Mercurial > repos > iuc > deseq2

annotate deseq2.xml @ 44:1cb33de18af5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
author iuc
date Tue, 09 Dec 2025 17:43:58 +0000
parents 621ddf5967d2
children 702bdf59d6c8
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1 <tool id="deseq2" name="DESeq2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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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>macros.xml</import>
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5 </macros>
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6 <expand macro='edam_ontology'/>
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7 <expand macro='xrefs'/>
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8 <expand macro='requirements'/>
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9 <stdio>
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10 <exit_code range="1:" level="fatal" />
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11 <regex match="Execution halted"
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12 source="both"
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13 level="fatal"
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14 description="Execution halted."/>
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15 <regex match="Error in"
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16 source="both"
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17 level="fatal"
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18 description="An undefined error occurred, please check your input carefully and contact your administrator."/>
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19 <regex match="Fatal error"
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20 source="both"
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21 level="fatal"
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22 description="An undefined error occurred, please check your input carefully and contact your administrator."/>
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23 </stdio>
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24 <version_command><![CDATA[
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25 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: ")
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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26 ]]></version_command>
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27 <command><![CDATA[
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28 #if $tximport.tximport_selector == 'tximport':
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29 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
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30 ln -s '$tximport.mapping_format.gtf_file' mapping.gff &&
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31 #else:
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32 ln -s '$tximport.mapping_format.tabular_file' mapping.txt &&
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33 #end if
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34 #end if
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35
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36 ## This is needed for Pulsar to transfer the file
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37 cat '$__tool_directory__/get_deseq_dataset.R' > /dev/null &&
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38
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39 #import json
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40 #import os
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41 Rscript '${__tool_directory__}/deseq2.R'
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42 --cores \${GALAXY_SLOTS:-1}
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43 -o '$deseq_out'
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44 #if 'pdf' in $output_options.output_selector:
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45 -p '$plots'
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46 #end if
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47 -A $output_options.alpha_ma
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48 #if 'normCounts' in $output_options.output_selector:
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49 -n '$counts_out'
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50 #end if
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51 #if 'sizefactors' in $output_options.output_selector:
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52 -F '$sizefactors_out'
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53 #end if
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54 #if 'normRLog' in $output_options.output_selector:
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55 -r '$rlog_out'
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56 #end if
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57 #if 'normVST' in $output_options.output_selector:
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58 -v '$vst_out'
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59 #end if
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60 #set $filename_to_element_identifiers = {}
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61 #set $temp_factor_names = list()
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62 #if $select_data.how == 'sample_sheet_contrasts':
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63 ## Pass collection file paths and element identifiers for sample sheet mode
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64 #set $count_files = list()
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65 #for $file in $select_data.countsFile:
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66 $count_files.append(str($file))
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67 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier)
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68 #end for
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69 --sample_sheet_mode
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70 --sample_sheet '$select_data.sample_sheet'
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71 --collection_files '#echo ",".join($count_files)#'
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72 #if $select_data.design_formula_mode.mode == 'custom':
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73 --custom_design_formula
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74 --design_formula '$select_data.design_formula_mode.design_formula'
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75 #else:
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76 --factor_columns '$select_data.design_formula_mode.factor'
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77 #end if
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78 #if str($select_data.design_formula_mode.reference_level).strip():
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79 --reference_level '${select_data.design_formula_mode.reference_level.strip()}'
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80 #end if
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81 #if str($select_data.design_formula_mode.target_level).strip():
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82 --target_level '${select_data.design_formula_mode.target_level.strip()}'
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83 #end if
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84 #else:
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85 #for $factor in $select_data.rep_factorName:
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86 #set $temp_factor = list()
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87 #for $level in $factor.rep_factorLevel:
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88 #set $count_files = list()
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89 #if $select_data.how == 'group_tags':
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90 #for $group in $level.groups.value:
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91 #for $file in $select_data.countsFile.get_datasets_for_group($group):
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92 $count_files.append(str($file))
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93 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier)
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94 #end for
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95 #end for
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96 #else:
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97 #for $file in $level.countsFile:
34
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98 $count_files.append(str($file))
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99 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier)
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100 #end for
44
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101 #end if
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102 $temp_factor.append( {str($level.factorLevel): $count_files} )
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103 #end for
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104 $temp_factor.reverse()
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105 $temp_factor_names.append([str($factor.factorName), $temp_factor])
23
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106 #end for
44
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107 #end if
27
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108
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109 $header
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110
44
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111 #if $select_data.how != 'sample_sheet_contrasts':
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112 -f '#echo json.dumps(temp_factor_names)#'
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113 #end if
24
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114 -l '#echo json.dumps(filename_to_element_identifiers)#'
43
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115 #if $advanced_options.esf_cond.esf:
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116 #if $advanced_options.esf_cond.esf == "user":
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117 -e $advanced_options.esf_cond.size_factor_input
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118 #else:
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119 -e $advanced_options.esf_cond.esf
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120 #end if
30
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121 #end if
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122 -t $advanced_options.fit_type
30
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123 #if $batch_factors:
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124 --batch_factors '$batch_factors'
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125 #end if
42
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126 #if $advanced_options.prefilter_conditional.prefilter:
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127 $advanced_options.prefilter_conditional.prefilter
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128 -V $advanced_options.prefilter_conditional.prefilter_value
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129 #end if
44
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130
43
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131 $advanced_options.outlier_replace_off
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132 $advanced_options.outlier_filter_off
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133 $advanced_options.auto_mean_filter_off
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134 $advanced_options.use_beta_priors
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135
39
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136 #if 'many_contrasts' in $output_options.output_selector
23
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137 -m
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138 #end if
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139 #if $tximport.tximport_selector == 'tximport':
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140 -i
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141 -y $tximport.txtype
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142 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
31
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143 -x mapping.gff
23
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144 #else:
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145 -x mapping.txt
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146 #end if
23
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147 #end if
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148 ]]></command>
0
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149 <inputs>
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150 <conditional name="select_data">
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151 <param name="how" type="select">
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152 <option value="datasets_per_level">Select datasets per level</option>
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153 <option value="group_tags">Select group tags corresponding to levels</option>
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154 <option value="sample_sheet_contrasts">Select contrasts from sample sheet columns</option>
0
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155 </param>
34
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156 <when value="group_tags">
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157 <param name="countsFile" type="data_collection" format="tabular" label="Count file(s) collection" multiple="true"/>
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158 <expand macro="factor_repeat">
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159 <param name="groups" type="group_tag" data_ref="countsFile" multiple="true" label="Select groups that correspond to this factor level"/>
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160 </expand>
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161 </when>
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162 <when value="datasets_per_level">
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163 <expand macro="factor_repeat">
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164 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
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165 </expand>
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166 </when>
44
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167 <when value="sample_sheet_contrasts">
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168 <param name="countsFile" type="data_collection" format="tabular" label="Count file(s) collection" multiple="true"/>
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169 <param name="sample_sheet" type="data" format="tabular" label="Sample sheet file" help="A tabular file containing at least two columns: one with the element identifiers (matching those in the collection) and one or more columns with factor levels."/>
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170 <conditional name="design_formula_mode">
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171 <param name="mode" type="select" label="Design formula specification">
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172 <option value="automatic" selected="true">Automatic (select factors from columns)</option>
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173 <option value="custom">Custom design formula</option>
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174 </param>
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175 <when value="automatic">
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176 <param name="factor" type="data_column" use_header_names="true" data_ref="sample_sheet" multiple="true" optional="false" label="Factor levels column(s)" help="Select one or more columns from the sample sheet to define factor levels for DESeq2 analysis. First selected factor is the primary factor"/>
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177 <param name="reference_level" type="text" label="Reference level for primary factor" help="Specify the reference level for the primary factor. If left blank, the first encountered level of the primary factor will be used as reference." optional="true"/>
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178 <param name="target_level" type="text" label="Target level for primary factor" help="Specify the target level for the primary factor. If left blank, all levels will be compared against the primary factor." optional="true"/>
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179 </when>
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180 <when value="custom">
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181 <param name="design_formula" type="text" label="Design formula" help="Specify the design formula using R formula syntax (e.g., '~ condition' or '~ batch + condition'). Column names must match those in the sample sheet. The last factor in the formula is used as the primary factor for contrasts.">
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182 <validator type="regex" message="Design formula must start with ~ and contain valid R variable names">^~\s*[a-zA-Z][a-zA-Z0-9_.]*(\s*[+*:]\s*[a-zA-Z][a-zA-Z0-9_.]*)*$</validator>
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183 <sanitizer>
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184 <valid initial="string.letters,string.digits">
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185 <add value="~"/>
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186 <add value=":"/>
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187 <add value="+"/>
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188 <add value="*"/>
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189 <add value="_"/>
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190 <add value="."/>
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191 <add value=" "/>
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192 </valid>
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193 </sanitizer>
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194 </param>
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195 <param name="reference_level" type="text" label="Reference level for primary factor" help="Specify the reference level for the primary factor. If left blank, the first encountered level of the primary factor will be used as reference." optional="true"/>
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196 <param name="target_level" type="text" label="Target level for primary factor" help="Specify the target level for the primary factor. If left blank, all levels will be compared against the primary factor." optional="true"/>
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197 </when>
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198 </conditional>
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199 </when>
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200 </conditional>
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201
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202 <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."/>
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203 <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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204
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205 <conditional name="tximport">
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206 <param name="tximport_selector" type="select" label="Choice of Input data">
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207 <option value="count" selected="True">Count data (e.g. from HTSeq-count, featureCounts or StringTie)</option>
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208 <option value="tximport">TPM values (e.g. from kallisto, sailfish or salmon)</option>
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209 </param>
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210 <when value="tximport">
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211 <param name="txtype" type="select" label="Program used to generate TPMs">
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212 <option value="kallisto">kallisto</option>
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213 <option value="sailfish">Sailfish</option>
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214 <option value="salmon">Salmon</option>
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215 </param>
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216 <conditional name="mapping_format">
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217 <param name="mapping_format_selector" type="select" label="Gene mapping format">
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218 <option value="gtf" selected="True">GTF/GFF3</option>
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219 <option value="tabular">Transcript-ID to Gene-ID mapping file</option>
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220 </param>
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221 <when value="gtf">
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222 <param name="gtf_file" type="data" format="gtf,gff3" label="GTF/GFF3 annotation file"/>
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223 </when>
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224 <when value="tabular">
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225 <param name="tabular_file" type="data" format="tabular" label="Tabular file with Transcript-ID to Gene-ID mapping"/>
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226 </when>
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227 </conditional>
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228 </when>
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229 <when value="count"/>
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230 </conditional>
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231 <section name="advanced_options" title="Advanced options">
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232 <conditional name="esf_cond">
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233 <param name="esf" type="select" label="Method for estimateSizeFactors"
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234 help="Method for estimation: either 'ratio', 'poscounts', or 'iterate'. 'ratio' uses the standard median ratio method introduced in DESeq.
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235 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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236 '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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237 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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238 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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239 use cases with Paul McMurdie's phyloseq package for metagenomic samples. The 'iterate' estimator iterates between estimating the dispersion
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240 with a design of ~1, and finding a size factor vector by numerically optimizing the likelihood of the ~1 model.">
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241 <option value="" selected="true">No Selection (use default)</option>
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242 <option value="ratio">ratio</option>
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243 <option value="poscounts">poscounts</option>
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244 <option value="iterate">iterate</option>
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245 <option value="user">User-provided</option>
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246 </param>
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247 <when value=""/>
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248 <when value="ratio"/>
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249 <when value="poscounts"/>
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250 <when value="iterate"/>
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251 <when value="user">
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252 <param name="size_factor_input" type="data" format="tabular" label="File with custom size factors" help="The input must be a 2-column file: col1 should have the input file names. Col2 should contain your custom size factors."/>
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253 </when>
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254 </conditional>
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255 <param name="fit_type" type="select" label="Fit type">
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256 <option value="1" selected="true">parametric</option>
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257 <option value="2">local</option>
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258 <option value="3">mean</option>
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259 </param>
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260 <param name="outlier_replace_off" type="boolean" truevalue="-a" falsevalue="" checked="false"
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261 label="Turn off outliers replacement (only affects with >6 replicates)"
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262 help="When there are more than 6 replicates for a given sample, the DESeq2 will automatically replace
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263 counts with large Cook’s distance with the trimmed mean over all samples, scaled up by the size factor
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264 or normalization factor for that sample"/>
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265 <param name="outlier_filter_off" type="boolean" truevalue="-b" falsevalue="" checked="false"
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266 label="Turn off outliers filtering (only affects with >2 replicates)"
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267 help="When there are more than 2 replicates for a given sample, the DESeq2 will automatically
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268 filter genes which contain a Cook’s distance above a cutoff"/>
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269 <param name="auto_mean_filter_off" type="boolean" truevalue="-c" falsevalue="" checked="false"
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270 label="Turn off independent filtering"
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271 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic"/>
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272 <conditional name="prefilter_conditional">
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273 <param name="prefilter" type="select" label="Perform pre-filtering" help="While it is not necessary to pre-filter
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274 low count genes before running the DESeq2 functions, there are two reasons which make pre-filtering useful:
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275 by removing rows in which there are very few reads, we reduce the required memory, and we increase the speed.
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276 It can also improve visualizations, as features with no information for differential expression are not plotted.">
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277 <option value="-P">Enabled</option>
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278 <option value="" selected="true">Disabled</option>
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279 </param>
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280 <when value="-P">
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281 <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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282 </when>
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283 <when value=""/>
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284 </conditional>
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285 <param name="use_beta_priors" type="boolean" truevalue="-d" falsevalue="" checked="false"
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286 label="Use beta priors"
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287 help="Whether or not to put a zero-mean normal prior on the non-intercept coefficients"/>
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288 </section>
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289 <section name="output_options" title="Output options">
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290 <param name="output_selector" type="select" multiple="True" optional="true" display="checkboxes" label="Output selector">
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291 <option value="pdf" selected="True">Generate plots for visualizing the analysis results</option>
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292 <option value="sizefactors">Output sample size factors</option>
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293 <option value="normCounts">Output normalised counts</option>
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294 <option value="normVST">Output VST normalized table</option>
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295 <option value="normRLog">Output rLog normalized table</option>
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296 <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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297 </param>
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298 <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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299 </section>
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300 </inputs>
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301 <outputs>
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302 <data name="deseq_out" format="tabular" label="DESeq2 result file on ${on_string}">
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303 <filter>'many_contrasts' not in output_options['output_selector']</filter>
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304 <actions>
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305 <action name="column_names" type="metadata" default="GeneID,Base mean,log2(FC),StdErr,Wald-Stats,P-value,P-adj"/>
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306 </actions>
0
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307 </data>
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308 <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}">
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309 <filter>output_options['output_selector'] and 'many_contrasts' in output_options['output_selector']</filter>
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310 <discover_datasets pattern="(?P&lt;designation&gt;.+_vs_.+)" format="tabular" directory="." visible="false"/>
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311 </collection>
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312 <data name="plots" format="pdf" label="DESeq2 plots on ${on_string}">
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313 <filter>output_options['output_selector'] and 'pdf' in output_options['output_selector']</filter>
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314 </data>
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315 <data name="sizefactors_out" format="tabular" label="Size Factors on ${on_string}">
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316 <filter>output_options['output_selector'] and 'sizefactors' in output_options['output_selector']</filter>
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317 </data>
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318 <data name="counts_out" format="tabular" label="Normalized counts file on ${on_string}">
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319 <filter>output_options['output_selector'] and 'normCounts' in output_options['output_selector']</filter>
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320 </data>
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321 <data name="rlog_out" format="tabular" label="rLog-Normalized counts file on ${on_string}">
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322 <filter>output_options['output_selector'] and 'normRLog' in output_options['output_selector']</filter>
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323 </data>
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324 <data name="vst_out" format="tabular" label="VST-Normalized counts file on ${on_string}">
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325 <filter>output_options['output_selector'] and 'normVST' in output_options['output_selector']</filter>
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326 </data>
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327 </outputs>
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328 <tests>
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329 <!-- Ensure counts files with header works -->
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330 <test expect_num_outputs="4">
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331 <repeat name="rep_factorName">
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332 <param name="factorName" value="Treatment"/>
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333 <repeat name="rep_factorLevel">
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334 <param name="factorLevel" value="Treated"/>
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335 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
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336 </repeat>
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337 <repeat name="rep_factorLevel">
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338 <param name="factorLevel" value="Untreated"/>
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339 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
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340 </repeat>
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341 </repeat>
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342 <section name="advanced_options">
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343 <param name="use_beta_priors" value="1"/>
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344 </section>
39
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345 <section name="output_options">
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346 <param name="output_selector" value="normCounts,normRLog,normVST"/>
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347 </section>
27
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348 <output name="counts_out">
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349 <assert_contents>
43
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350 <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"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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351 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0"/>
27
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352 </assert_contents>
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353 </output>
30
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diff changeset
354 <output name="rlog_out">
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355 <assert_contents>
43
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356 <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"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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diff changeset
357 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0"/>
30
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358 </assert_contents>
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359 </output>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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diff changeset
360 <output name="vst_out">
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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diff changeset
361 <assert_contents>
43
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diff changeset
362 <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"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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363 <has_text_matching expression="FBgn0000003\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*"/>
30
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diff changeset
364 </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
365 </output>
27
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diff changeset
366 <output name="deseq_out" >
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367 <assert_contents>
43
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368 <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
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diff changeset
369 <has_n_lines n="3999"/>
27
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370 </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
371 </output>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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diff changeset
372 </test>
44
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diff changeset
373 <!-- Ensure additional batch factor correction works -->
29
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diff changeset
374 <test expect_num_outputs="2">
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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375 <repeat name="rep_factorName">
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376 <param name="factorName" value="Treatment"/>
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377 <repeat name="rep_factorLevel">
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378 <param name="factorLevel" value="Treated"/>
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379 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
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iuc
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diff changeset
380 </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
381 <repeat name="rep_factorLevel">
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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diff changeset
382 <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
383 <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
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diff changeset
384 </repeat>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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diff changeset
385 </repeat>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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diff changeset
386 <param name="batch_factors" value="batch_factors.tab"/>
43
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diff changeset
387 <section name="advanced_options">
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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diff changeset
388 <param name="use_beta_priors" value="1"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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389 </section>
39
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diff changeset
390 <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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391 <param name="output_selector" value="normCounts"/>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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392 </section>
29
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393 <output name="deseq_out">
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394 <assert_contents>
43
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diff changeset
395 <has_text_matching expression="FBgn0003360\t1933.*\t-2.9.*\t0.1.*\t-26.*\t1.*-152\t4.*-149"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
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396 </assert_contents>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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diff changeset
397 </output>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
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diff changeset
398 </test>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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diff changeset
399 <!-- Same as above, but without beta priors -->
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iuc
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diff changeset
400 <test expect_num_outputs="2">
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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diff changeset
401 <repeat name="rep_factorName">
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
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diff changeset
402 <param name="factorName" value="Treatment"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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diff changeset
403 <repeat name="rep_factorLevel">
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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diff changeset
404 <param name="factorLevel" value="Treated"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
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diff changeset
405 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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diff changeset
406 </repeat>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
407 <repeat name="rep_factorLevel">
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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diff changeset
408 <param name="factorLevel" value="Untreated"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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diff changeset
409 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
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diff changeset
410 </repeat>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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diff changeset
411 </repeat>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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diff changeset
412 <param name="batch_factors" value="batch_factors.tab"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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diff changeset
413 <section name="advanced_options">
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diff changeset
414 <param name="use_beta_priors" value="0"/>
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diff changeset
415 </section>
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iuc
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diff changeset
416 <section name="output_options">
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
417 <param name="output_selector" value="normCounts"/>
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diff changeset
418 </section>
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iuc
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diff changeset
419 <output name="deseq_out">
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diff changeset
420 <assert_contents>
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diff changeset
421 <has_text_matching expression="FBgn0003360\t1933.*\t-3.*\t0.1.*\t-26.*\t6.*-151\t1.*-147"/>
29
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diff changeset
422 </assert_contents>
66203279224f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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diff changeset
423 </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
424 </test>
44
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parents: 43
diff changeset
425 <!-- Ensure counts files without header works -->
30
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diff changeset
426 <test expect_num_outputs="4">
27
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parents: 26
diff changeset
427 <repeat name="rep_factorName">
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
428 <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
429 <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
430 <param name="factorLevel" value="Treated"/>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
431 <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
432 </repeat>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
433 <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
434 <param name="factorLevel" value="Untreated"/>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
435 <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
parents: 26
diff changeset
436 </repeat>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
437 </repeat>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
438 <param name="header" value="False"/>
43
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iuc
parents: 42
diff changeset
439 <section name="advanced_options">
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
440 <param name="use_beta_priors" value="1"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
441 </section>
39
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iuc
parents: 38
diff changeset
442 <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
443 <param name="output_selector" value="normCounts,normRLog,normVST"/>
44
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iuc
parents: 43
diff changeset
444 </section>
27
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iuc
parents: 26
diff changeset
445 <output name="counts_out">
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
446 <assert_contents>
43
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iuc
parents: 42
diff changeset
447 <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"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
448 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0"/>
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
449 </assert_contents>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
450 </output>
30
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iuc
parents: 29
diff changeset
451 <output name="rlog_out">
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
452 <assert_contents>
43
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iuc
parents: 42
diff changeset
453 <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"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
454 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0"/>
30
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
455 </assert_contents>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
456 </output>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
457 <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
458 <assert_contents>
43
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
459 <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"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
460 <has_text_matching expression="FBgn0000003\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*"/>
30
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
461 </assert_contents>
3b9af9a27b5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 29
diff changeset
462 </output>
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
463 <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
464 <assert_contents>
43
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
465 <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
466 </assert_contents>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
467 </output>
17
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iuc
parents: 16
diff changeset
468 </test>
44
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iuc
parents: 43
diff changeset
469 <!-- Ensure Sailfish/Salmon input with tx2gene table works -->
23
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iuc
parents: 22
diff changeset
470 <test expect_num_outputs="1">
17
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents: 16
diff changeset
471 <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
472 <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
473 <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
474 <param name="factorLevel" value="Treated"/>
23
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
475 <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
476 </repeat>
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents: 16
diff changeset
477 <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
478 <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
479 <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
480 </repeat>
24930eeff731 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 23559e873291b04840f186edb0b4b85e76359e05
iuc
parents: 16
diff changeset
481 </repeat>
43
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iuc
parents: 42
diff changeset
482 <section name="advanced_options">
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
483 <param name="use_beta_priors" value="1"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
484 </section>
39
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
485 <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
486 <param name="output_selector" value=""/>
44
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parents: 43
diff changeset
487 </section>
17
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iuc
parents: 16
diff changeset
488 <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
489 <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
490 <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
491 <param name="tabular_file" value="tx2gene.tab"/>
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
492 <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
493 <assert_contents>
43
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iuc
parents: 42
diff changeset
494 <has_text_matching expression="UGT3A2\t1.8841.*\t-0.1329.*\t0.6936.*\t-0.1917.*\t0.8479.*\t0.9999.*"/>
31
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 30
diff changeset
495 </assert_contents>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 30
diff changeset
496 </output>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 30
diff changeset
497 </test>
44
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iuc
parents: 43
diff changeset
498 <!-- Ensure Sailfish/Salmon input with GFF3 annotation from NCBI works -->
31
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 30
diff changeset
499 <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
500 <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
501 <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
502 <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
503 <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
504 <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
505 </repeat>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 30
diff changeset
506 <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
507 <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
508 <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
509 </repeat>
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 30
diff changeset
510 </repeat>
43
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
511 <section name="advanced_options">
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
512 <param name="use_beta_priors" value="1"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
513 </section>
39
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
514 <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
515 <param name="output_selector" value=""/>
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
516 </section>
31
7a189a7634c7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 30
diff changeset
517 <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
518 <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
519 <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
520 <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
521 <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
522 <assert_contents>
43
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
523 <has_text_matching expression="UGT3A2\t1.8841.*\t-0.1329.*\t0.6936.*\t-0.1917.*\t0.8479.*\t0.9999.*"/>
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
524 </assert_contents>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
525 </output>
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
526 </test>
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
527 <!-- Ensure Sailfish/Salmon input with GTF annotation from Ensembl works -->
32
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
528 <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
529 <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
530 <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
531 <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
532 <param name="factorLevel" value="Treated"/>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
533 <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
534 </repeat>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
535 <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
536 <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
537 <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
538 </repeat>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
539 </repeat>
43
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
540 <section name="advanced_options">
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
541 <param name="use_beta_priors" value="1"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
542 </section>
39
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
543 <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
544 <param name="output_selector" value=""/>
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
545 </section>
32
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
546 <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
547 <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
548 <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
549 <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
550 <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
551 <assert_contents>
43
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
552 <has_text_matching expression="ENSG00000168671\t1.8841.*\t-0.1180.*\t0.7429.*\t-0.1589.*\t0.8737.*\t0.9999.*"/>
32
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
553 </assert_contents>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
554 </output>
13f324f9cdb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 31
diff changeset
555 </test>
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
556 <!-- Ensure group tags can be used to select factor levels -->
34
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
557 <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
558 <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
559 <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
560 <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
561 <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
562 <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
563 <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
564 <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
565 <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
566 <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
567 </collection>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
568 </param>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
569 <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
570 <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
571 <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
572 <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
573 <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
574 </repeat>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
575 <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
576 <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
577 <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
578 </repeat>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
579 </repeat>
43
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
580 <section name="advanced_options">
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
581 <param name="use_beta_priors" value="1"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
582 </section>
39
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
583 <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
584 <param name="output_selector" value=""/>
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
585 </section>
34
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
586 <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
587 <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
588 <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
589 <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
590 <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
591 <assert_contents>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
592 <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
593 </assert_contents>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
594 </output>
f98981133ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 33
diff changeset
595 </test>
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
596 <!-- Ensure many_contrasts produces output collection -->
36
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
597 <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
598 <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
599 <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
600 <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
601 <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
602 <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
603 <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
604 <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
605 <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
606 <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
607 </collection>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
608 </param>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
609 <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
610 <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
611 <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
612 <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
613 <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
614 </repeat>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
615 <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
616 <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
617 <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
618 </repeat>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
619 </repeat>
43
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
620 <section name="advanced_options">
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
621 <param name="use_beta_priors" value="1"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
622 </section>
39
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
623 <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
624 <param name="output_selector" value="many_contrasts"/>
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
625 </section>
36
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
626 <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
627 <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
628 <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
629 <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
630 <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
631 <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
632 <assert_contents>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
633 <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
634 </assert_contents>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
635 </element>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
636 </output_collection>
d9f48120c02b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 34
diff changeset
637 </test>
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
638 <!-- Test alpha_ma option -->
39
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
639 <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
640 <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
641 <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
642 <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
643 <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
644 <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
645 </repeat>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
646 <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
647 <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
648 <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
649 </repeat>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
650 </repeat>
43
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
651 <section name="advanced_options">
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
652 <param name="use_beta_priors" value="1"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
653 </section>
39
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
654 <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
655 <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
656 <param name="alpha_ma" value="0.05"/>
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
657 </section>
39
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
658 <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
659 <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
660 <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
661 <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
662 <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
663 <assert_contents>
43
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
664 <has_text_matching expression="ENSG00000168671\t1.8841.*\t-0.1180.*\t0.7429.*\t-0.1589.*\t0.8737.*\t0.9999.*"/>
39
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
665 </assert_contents>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
666 </output>
b30a443484ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 38
diff changeset
667 </test>
41
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
668 <!-- 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
669 <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
670 <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
671 <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
672 <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
673 <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
674 <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
675 </repeat>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
676 <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
677 <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
678 <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
679 </repeat>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
680 </repeat>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
681 <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
682 <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
683 <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
684 </section>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
685 <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
686 <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
687 <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
688 <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
689 <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
690 <assert_contents>
43
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
691 <has_text_matching expression="sailfish_quant\.sf4\.tab\t0\.8\d+"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
692 <has_text_matching expression="sailfish_quant\.sf3\.tab\t1\.0\d+"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
693 </assert_contents>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
694 </output>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
695 </test>
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
696 <!-- Test alpha_ma option, but with user-provided size factors -->
43
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
697 <test expect_num_outputs="1">
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
698 <repeat name="rep_factorName">
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
699 <param name="factorName" value="Treatment"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
700 <repeat name="rep_factorLevel">
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
701 <param name="factorLevel" value="Treated"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
702 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
703 </repeat>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
704 <repeat name="rep_factorLevel">
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
705 <param name="factorLevel" value="Untreated"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
706 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
707 </repeat>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
708 </repeat>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
709 <section name="advanced_options">
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
710 <param name="use_beta_priors" value="1"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
711 <conditional name="esf_cond">
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
712 <param name="esf" value="user"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
713 <param name="size_factor_input" value="size_factors_out.tsv"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
714 </conditional>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
715 </section>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
716 <section name="output_options">
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
717 <param name="output_selector" value=""/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
718 <param name="alpha_ma" value="0.05"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
719 </section>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
720 <param name="tximport_selector" value="tximport"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
721 <param name="txtype" value="sailfish"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
722 <param name="mapping_format_selector" value="gtf"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
723 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
724 <output name="deseq_out">
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
725 <assert_contents>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
726 <has_text_matching expression="ENSG00000168671\t1.90.*\t-0.05.*\t0.75.*\t-0.07.*\t0.94.*\t0.95.*"/>
41
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
727 </assert_contents>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
728 </output>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
729 </test>
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
730 <!-- Same as above alpha_ma size factor test, but with a non-default estimator -->
41
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
731 <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
732 <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
733 <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
734 <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
735 <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
736 <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
737 </repeat>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
738 <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
739 <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
740 <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
741 </repeat>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
742 </repeat>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
743 <section name="advanced_options">
43
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
744 <param name="esf" value="poscounts"/>
41
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
745 </section>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
746 <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
747 <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
748 <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
749 </section>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
750 <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
751 <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
752 <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
753 <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
754 <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
755 <assert_contents>
43
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
756 <has_text_matching expression="sailfish_quant\.sf4\.tab\t0\.8\d+"/>
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 42
diff changeset
757 <has_text_matching expression="sailfish_quant\.sf3\.tab\t1\.0\d+"/>
41
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
758 </assert_contents>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
759 </output>
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 40
diff changeset
760 </test>
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
761 <!-- Test prefilter parameter -->
42
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
762 <test expect_num_outputs="2">
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
763 <repeat name="rep_factorName">
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
764 <param name="factorName" value="Treatment"/>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
765 <repeat name="rep_factorLevel">
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
766 <param name="factorLevel" value="Treated"/>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
767 <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
iuc
parents: 41
diff changeset
768 </repeat>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
769 <repeat name="rep_factorLevel">
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
770 <param name="factorLevel" value="Untreated"/>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
771 <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
iuc
parents: 41
diff changeset
772 </repeat>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
773 </repeat>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
774 <section name="advanced_options">
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
775 <conditional name="prefilter_conditional">
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
776 <param name="prefilter" value="-P"/>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
777 <param name="prefilter_value" value="10"/>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
778 </conditional>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
779 </section>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
780 <section name="output_options">
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
781 <param name="output_selector" value="normCounts"/>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
782 </section>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
783 <output name="counts_out">
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
784 <assert_contents>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
785 <has_n_lines n="2922"/>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
786 </assert_contents>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
787 </output>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
788 <output name="deseq_out" >
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
789 <assert_contents>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
790 <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
iuc
parents: 41
diff changeset
791 </assert_contents>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
792 </output>
6ef2cba4e35a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 41
diff changeset
793 </test>
44
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
794
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
795 <!--Test sample_sheet_contrasts mode -->
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
796 <test expect_num_outputs="2">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
797 <param name="select_data|how" value="sample_sheet_contrasts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
798 <param name="select_data|countsFile">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
799 <collection type="list">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
800 <element name="GSM461179_treat_single.counts" value="GSM461179_treat_single.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
801 <element name="GSM461180_treat_paired.counts" value="GSM461180_treat_paired.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
802 <element name="GSM461181_treat_paired.counts" value="GSM461181_treat_paired.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
803 <element name="GSM461176_untreat_single.counts" value="GSM461176_untreat_single.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
804 <element name="GSM461177_untreat_paired.counts" value="GSM461177_untreat_paired.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
805 <element name="GSM461178_untreat_paired.counts" value="GSM461178_untreat_paired.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
806 <element name="GSM461182_untreat_single.counts" value="GSM461182_untreat_single.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
807 </collection>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
808 </param>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
809 <param name="select_data|sample_sheet" value="sample_sheet.tab"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
810 <param name="select_data|design_formula_mode|mode" value="automatic"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
811 <param name="select_data|design_formula_mode|factor" value="2"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
812 <section name="advanced_options">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
813 <param name="use_beta_priors" value="1"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
814 </section>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
815 <section name="output_options">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
816 <param name="output_selector" value="normCounts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
817 </section>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
818 <output name="counts_out">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
819 <assert_contents>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
820 <has_text_matching expression="GSM461179_treat_single.counts\tGSM461180_treat_paired.counts\tGSM461181_treat_paired.counts\tGSM461176_untreat_single.counts\tGSM461177_untreat_paired.counts\tGSM461178_untreat_paired.counts\tGSM461182_untreat_single.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
821 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
822 </assert_contents>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
823 </output>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
824 <output name="deseq_out">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
825 <assert_contents>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
826 <!-- Contrast direction: first level (Treated) is reference, comparing Untreated vs Treated -->
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
827 <has_text_matching expression="FBgn0003360\t1933\.9504.*\t2\.8399.*\t0\.1309.*\t21\.68.*\t.*e-104\t.*e-101"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
828 <has_n_lines n="3999"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
829 </assert_contents>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
830 </output>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
831 </test>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
832 <!--Test sample_sheet_contrasts mode with explicit reference_level -->
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
833 <test expect_num_outputs="2">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
834 <param name="select_data|how" value="sample_sheet_contrasts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
835 <param name="select_data|countsFile">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
836 <collection type="list">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
837 <element name="GSM461179_treat_single.counts" value="GSM461179_treat_single.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
838 <element name="GSM461180_treat_paired.counts" value="GSM461180_treat_paired.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
839 <element name="GSM461181_treat_paired.counts" value="GSM461181_treat_paired.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
840 <element name="GSM461176_untreat_single.counts" value="GSM461176_untreat_single.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
841 <element name="GSM461177_untreat_paired.counts" value="GSM461177_untreat_paired.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
842 <element name="GSM461178_untreat_paired.counts" value="GSM461178_untreat_paired.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
843 <element name="GSM461182_untreat_single.counts" value="GSM461182_untreat_single.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
844 </collection>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
845 </param>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
846 <param name="select_data|sample_sheet" value="sample_sheet.tab"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
847 <param name="select_data|design_formula_mode|mode" value="automatic"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
848 <param name="select_data|design_formula_mode|factor" value="2"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
849 <param name="select_data|design_formula_mode|reference_level" value="Untreated"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
850 <section name="advanced_options">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
851 <param name="use_beta_priors" value="1"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
852 </section>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
853 <section name="output_options">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
854 <param name="output_selector" value="normCounts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
855 </section>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
856 <output name="counts_out">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
857 <assert_contents>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
858 <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"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
859 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
860 </assert_contents>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
861 </output>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
862 <output name="deseq_out">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
863 <assert_contents>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
864 <!-- With reference_level=Untreated, compares Treated vs Untreated = log2(Treated/Untreated) -->
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
865 <has_text_matching expression="FBgn0003360\t1933\.9504.*\t-2\.8399.*\t0\.1309.*\t-21\.68.*\t.*e-104\t.*e-101"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
866 <has_n_lines n="3999"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
867 </assert_contents>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
868 </output>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
869 </test>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
870 <!--Test sample_sheet_contrasts mode with reference_level and target_level -->
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
871 <test expect_num_outputs="2">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
872 <param name="select_data|how" value="sample_sheet_contrasts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
873 <param name="select_data|countsFile">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
874 <collection type="list">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
875 <element name="GSM461179_treat_single.counts" value="GSM461179_treat_single.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
876 <element name="GSM461180_treat_paired.counts" value="GSM461180_treat_paired.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
877 <element name="GSM461181_treat_paired.counts" value="GSM461181_treat_paired.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
878 <element name="GSM461176_untreat_single.counts" value="GSM461176_untreat_single.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
879 <element name="GSM461177_untreat_paired.counts" value="GSM461177_untreat_paired.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
880 <element name="GSM461178_untreat_paired.counts" value="GSM461178_untreat_paired.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
881 <element name="GSM461182_untreat_single.counts" value="GSM461182_untreat_single.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
882 </collection>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
883 </param>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
884 <param name="select_data|sample_sheet" value="sample_sheet.tab"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
885 <param name="select_data|design_formula_mode|mode" value="automatic"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
886 <param name="select_data|design_formula_mode|factor" value="2"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
887 <param name="select_data|design_formula_mode|reference_level" value="Untreated"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
888 <param name="select_data|design_formula_mode|target_level" value="Treated"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
889 <section name="advanced_options">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
890 <param name="use_beta_priors" value="1"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
891 </section>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
892 <section name="output_options">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
893 <param name="output_selector" value="normCounts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
894 </section>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
895 <output name="counts_out">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
896 <assert_contents>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
897 <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"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
898 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
899 </assert_contents>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
900 </output>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
901 <output name="deseq_out">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
902 <assert_contents>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
903 <!-- With reference=Untreated and target=Treated, compares Treated vs Untreated -->
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
904 <has_text_matching expression="FBgn0003360\t1933\.9504.*\t-2\.8399.*\t0\.1309.*\t-21\.68.*\t.*e-104\t.*e-101"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
905 <has_n_lines n="3999"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
906 </assert_contents>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
907 </output>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
908 </test>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
909 <!--Test sample_sheet_contrasts with custom design formula -->
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
910 <test expect_num_outputs="2">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
911 <param name="select_data|how" value="sample_sheet_contrasts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
912 <param name="select_data|countsFile">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
913 <collection type="list">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
914 <element name="GSM461179_treat_single.counts" value="GSM461179_treat_single.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
915 <element name="GSM461180_treat_paired.counts" value="GSM461180_treat_paired.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
916 <element name="GSM461181_treat_paired.counts" value="GSM461181_treat_paired.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
917 <element name="GSM461176_untreat_single.counts" value="GSM461176_untreat_single.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
918 <element name="GSM461177_untreat_paired.counts" value="GSM461177_untreat_paired.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
919 <element name="GSM461178_untreat_paired.counts" value="GSM461178_untreat_paired.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
920 <element name="GSM461182_untreat_single.counts" value="GSM461182_untreat_single.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
921 </collection>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
922 </param>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
923 <param name="select_data|sample_sheet" value="sample_sheet.tab"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
924 <param name="select_data|design_formula_mode|mode" value="custom"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
925 <param name="select_data|design_formula_mode|design_formula" value="~ treatment"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
926 <param name="select_data|design_formula_mode|reference_level" value="Untreated"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
927 <section name="advanced_options">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
928 <param name="use_beta_priors" value="1"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
929 </section>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
930 <section name="output_options">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
931 <param name="output_selector" value="normCounts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
932 </section>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
933 <output name="counts_out">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
934 <assert_contents>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
935 <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"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
936 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
937 </assert_contents>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
938 </output>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
939 <output name="deseq_out">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
940 <assert_contents>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
941 <!-- Custom formula ~treatment with reference=Untreated, compares Treated vs Untreated -->
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
942 <has_text_matching expression="FBgn0003360\t1933\.9504.*\t-2\.8399.*\t0\.1309.*\t-21\.68.*\t.*e-104\t.*e-101"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
943 <has_n_lines n="3999"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
944 </assert_contents>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
945 </output>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
946 </test>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
947 <!--Test sample_sheet_contrasts with multi-factor custom design formula -->
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
948 <test expect_num_outputs="2">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
949 <param name="select_data|how" value="sample_sheet_contrasts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
950 <param name="select_data|countsFile">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
951 <collection type="list">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
952 <element name="GSM461179_treat_single.counts" value="GSM461179_treat_single.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
953 <element name="GSM461180_treat_paired.counts" value="GSM461180_treat_paired.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
954 <element name="GSM461181_treat_paired.counts" value="GSM461181_treat_paired.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
955 <element name="GSM461176_untreat_single.counts" value="GSM461176_untreat_single.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
956 <element name="GSM461177_untreat_paired.counts" value="GSM461177_untreat_paired.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
957 <element name="GSM461178_untreat_paired.counts" value="GSM461178_untreat_paired.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
958 <element name="GSM461182_untreat_single.counts" value="GSM461182_untreat_single.counts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
959 </collection>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
960 </param>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
961 <param name="select_data|sample_sheet" value="sample_sheet.tab"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
962 <param name="select_data|design_formula_mode|mode" value="custom"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
963 <param name="select_data|design_formula_mode|design_formula" value="~ sequencing + treatment"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
964 <param name="select_data|design_formula_mode|reference_level" value="Untreated"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
965 <section name="advanced_options">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
966 <param name="use_beta_priors" value="1"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
967 </section>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
968 <section name="output_options">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
969 <param name="output_selector" value="normCounts"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
970 </section>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
971 <output name="counts_out">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
972 <assert_contents>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
973 <!-- Verify all 7 samples present with correct values (column order may vary) -->
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
974 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
975 <has_n_columns n="8"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
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diff changeset
976 </assert_contents>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
977 </output>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
978 <output name="deseq_out">
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
979 <assert_contents>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
980 <!-- Multi-factor design ~sequencing + treatment controls for sequencing type -->
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
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diff changeset
981 <!-- Effect estimates differ from single-factor design due to covariate adjustment -->
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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diff changeset
982 <has_text_matching expression="FBgn0003360\t1933\.950.*\t-2\.88.*\t0\.111.*\t-25\.8.*\t.*e-14[0-9]\t.*e-14[0-9]"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
parents: 43
diff changeset
983 <has_n_lines n="3999"/>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
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diff changeset
984 </assert_contents>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
iuc
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diff changeset
985 </output>
1cb33de18af5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5bf5011af827e93ddeecbfba4815fe9b85f02594
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986 </test>
0
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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987 </tests>
23
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988 <help><![CDATA[
0
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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989 .. class:: infomark
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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990
15
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991 **What it does**
0
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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992
43
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993 Uses DESeq2 version @DESEQ2_VERSION@ to 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.
0
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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994
23
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995 -----
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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996
0
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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997 **Inputs**
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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998
23
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999 **Count Files**
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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1000
27
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1001 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
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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1002
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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1003 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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1004
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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1005 ========= ============== ===============
15
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diff changeset
1006 Factor Factor level 1 Factor level 2
0
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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1007 --------- -------------- ---------------
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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1008 Treatment Treated Untreated
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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1009 --------- -------------- ---------------
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1010 Condition Knockdown Wildtype
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1011 --------- -------------- ---------------
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1012 TimePoint Day4 Day1
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1013 --------- -------------- ---------------
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1014 SeqType SingleEnd PairedEnd
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1015 --------- -------------- ---------------
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diff changeset
1016 Gender Female Male
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff changeset
1017 ========= ============== ===============
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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parents:
diff changeset
1018
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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parents:
diff changeset
1019 *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
iuc
parents:
diff changeset
1020
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
1021 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
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
1022
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
1023 **Salmon or Sailfish Files**
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
1024
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
1025 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
1026
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
1027 Example:
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
1028
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
1029 ============ ========== =============== =========== ===========
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
1030 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
1031 ------------ ---------- --------------- ----------- -----------
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
1032 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
1033 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
1034 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
1035 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
1036 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
1037 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
1038 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
1039 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
1040 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
1041 ============ ========== =============== =========== ===========
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
1042
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
1043 **kallisto Files**
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
1044
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
1045 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
1046
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
1047 Example:
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
1048
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
1049 ============ ========== =============== =========== ===========
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
1050 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
1051 ------------ ---------- --------------- ----------- -----------
27
dc6bc19f05ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 26
diff changeset
1052 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
1053 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
1054 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
1055 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
1056 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
1057 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
1058 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
1059 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
1060 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
1061 ============ ========== =============== =========== ===========
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
1062
d1241c2b81a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 22
diff changeset
1063 -----
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
1064
0
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
1065 **Output**
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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1066
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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diff changeset
1067 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
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diff changeset
1068
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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parents:
diff changeset
1069 ====== ==========================================================
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff changeset
1070 Column Description
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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diff changeset
1071 ------ ----------------------------------------------------------
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff changeset
1072 1 Gene Identifiers
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff changeset
1073 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
1074 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
1075 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
1076 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
1077 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
1078 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
1079 which controls false discovery rate (FDR)
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
1080 ====== ==========================================================
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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diff changeset
1081
41
0a0a3388e3f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
1082 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
1083 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
1084 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
1085
0
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff changeset
1086 .. _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
1087 .. _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
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diff changeset
1088 ]]></help>
43
621ddf5967d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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diff changeset
1089 <expand macro="citations"/>
0
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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diff changeset
1090 </tool>