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71 #end for
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72 #else:
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73 #for $file in $level.countsFile:
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74 $count_files.append(str($file))
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75 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier)
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76 #end for
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77 #end if
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78 $temp_factor.append( {str($level.factorLevel): $count_files} )
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79 #end for
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80 $temp_factor.reverse()
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81 $temp_factor_names.append([str($factor.factorName), $temp_factor])
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82 #end for
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83
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84 $header
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85
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86 -f '#echo json.dumps(temp_factor_names)#'
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87 -l '#echo json.dumps(filename_to_element_identifiers)#'
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88 #if $advanced_options.esf:
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89 -e $advanced_options.esf
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90 #end if
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91 -t $advanced_options.fit_type
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92 #if $batch_factors:
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93 --batch_factors '$batch_factors'
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94 #end if
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95 #if $advanced_options.prefilter_conditional.prefilter:
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96 $advanced_options.prefilter_conditional.prefilter
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97 -V $advanced_options.prefilter_conditional.prefilter_value
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98 #end if
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99 #if $advanced_options.outlier_replace_off:
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100 -a
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101 #end if
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102 #if $advanced_options.outlier_filter_off:
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103 -b
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104 #end if
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105 #if $advanced_options.auto_mean_filter_off:
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106 -c
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107 #end if
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108 #if 'many_contrasts' in $output_options.output_selector
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109 -m
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110 #end if
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111 #if $tximport.tximport_selector == 'tximport':
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112 -i
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113 -y $tximport.txtype
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114 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
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115 -x mapping.gff
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116 #else:
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117 -x mapping.txt
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118 #end if
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119
23
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120 #end if
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121 ]]></command>
0
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122 <inputs>
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123 <conditional name="select_data">
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124 <param name="how" type="select">
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125 <option value="datasets_per_level">Select datasets per level</option>
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126 <option value="group_tags">Select group tags corresponding to levels</option>
0
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127 </param>
34
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128 <when value="group_tags">
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129 <param name="countsFile" type="data_collection" format="tabular" label="Count file(s) collection" multiple="true"/>
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130 <expand macro="factor_repeat">
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131 <param name="groups" type="group_tag" data_ref="countsFile" multiple="true" label="Select groups that correspond to this factor level"/>
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132 </expand>
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133 </when>
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134 <when value="datasets_per_level">
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135 <expand macro="factor_repeat">
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136 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
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137 </expand>
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138 </when>
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139 </conditional>
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140
29
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141 <param name="batch_factors" type="data" format="tabular" optional="true" label="(Optional) provide a tabular file with additional batch factors to include in the model." help="You can produce this file using RUVSeq or svaseq."/>
27
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142 <param name="header" type="boolean" truevalue="-H" falsevalue="" checked="true" label="Files have header?" help="If this option is set to Yes, the tool will assume that the count files have column headers in the first row. Default: Yes" />
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143
17
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144 <conditional name="tximport">
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145 <param name="tximport_selector" type="select" label="Choice of Input data">
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146 <option value="count" selected="True">Count data (e.g. from HTSeq-count, featureCounts or StringTie)</option>
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147 <option value="tximport">TPM values (e.g. from kallisto, sailfish or salmon)</option>
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148 </param>
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149 <when value="tximport">
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150 <param name="txtype" type="select" label="Program used to generate TPMs">
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151 <option value="kallisto">kallisto</option>
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152 <option value="sailfish">Sailfish</option>
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153 <option value="salmon">Salmon</option>
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154 </param>
17
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155 <conditional name="mapping_format">
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156 <param name="mapping_format_selector" type="select" label="Gene mapping format">
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157 <option value="gtf" selected="True">GTF/GFF3</option>
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158 <option value="tabular">Transcript-ID to Gene-ID mapping file</option>
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159 </param>
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160 <when value="gtf">
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161 <param name="gtf_file" type="data" format="gtf,gff3" label="GTF/GFF3 annotation file"/>
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162 </when>
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163 <when value="tabular">
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164 <param name="tabular_file" type="data" format="tabular" label="Tabular file with Transcript-ID to Gene-ID mapping"/>
17
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165 </when>
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166 </conditional>
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167 </when>
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168 <when value="count" />
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169 </conditional>
39
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170 <section name="advanced_options" title="Advanced options">
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171 <param name="esf" type="select" label="Method for estimateSizeFactors"
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172 help="Method for estimation: either 'ratio', 'poscounts', or 'iterate'. 'ratio' uses the standard median ratio method introduced in DESeq.
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173 The size factor is the median ratio of the sample over a 'pseudosample': for each gene, the geometric mean of all samples.
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174 'poscounts' and 'iterate' offer alternative estimators, which can be used even when all genes contain a sample with a zero (a problem
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175 for the default method, as the geometric mean becomes zero, and the ratio undefined). The 'poscounts' estimator deals with a gene with
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176 some zeros, by calculating a modified geometric mean by taking the n-th root of the product of the non-zero counts. This evolved out of
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177 use cases with Paul McMurdie's phyloseq package for metagenomic samples. The 'iterate' estimator iterates between estimating the dispersion
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178 with a design of ~1, and finding a size factor vector by numerically optimizing the likelihood of the ~1 model.">
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179 <option value="" selected="true">No Selection (use default)</option>
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180 <option value="ratio">ratio</option>
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181 <option value="poscounts">poscounts</option>
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182 <option value="iterate">iterate</option>
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183 </param>
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184 <param name="fit_type" type="select" label="Fit type">
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185 <option value="1" selected="true">parametric</option>
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186 <option value="2">local</option>
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187 <option value="3">mean</option>
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188 </param>
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189 <param name="outlier_replace_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
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190 label="Turn off outliers replacement (only affects with >6 replicates)"
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191 help="When there are more than 6 replicates for a given sample, the DESeq2 will automatically replace
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192 counts with large Cook’s distance with the trimmed mean over all samples, scaled up by the size factor
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193 or normalization factor for that sample" />
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194 <param name="outlier_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
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195 label="Turn off outliers filtering (only affects with >2 replicates)"
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196 help="When there are more than 2 replicates for a given sample, the DESeq2 will automatically
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197 filter genes which contain a Cook’s distance above a cutoff" />
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198 <param name="auto_mean_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false"
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199 label="Turn off independent filtering"
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200 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" />
42
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201 <conditional name="prefilter_conditional">
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202 <param name="prefilter" type="select" label="Perform pre-filtering" help="While it is not necessary to pre-filter
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203 low count genes before running the DESeq2 functions, there are two reasons which make pre-filtering useful:
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204 by removing rows in which there are very few reads, we reduce the required memory, and we increase the speed.
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205 It can also improve visualizations, as features with no information for differential expression are not plotted.">
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206 <option value="-P">Enabled</option>
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207 <option value="" selected="true">Disabled</option>
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208 </param>
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209 <when value="-P">
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210 <param name="prefilter_value" type="integer" min="0" value="10" label="Pre-filter value" help="Keep only rows that have at least N reads total." />
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211 </when>
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212 <when value=""/>
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213 </conditional>
39
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214 </section>
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215 <section name="output_options" title="Output options">
40
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216 <param name="output_selector" type="select" multiple="True" optional="true" display="checkboxes" label="Output selector">
39
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217 <option value="pdf" selected="True">Generate plots for visualizing the analysis results</option>
41
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218 <option value="sizefactors" >Output sample size factors</option>
40
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219 <option value="normCounts">Output normalised counts</option>
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220 <option value="normVST">Output VST normalized table</option>
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221 <option value="normRLog">Output rLog normalized table</option>
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222 <option value="many_contrasts">Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)</option>
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223 </param>
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224 <param name="alpha_ma" type="float" min="0" max="0.5" value="0.1" label="Alpha value for MA-plot" help="Default value is 0.1. This option is only meaninful when plots are generated" />
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225 </section>
0
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226 </inputs>
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227 <outputs>
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228 <data name="deseq_out" format="tabular" label="DESeq2 result file on ${on_string}">
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229 <filter>'many_contrasts' not in output_options['output_selector']</filter>
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230 <actions>
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231 <action name="column_names" type="metadata" default="GeneID,Base mean,log2(FC),StdErr,Wald-Stats,P-value,P-adj" />
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232 </actions>
0
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233 </data>
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234 <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}">
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235 <filter>output_options['output_selector'] and 'many_contrasts' in output_options['output_selector']</filter>
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236 <discover_datasets pattern="(?P&lt;designation&gt;.+_vs_.+)" format="tabular" directory="." visible="false"/>
0
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237 </collection>
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238 <data name="plots" format="pdf" label="DESeq2 plots on ${on_string}">
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239 <filter>output_options['output_selector'] and 'pdf' in output_options['output_selector']</filter>
0
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240 </data>
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241 <data name="sizefactors_out" format="tabular" label="Size Factors on ${on_string}">
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242 <filter>output_options['output_selector'] and 'sizefactors' in output_options['output_selector']</filter>
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243 </data>
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244 <data name="counts_out" format="tabular" label="Normalized counts file on ${on_string}">
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245 <filter>output_options['output_selector'] and 'normCounts' in output_options['output_selector']</filter>
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246 </data>
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247 <data name="rlog_out" format="tabular" label="rLog-Normalized counts file on ${on_string}">
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248 <filter>output_options['output_selector'] and 'normRLog' in output_options['output_selector']</filter>
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249 </data>
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250 <data name="vst_out" format="tabular" label="VST-Normalized counts file on ${on_string}">
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251 <filter>output_options['output_selector'] and 'normVST' in output_options['output_selector']</filter>
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252 </data>
0
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253 </outputs>
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diff changeset
254 <tests>
27
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255 <!--Ensure counts files with header works -->
30
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256 <test expect_num_outputs="4">
0
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257 <repeat name="rep_factorName">
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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258 <param name="factorName" value="Treatment"/>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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259 <repeat name="rep_factorLevel">
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
260 <param name="factorLevel" value="Treated"/>
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iuc
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261 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
262 </repeat>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
263 <repeat name="rep_factorLevel">
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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264 <param name="factorLevel" value="Untreated"/>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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265 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
266 </repeat>
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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267 </repeat>
39
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268 <section name="output_options">
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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269 <param name="output_selector" value="normCounts,normRLog,normVST"/>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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270 </section>
27
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271 <output name="counts_out">
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272 <assert_contents>
28
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273 <has_text_matching expression="GSM461176_untreat_single.counts\tGSM461177_untreat_paired.counts\tGSM461178_untreat_paired.counts\tGSM461182_untreat_single.counts\tGSM461179_treat_single.counts\tGSM461180_treat_paired.counts\tGSM461181_treat_paired.counts" />
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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diff changeset
274 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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275 </assert_contents>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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276 </output>
30
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iuc
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diff changeset
277 <output name="rlog_out">
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
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diff changeset
278 <assert_contents>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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diff changeset
279 <has_text_matching expression="GSM461176_untreat_single.counts\tGSM461177_untreat_paired.counts\tGSM461178_untreat_paired.counts\tGSM461182_untreat_single.counts\tGSM461179_treat_single.counts\tGSM461180_treat_paired.counts\tGSM461181_treat_paired.counts" />
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
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diff changeset
280 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
281 </assert_contents>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
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diff changeset
282 </output>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
283 <output name="vst_out">
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
284 <assert_contents>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
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diff changeset
285 <has_text_matching expression="GSM461176_untreat_single.counts\tGSM461177_untreat_paired.counts\tGSM461178_untreat_paired.counts\tGSM461182_untreat_single.counts\tGSM461179_treat_single.counts\tGSM461180_treat_paired.counts\tGSM461181_treat_paired.counts" />
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
286 <has_text_matching expression="FBgn0000003\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*" />
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
287 </assert_contents>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
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diff changeset
288 </output>
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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diff changeset
289 <output name="deseq_out" >
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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diff changeset
290 <assert_contents>
31
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 30
diff changeset
291 <has_text_matching expression="FBgn0003360\t1933\.9504.*\t-2\.8399.*\t0\.1309.*\t-21\.68.*\t.*e-104\t.*e-101" />
42
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
292 <has_n_lines n="3999"/>
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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diff changeset
293 </assert_contents>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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diff changeset
294 </output>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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diff changeset
295 </test>
29
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iuc
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diff changeset
296 <!--Ensure additional batch factor correction works -->
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
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diff changeset
297 <test expect_num_outputs="2">
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
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diff changeset
298 <repeat name="rep_factorName">
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 28
diff changeset
299 <param name="factorName" value="Treatment"/>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 28
diff changeset
300 <repeat name="rep_factorLevel">
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 28
diff changeset
301 <param name="factorLevel" value="Treated"/>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
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diff changeset
302 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 28
diff changeset
303 </repeat>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 28
diff changeset
304 <repeat name="rep_factorLevel">
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 28
diff changeset
305 <param name="factorLevel" value="Untreated"/>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
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diff changeset
306 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 28
diff changeset
307 </repeat>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 28
diff changeset
308 </repeat>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
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diff changeset
309 <param name="batch_factors" value="batch_factors.tab"/>
39
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
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diff changeset
310 <section name="output_options">
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
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diff changeset
311 <param name="output_selector" value="normCounts"/>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
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diff changeset
312 </section>
29
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diff changeset
313 <output name="deseq_out">
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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diff changeset
314 <assert_contents>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
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diff changeset
315 <has_text_matching expression="FBgn0003360\t1933.*\t-2.9.*\t0.1.*\t-26.*\t1.*-152\t4.*-149" />
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 28
diff changeset
316 </assert_contents>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
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diff changeset
317 </output>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
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diff changeset
318 </test>
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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diff changeset
319 <!--Ensure counts files without header works -->
30
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
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diff changeset
320 <test expect_num_outputs="4">
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
321 <repeat name="rep_factorName">
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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diff changeset
322 <param name="factorName" value="Treatment"/>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
323 <repeat name="rep_factorLevel">
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
324 <param name="factorLevel" value="Treated"/>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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diff changeset
325 <param name="countsFile" value="GSM461179_treat_single.counts.noheader,GSM461180_treat_paired.counts.noheader,GSM461181_treat_paired.counts.noheader"/>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
326 </repeat>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
327 <repeat name="rep_factorLevel">
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
328 <param name="factorLevel" value="Untreated"/>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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diff changeset
329 <param name="countsFile" value="GSM461176_untreat_single.counts.noheader,GSM461177_untreat_paired.counts.noheader,GSM461178_untreat_paired.counts.noheader,GSM461182_untreat_single.counts.noheader"/>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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diff changeset
330 </repeat>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
331 </repeat>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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diff changeset
332 <param name="header" value="False"/>
39
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iuc
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diff changeset
333 <section name="output_options">
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
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diff changeset
334 <param name="output_selector" value="normCounts,normRLog,normVST"/>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
335 </section>
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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diff changeset
336 <output name="counts_out">
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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diff changeset
337 <assert_contents>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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338 <has_text_matching expression="GSM461176_untreat_single.counts.noheader\tGSM461177_untreat_paired.counts.noheader\tGSM461178_untreat_paired.counts.noheader\tGSM461182_untreat_single.counts.noheader\tGSM461179_treat_single.counts.noheader\tGSM461180_treat_paired.counts.noheader\tGSM461181_treat_paired.counts.noheader" />
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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diff changeset
339 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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340 </assert_contents>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
341 </output>
30
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
342 <output name="rlog_out">
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
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343 <assert_contents>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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diff changeset
344 <has_text_matching expression="GSM461176_untreat_single.counts.noheader\tGSM461177_untreat_paired.counts.noheader\tGSM461178_untreat_paired.counts.noheader\tGSM461182_untreat_single.counts.noheader\tGSM461179_treat_single.counts.noheader\tGSM461180_treat_paired.counts.noheader\tGSM461181_treat_paired.counts.noheader" />
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
345 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0" />
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
346 </assert_contents>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
347 </output>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
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348 <output name="vst_out">
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
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diff changeset
349 <assert_contents>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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diff changeset
350 <has_text_matching expression="GSM461176_untreat_single.counts.noheader\tGSM461177_untreat_paired.counts.noheader\tGSM461178_untreat_paired.counts.noheader\tGSM461182_untreat_single.counts.noheader\tGSM461179_treat_single.counts.noheader\tGSM461180_treat_paired.counts.noheader\tGSM461181_treat_paired.counts.noheader" />
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
351 <has_text_matching expression="FBgn0000003\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*" />
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
352 </assert_contents>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
353 </output>
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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diff changeset
354 <output name="deseq_out" >
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
355 <assert_contents>
31
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iuc
parents: 30
diff changeset
356 <has_text_matching expression="FBgn0003360\t1933\.9504.*\t-2\.8399.*\t0\.1309.*\t-21\.68.*\t.*e-104\t.*e-101" />
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
357 </assert_contents>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
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diff changeset
358 </output>
17
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iuc
parents: 16
diff changeset
359 </test>
23
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parents: 22
diff changeset
360 <!--Ensure Sailfish/Salmon input with tx2gene table works-->
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
361 <test expect_num_outputs="1">
17
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iuc
parents: 16
diff changeset
362 <repeat name="rep_factorName">
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents: 16
diff changeset
363 <param name="factorName" value="Treatment"/>
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents: 16
diff changeset
364 <repeat name="rep_factorLevel">
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents: 16
diff changeset
365 <param name="factorLevel" value="Treated"/>
23
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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parents: 22
diff changeset
366 <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/>
17
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents: 16
diff changeset
367 </repeat>
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents: 16
diff changeset
368 <repeat name="rep_factorLevel">
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
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diff changeset
369 <param name="factorLevel" value="Untreated"/>
23
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
370 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/>
17
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents: 16
diff changeset
371 </repeat>
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents: 16
diff changeset
372 </repeat>
39
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iuc
parents: 38
diff changeset
373 <section name="output_options">
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
374 <param name="output_selector" value=""/>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
375 </section>
17
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diff changeset
376 <param name="tximport_selector" value="tximport"/>
23
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
377 <param name="txtype" value="sailfish"/>
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
378 <param name="mapping_format_selector" value="tabular"/>
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
379 <param name="tabular_file" value="tx2gene.tab"/>
27
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iuc
parents: 26
diff changeset
380 <output name="deseq_out" >
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
381 <assert_contents>
31
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iuc
parents: 30
diff changeset
382 <has_text_matching expression="UGT3A2\t1.8841.*\t-0.1329.*\t0.6936.*\t-0.1917.*\t0.8479.*\t0.9999.*" />
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 30
diff changeset
383 </assert_contents>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 30
diff changeset
384 </output>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
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diff changeset
385 </test>
32
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diff changeset
386 <!--Ensure Sailfish/Salmon input with GFF3 annotation from NCBI works-->
31
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iuc
parents: 30
diff changeset
387 <test expect_num_outputs="1">
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 30
diff changeset
388 <repeat name="rep_factorName">
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 30
diff changeset
389 <param name="factorName" value="Treatment"/>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 30
diff changeset
390 <repeat name="rep_factorLevel">
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 30
diff changeset
391 <param name="factorLevel" value="Treated"/>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 30
diff changeset
392 <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 30
diff changeset
393 </repeat>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 30
diff changeset
394 <repeat name="rep_factorLevel">
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 30
diff changeset
395 <param name="factorLevel" value="Untreated"/>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 30
diff changeset
396 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 30
diff changeset
397 </repeat>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 30
diff changeset
398 </repeat>
39
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iuc
parents: 38
diff changeset
399 <section name="output_options">
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
400 <param name="output_selector" value=""/>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
401 </section>
31
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 30
diff changeset
402 <param name="tximport_selector" value="tximport"/>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 30
diff changeset
403 <param name="txtype" value="sailfish"/>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 30
diff changeset
404 <param name="mapping_format_selector" value="gtf"/>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 30
diff changeset
405 <param name="gtf_file" value="GRCh38_latest_genomic.gff"/>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 30
diff changeset
406 <output name="deseq_out" >
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 30
diff changeset
407 <assert_contents>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 30
diff changeset
408 <has_text_matching expression="UGT3A2\t1.8841.*\t-0.1329.*\t0.6936.*\t-0.1917.*\t0.8479.*\t0.9999.*" />
27
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iuc
parents: 26
diff changeset
409 </assert_contents>
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iuc
parents: 26
diff changeset
410 </output>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
411 </test>
32
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parents: 31
diff changeset
412 <!--Ensure Sailfish/Salmon input with GTF annotation from Ensembl works-->
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
413 <test expect_num_outputs="1">
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
414 <repeat name="rep_factorName">
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
415 <param name="factorName" value="Treatment"/>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
416 <repeat name="rep_factorLevel">
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
417 <param name="factorLevel" value="Treated"/>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
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parents: 31
diff changeset
418 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
419 </repeat>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
420 <repeat name="rep_factorLevel">
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
421 <param name="factorLevel" value="Untreated"/>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
422 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
423 </repeat>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
424 </repeat>
39
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
425 <section name="output_options">
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
426 <param name="output_selector" value=""/>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
427 </section>
32
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
428 <param name="tximport_selector" value="tximport"/>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
429 <param name="txtype" value="sailfish"/>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
430 <param name="mapping_format_selector" value="gtf"/>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
431 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
432 <output name="deseq_out" >
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
433 <assert_contents>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
434 <has_text_matching expression="ENSG00000168671\t1.8841.*\t-0.1180.*\t0.7429.*\t-0.1589.*\t0.8737.*\t0.9999.*" />
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
435 </assert_contents>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
436 </output>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
437 </test>
34
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
438 <!--Ensure group tags can be used to select factor levels -->
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
439 <test expect_num_outputs="1">
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
440 <param name="select_data|how" value="group_tags"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
441 <param name="select_data|countsFile">
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
442 <collection type="list">
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
443 <element name="1" value="sailfish/sailfish_quant.sf1.tab" tags="group:primary:treated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
444 <element name="2" value="sailfish/sailfish_quant.sf2.tab" tags="group:primary:treated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
445 <element name="3" value="sailfish/sailfish_quant.sf3.tab" tags="group:primary:treated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
446 <element name="4" value="sailfish/sailfish_quant.sf4.tab" tags="group:primary:untreated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
447 <element name="5" value="sailfish/sailfish_quant.sf5.tab" tags="group:primary:untreated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
448 <element name="6" value="sailfish/sailfish_quant.sf6.tab" tags="group:primary:untreated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
449 </collection>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
450 </param>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
451 <repeat name="rep_factorName">
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
452 <param name="factorName" value="Treatment"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
453 <repeat name="rep_factorLevel">
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
454 <param name="factorLevel" value="Treated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
455 <param name="groups" value="primary:treated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
456 </repeat>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
457 <repeat name="rep_factorLevel">
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
458 <param name="factorLevel" value="Untreated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
459 <param name="groups" value="primary:untreated"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
460 </repeat>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
461 </repeat>
39
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
462 <section name="output_options">
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
463 <param name="output_selector" value=""/>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
464 </section>
34
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
465 <param name="tximport_selector" value="tximport"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
466 <param name="txtype" value="sailfish"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
467 <param name="mapping_format_selector" value="tabular"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
468 <param name="tabular_file" value="tx2gene.tab"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
469 <output name="deseq_out" >
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
470 <assert_contents>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
471 <has_text_matching expression="HOXC11\t0.557.*\t0.324.*\t0.437.*\t0.741.*\t0.458.*\t0.999.*"/>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
472 </assert_contents>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
473 </output>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
474 </test>
36
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
475 <!--Ensure many_contrasts produces output collection -->
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
476 <test expect_num_outputs="1">
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
477 <param name="select_data|how" value="group_tags"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
478 <param name="select_data|countsFile">
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
479 <collection type="list">
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
480 <element name="1" value="sailfish/sailfish_quant.sf1.tab" tags="group:primary:treated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
481 <element name="2" value="sailfish/sailfish_quant.sf2.tab" tags="group:primary:treated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
482 <element name="3" value="sailfish/sailfish_quant.sf3.tab" tags="group:primary:treated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
483 <element name="4" value="sailfish/sailfish_quant.sf4.tab" tags="group:primary:untreated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
484 <element name="5" value="sailfish/sailfish_quant.sf5.tab" tags="group:primary:untreated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
485 <element name="6" value="sailfish/sailfish_quant.sf6.tab" tags="group:primary:untreated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
486 </collection>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
487 </param>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
488 <repeat name="rep_factorName">
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
489 <param name="factorName" value="Treatment"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
490 <repeat name="rep_factorLevel">
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
491 <param name="factorLevel" value="Treated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
492 <param name="groups" value="primary:treated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
493 </repeat>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
494 <repeat name="rep_factorLevel">
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
495 <param name="factorLevel" value="Untreated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
496 <param name="groups" value="primary:untreated"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
497 </repeat>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
498 </repeat>
39
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
499 <section name="output_options">
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
500 <param name="output_selector" value="many_contrasts"/>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
501 </section>
36
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
502 <param name="tximport_selector" value="tximport"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
503 <param name="txtype" value="sailfish"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
504 <param name="mapping_format_selector" value="tabular"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
505 <param name="tabular_file" value="tx2gene.tab"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
506 <output_collection name="split_output" type="list" count="1">
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
507 <element name="Treatment_Treated_vs_Untreated">
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
508 <assert_contents>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
509 <has_text_matching expression="HOXC11\t0.557.*\t0.324.*\t0.437.*\t0.741.*\t0.458.*\t0.999.*"/>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
510 </assert_contents>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
511 </element>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
512 </output_collection>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
513 </test>
39
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
514 <!--Test alpha_ma option-->
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
515 <test expect_num_outputs="1">
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
516 <repeat name="rep_factorName">
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
517 <param name="factorName" value="Treatment"/>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
518 <repeat name="rep_factorLevel">
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
519 <param name="factorLevel" value="Treated"/>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
520 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
521 </repeat>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
522 <repeat name="rep_factorLevel">
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
523 <param name="factorLevel" value="Untreated"/>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
524 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
525 </repeat>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
526 </repeat>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
527 <section name="output_options">
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
528 <param name="output_selector" value=""/>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
529 <param name="alpha_ma" value="0.05"/>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
530 </section>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
531 <param name="tximport_selector" value="tximport"/>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
532 <param name="txtype" value="sailfish"/>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
533 <param name="mapping_format_selector" value="gtf"/>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
534 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
535 <output name="deseq_out" >
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
536 <assert_contents>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
537 <has_text_matching expression="ENSG00000168671\t1.8841.*\t-0.1180.*\t0.7429.*\t-0.1589.*\t0.8737.*\t0.9999.*" />
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
538 </assert_contents>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
539 </output>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
540 </test>
41
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
541 <!-- Same as above alpha_ma test, but with size factors -->
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
542 <test expect_num_outputs="2">
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
543 <repeat name="rep_factorName">
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
544 <param name="factorName" value="Treatment"/>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
545 <repeat name="rep_factorLevel">
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
546 <param name="factorLevel" value="Treated"/>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
547 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
548 </repeat>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
549 <repeat name="rep_factorLevel">
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
550 <param name="factorLevel" value="Untreated"/>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
551 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
552 </repeat>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
553 </repeat>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
554 <section name="output_options">
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
555 <param name="output_selector" value="sizefactors"/>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
556 <param name="alpha_ma" value="0.05"/>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
557 </section>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
558 <param name="tximport_selector" value="tximport"/>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
559 <param name="txtype" value="sailfish"/>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
560 <param name="mapping_format_selector" value="gtf"/>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
561 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
562 <output name="sizefactors_out">
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
563 <assert_contents>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
564 <has_text_matching expression="sailfish_quant\.sf4\.tab\t0\.8\d+" />
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
565 <has_text_matching expression="sailfish_quant\.sf3\.tab\t1\.0\d+" />
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
566 </assert_contents>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
567 </output>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
568 </test>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
569 <!-- Same as above alpha_ma size factor test, but with a non-default estimator-->
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
570 <test expect_num_outputs="2">
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
571 <repeat name="rep_factorName">
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
572 <param name="factorName" value="Treatment"/>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
573 <repeat name="rep_factorLevel">
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
574 <param name="factorLevel" value="Treated"/>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
575 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
576 </repeat>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
577 <repeat name="rep_factorLevel">
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
578 <param name="factorLevel" value="Untreated"/>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
579 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
580 </repeat>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
581 </repeat>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
582 <section name="advanced_options">
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
583 <param name="esf" value="poscounts" />
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
584 </section>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
585 <section name="output_options">
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
586 <param name="output_selector" value="sizefactors"/>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
587 <param name="alpha_ma" value="0.05"/>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
588 </section>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
589 <param name="tximport_selector" value="tximport"/>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
590 <param name="txtype" value="sailfish"/>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
591 <param name="mapping_format_selector" value="gtf"/>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
592 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
593 <output name="sizefactors_out" >
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
594 <assert_contents>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
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diff changeset
595 <has_text_matching expression="sailfish_quant\.sf4\.tab\t0\.8\d+" />
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
596 <has_text_matching expression="sailfish_quant\.sf3\.tab\t1\.0\d+" />
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
597 </assert_contents>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
598 </output>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
599 </test>
42
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diff changeset
600 <!--Test prefilter parameter -->
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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601 <test expect_num_outputs="2">
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
602 <repeat name="rep_factorName">
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
603 <param name="factorName" value="Treatment"/>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
604 <repeat name="rep_factorLevel">
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
605 <param name="factorLevel" value="Treated"/>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
606 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
607 </repeat>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
608 <repeat name="rep_factorLevel">
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
609 <param name="factorLevel" value="Untreated"/>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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610 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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parents: 41
diff changeset
611 </repeat>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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612 </repeat>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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parents: 41
diff changeset
613 <section name="advanced_options">
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
614 <conditional name="prefilter_conditional">
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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parents: 41
diff changeset
615 <param name="prefilter" value="-P"/>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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616 <param name="prefilter_value" value="10"/>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
617 </conditional>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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618 </section>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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parents: 41
diff changeset
619 <section name="output_options">
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
620 <param name="output_selector" value="normCounts"/>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
621 </section>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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622 <output name="counts_out">
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
623 <assert_contents>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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624 <has_n_lines n="2922"/>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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625 </assert_contents>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
626 </output>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
627 <output name="deseq_out" >
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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628 <assert_contents>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
629 <has_n_lines n="2921"/> <!-- Smallen value when compared with the first test-->
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
630 </assert_contents>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
631 </output>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
632 </test>
0
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633 </tests>
23
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diff changeset
634 <help><![CDATA[
0
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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635 .. class:: infomark
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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636
15
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637 **What it does**
0
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638
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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639 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
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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640
23
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641 -----
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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642
0
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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643 **Inputs**
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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644
23
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645 **Count Files**
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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646
27
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647 DESeq2_ takes count tables generated from **featureCounts**, **HTSeq-count** or **StringTie** as input. Count tables must be generated for each sample individually. One header row is assumed, but files with no header (e.g from HTSeq) can be input with the *Files have header?* option set to No. DESeq2 is capable of handling multiple factors that affect your experiment. The first factor you input is considered as the primary factor that affects gene expressions. Optionally, you can input one or more secondary factors that might influence your experiment. But the final output will be changes in genes due to primary factor in presence of secondary factors. Each factor has two levels/states. You need to select appropriate count table from your history for each factor level.
0
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648
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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649 The following table gives some examples of factors and their levels:
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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650
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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651 ========= ============== ===============
15
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652 Factor Factor level 1 Factor level 2
0
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653 --------- -------------- ---------------
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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654 Treatment Treated Untreated
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655 --------- -------------- ---------------
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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656 Condition Knockdown Wildtype
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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657 --------- -------------- ---------------
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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658 TimePoint Day4 Day1
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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659 --------- -------------- ---------------
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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660 SeqType SingleEnd PairedEnd
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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661 --------- -------------- ---------------
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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662 Gender Female Male
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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663 ========= ============== ===============
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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664
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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665 *Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level2. Here the order of factor levels is important. For example, for the factor 'Treatment' given in above table, DESeq2 computes fold changes of 'Treated' samples against 'Untreated', i.e. the values correspond to up or down regulations of genes in Treated samples.
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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666
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667 DESeq2_ can also take transcript-level counts from quantification tools such as, **kallisto**, **Salmon** and **Sailfish**, and this Galaxy wrapper incorporates the Bioconductor tximport_ package to process the transcript counts for DESeq2.
23
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diff changeset
668
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diff changeset
669 **Salmon or Sailfish Files**
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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diff changeset
670
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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671 Salmon or Sailfish ``quant.sf`` files can be imported by setting type to *Salmon* or *Sailfish* respectively above. Note: for previous version of Salmon or Sailfish, in which the quant.sf files start with comment lines you will need to remove the comment lines before inputting here. An example of the format is shown below.
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
672
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
673 Example:
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
674
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
675 ============ ========== =============== =========== ===========
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
676 Name Length EffectiveLength TPM NumReads
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
677 ------------ ---------- --------------- ----------- -----------
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
678 NR_001526 164 20.4518 0 0
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
679 NR_001526_1 164 20.4518 0 0
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
680 NR_001526_2 164 20.4518 0 0
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
681 NM_130786 1764 1956.04 2.47415 109.165
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
682 NR_015380 2129 2139.53 1.77331 85.5821
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
683 NM_001198818 9360 7796.58 2.38616e-07 4.19648e-05
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
684 NM_001198819 9527 7964.62 0 0
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
685 NM_001198820 9410 7855.78 0 0
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
686 NM_014576 9267 7714.88 0.0481114 8.37255
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
687 ============ ========== =============== =========== ===========
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
688
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
689 **kallisto Files**
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
690
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
691 kallisto ``abundance.tsv`` files can be imported by setting type to *kallisto* above. An example of the format is shown below.
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
692
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
693 Example:
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
694
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
695 ============ ========== =============== =========== ===========
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
696 target_id length eff_length est_counts tpm
23
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
697 ------------ ---------- --------------- ----------- -----------
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
698 NR_001526 164 20.4518 0 0
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
699 NR_001526_1 164 20.4518 0 0
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
700 NR_001526_2 164 20.4518 0 0
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
701 NM_130786 1764 1956.04 109.165 2.47415
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
702 NR_015380 2129 2139.53 85.5821 1.77331
23
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
703 NM_001198818 9360 7796.58 4.19648e-05 2.38616e-07
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
704 NM_001198819 9527 7964.62 0 0
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
705 NM_001198820 9410 7855.78 0 0
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
706 NM_014576 9267 7714.88 8.37255 0.0481114
23
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
707 ============ ========== =============== =========== ===========
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
708
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
709 -----
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
710
0
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff changeset
711 **Output**
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff changeset
712
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff changeset
713 DESeq2_ generates a tabular file containing the different columns and optional visualized results as PDF.
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff changeset
714
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff changeset
715 ====== ==========================================================
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff changeset
716 Column Description
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff changeset
717 ------ ----------------------------------------------------------
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff changeset
718 1 Gene Identifiers
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff changeset
719 2 mean normalised counts, averaged over all samples from both conditions
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff changeset
720 3 the logarithm (to basis 2) of the fold change (See the note in inputs section)
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff changeset
721 4 standard error estimate for the log2 fold change estimate
13
00ff49f9e750 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1c0a208ea184713d5b38c5575861ecf6ce7decdd
iuc
parents: 12
diff changeset
722 5 Wald statistic
00ff49f9e750 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1c0a208ea184713d5b38c5575861ecf6ce7decdd
iuc
parents: 12
diff changeset
723 6 p value for the statistical significance of this change
00ff49f9e750 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1c0a208ea184713d5b38c5575861ecf6ce7decdd
iuc
parents: 12
diff changeset
724 7 p value adjusted for multiple testing with the Benjamini-Hochberg procedure
0
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff changeset
725 which controls false discovery rate (FDR)
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff changeset
726 ====== ==========================================================
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff changeset
727
41
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
728 By selecting ``Output sample size factors`` in the "Output options"
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
729 selection box, the size factors used to normalize the samples can also
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
730 be output as a tabular file.
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
731
0
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff changeset
732 .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html
23
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
733 .. _tximport: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
734 ]]></help>
39
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
735 <expand macro="citations" />
0
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff changeset
736 </tool>