Mercurial > repos > iuc > deseq2

annotate deseq2.xml @ 31:9a882d108833 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
author iuc
date Tue, 18 Jul 2023 14:58:52 +0000
parents 8fe98f7094de
children
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9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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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 <regex match="Execution halted"
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11 source="both"
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12 level="fatal"
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13 description="Execution halted."/>
0
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14 <regex match="Error in"
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15 source="both"
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16 level="fatal"
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17 description="An undefined error occurred, please check your input carefully and contact your administrator."/>
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18 <regex match="Fatal error"
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19 source="both"
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20 level="fatal"
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21 description="An undefined error occurred, please check your input carefully and contact your administrator."/>
0
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22 </stdio>
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23 <version_command><![CDATA[
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24 echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
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25 ]]></version_command>
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26 <command><![CDATA[
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27 #if $tximport.tximport_selector == 'tximport':
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28 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
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29 ln -s '$tximport.mapping_format.gtf_file' mapping.gff &&
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30 #else:
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31 ln -s '$tximport.mapping_format.tabular_file' mapping.txt &&
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32 #end if
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33 #end if
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34
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35 ## This is needed for Pulsar to transfer the file
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36 cat '$__tool_directory__/get_deseq_dataset.R' > /dev/null &&
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37
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38 #import json
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39 #import os
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40 Rscript '${__tool_directory__}/deseq2.R'
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41 --cores \${GALAXY_SLOTS:-1}
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42 -o '$deseq_out'
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43 #if 'pdf' in $output_options.output_selector:
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44 -p '$plots'
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45 #end if
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46 -A $output_options.alpha_ma
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47 #if 'normCounts' in $output_options.output_selector:
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48 -n '$counts_out'
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49 #end if
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50 #if 'sizefactors' in $output_options.output_selector:
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51 -F '$sizefactors_out'
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52 #end if
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53 #if 'normRLog' in $output_options.output_selector:
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54 -r '$rlog_out'
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55 #end if
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56 #if 'normVST' in $output_options.output_selector:
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57 -v '$vst_out'
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58 #end if
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59 #set $filename_to_element_identifiers = {}
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60 #set $temp_factor_names = list()
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61 #for $factor in $select_data.rep_factorName:
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62 #set $temp_factor = list()
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63 #for $level in $factor.rep_factorLevel:
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64 #set $count_files = list()
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65 #if $select_data.how == 'group_tags':
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66 #for $group in $level.groups.value:
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67 #for $file in $select_data.countsFile.get_datasets_for_group($group):
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68 $count_files.append(str($file))
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69 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier)
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70 #end for
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71 #end for
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72 #else:
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73 #for $file in $level.countsFile:
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74 $count_files.append(str($file))
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75 $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)), $file.element_identifier)
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76 #end for
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77 #end if
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78 $temp_factor.append( {str($level.factorLevel): $count_files} )
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79 #end for
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80 $temp_factor.reverse()
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81 $temp_factor_names.append([str($factor.factorName), $temp_factor])
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82 #end for
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83
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84 $header
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85
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86 -f '#echo json.dumps(temp_factor_names)#'
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87 -l '#echo json.dumps(filename_to_element_identifiers)#'
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88 #if $advanced_options.esf_cond.esf:
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89 #if $advanced_options.esf_cond.esf == "user":
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90 -e $advanced_options.esf_cond.size_factor_input
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91 #else:
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92 -e $advanced_options.esf_cond.esf
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93 #end if
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94 #end if
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95 -t $advanced_options.fit_type
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96 #if $batch_factors:
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97 --batch_factors '$batch_factors'
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98 #end if
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99 #if $advanced_options.prefilter_conditional.prefilter:
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100 $advanced_options.prefilter_conditional.prefilter
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101 -V $advanced_options.prefilter_conditional.prefilter_value
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102 #end if
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103
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104 $advanced_options.outlier_replace_off
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105 $advanced_options.outlier_filter_off
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106 $advanced_options.auto_mean_filter_off
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107 $advanced_options.use_beta_priors
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108
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109 #if 'many_contrasts' in $output_options.output_selector
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110 -m
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111 #end if
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112 #if $tximport.tximport_selector == 'tximport':
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113 -i
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114 -y $tximport.txtype
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115 #if $tximport.mapping_format.mapping_format_selector == 'gtf':
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116 -x mapping.gff
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117 #else:
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118 -x mapping.txt
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119 #end if
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120 #end if
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121 ]]></command>
0
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122 <inputs>
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123 <conditional name="select_data">
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124 <param name="how" type="select">
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125 <option value="datasets_per_level">Select datasets per level</option>
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126 <option value="group_tags">Select group tags corresponding to levels</option>
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127 </param>
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128 <when value="group_tags">
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129 <param name="countsFile" type="data_collection" format="tabular" label="Count file(s) collection" multiple="true"/>
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130 <expand macro="factor_repeat">
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131 <param name="groups" type="group_tag" data_ref="countsFile" multiple="true" label="Select groups that correspond to this factor level"/>
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132 </expand>
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133 </when>
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134 <when value="datasets_per_level">
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135 <expand macro="factor_repeat">
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136 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
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137 </expand>
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138 </when>
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139 </conditional>
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140
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141 <param name="batch_factors" type="data" format="tabular" optional="true" label="(Optional) provide a tabular file with additional batch factors to include in the model." help="You can produce this file using RUVSeq or svaseq."/>
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142 <param name="header" type="boolean" truevalue="-H" falsevalue="" checked="true" label="Files have header?" help="If this option is set to Yes, the tool will assume that the count files have column headers in the first row. Default: Yes"/>
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143
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144 <conditional name="tximport">
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145 <param name="tximport_selector" type="select" label="Choice of Input data">
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146 <option value="count" selected="True">Count data (e.g. from HTSeq-count, featureCounts or StringTie)</option>
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147 <option value="tximport">TPM values (e.g. from kallisto, sailfish or salmon)</option>
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148 </param>
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149 <when value="tximport">
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150 <param name="txtype" type="select" label="Program used to generate TPMs">
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151 <option value="kallisto">kallisto</option>
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152 <option value="sailfish">Sailfish</option>
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153 <option value="salmon">Salmon</option>
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154 </param>
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155 <conditional name="mapping_format">
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156 <param name="mapping_format_selector" type="select" label="Gene mapping format">
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157 <option value="gtf" selected="True">GTF/GFF3</option>
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158 <option value="tabular">Transcript-ID to Gene-ID mapping file</option>
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159 </param>
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160 <when value="gtf">
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161 <param name="gtf_file" type="data" format="gtf,gff3" label="GTF/GFF3 annotation file"/>
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162 </when>
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163 <when value="tabular">
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164 <param name="tabular_file" type="data" format="tabular" label="Tabular file with Transcript-ID to Gene-ID mapping"/>
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165 </when>
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166 </conditional>
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167 </when>
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168 <when value="count"/>
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169 </conditional>
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170 <section name="advanced_options" title="Advanced options">
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171 <conditional name="esf_cond">
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172 <param name="esf" type="select" label="Method for estimateSizeFactors"
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173 help="Method for estimation: either 'ratio', 'poscounts', or 'iterate'. 'ratio' uses the standard median ratio method introduced in DESeq.
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174 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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175 '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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176 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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177 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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178 use cases with Paul McMurdie's phyloseq package for metagenomic samples. The 'iterate' estimator iterates between estimating the dispersion
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179 with a design of ~1, and finding a size factor vector by numerically optimizing the likelihood of the ~1 model.">
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180 <option value="" selected="true">No Selection (use default)</option>
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181 <option value="ratio">ratio</option>
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182 <option value="poscounts">poscounts</option>
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183 <option value="iterate">iterate</option>
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184 <option value="user">User-provided</option>
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185 </param>
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186 <when value=""/>
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187 <when value="ratio"/>
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188 <when value="poscounts"/>
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189 <when value="iterate"/>
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190 <when value="user">
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191 <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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192 </when>
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193 </conditional>
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194 <param name="fit_type" type="select" label="Fit type">
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195 <option value="1" selected="true">parametric</option>
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196 <option value="2">local</option>
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197 <option value="3">mean</option>
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198 </param>
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199 <param name="outlier_replace_off" type="boolean" truevalue="-a" falsevalue="" checked="false"
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200 label="Turn off outliers replacement (only affects with >6 replicates)"
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201 help="When there are more than 6 replicates for a given sample, the DESeq2 will automatically replace
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202 counts with large Cook’s distance with the trimmed mean over all samples, scaled up by the size factor
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203 or normalization factor for that sample"/>
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204 <param name="outlier_filter_off" type="boolean" truevalue="-b" falsevalue="" checked="false"
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205 label="Turn off outliers filtering (only affects with >2 replicates)"
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206 help="When there are more than 2 replicates for a given sample, the DESeq2 will automatically
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207 filter genes which contain a Cook’s distance above a cutoff"/>
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208 <param name="auto_mean_filter_off" type="boolean" truevalue="-c" falsevalue="" checked="false"
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209 label="Turn off independent filtering"
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210 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic"/>
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211 <conditional name="prefilter_conditional">
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212 <param name="prefilter" type="select" label="Perform pre-filtering" help="While it is not necessary to pre-filter
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213 low count genes before running the DESeq2 functions, there are two reasons which make pre-filtering useful:
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214 by removing rows in which there are very few reads, we reduce the required memory, and we increase the speed.
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215 It can also improve visualizations, as features with no information for differential expression are not plotted.">
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216 <option value="-P">Enabled</option>
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217 <option value="" selected="true">Disabled</option>
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218 </param>
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219 <when value="-P">
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220 <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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221 </when>
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222 <when value=""/>
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223 </conditional>
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224 <param name="use_beta_priors" type="boolean" truevalue="-d" falsevalue="" checked="false"
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225 label="Use beta priors"
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226 help="Whether or not to put a zero-mean normal prior on the non-intercept coefficients"/>
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227 </section>
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228 <section name="output_options" title="Output options">
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229 <param name="output_selector" type="select" multiple="True" optional="true" display="checkboxes" label="Output selector">
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230 <option value="pdf" selected="True">Generate plots for visualizing the analysis results</option>
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231 <option value="sizefactors">Output sample size factors</option>
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232 <option value="normCounts">Output normalised counts</option>
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233 <option value="normVST">Output VST normalized table</option>
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234 <option value="normRLog">Output rLog normalized table</option>
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235 <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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236 </param>
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237 <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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238 </section>
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239 </inputs>
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240 <outputs>
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241 <data name="deseq_out" format="tabular" label="DESeq2 result file on ${on_string}">
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242 <filter>'many_contrasts' not in output_options['output_selector']</filter>
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243 <actions>
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244 <action name="column_names" type="metadata" default="GeneID,Base mean,log2(FC),StdErr,Wald-Stats,P-value,P-adj"/>
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245 </actions>
0
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246 </data>
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247 <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}">
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248 <filter>output_options['output_selector'] and 'many_contrasts' in output_options['output_selector']</filter>
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249 <discover_datasets pattern="(?P&lt;designation&gt;.+_vs_.+)" format="tabular" directory="." visible="false"/>
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250 </collection>
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251 <data name="plots" format="pdf" label="DESeq2 plots on ${on_string}">
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252 <filter>output_options['output_selector'] and 'pdf' in output_options['output_selector']</filter>
0
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253 </data>
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254 <data name="sizefactors_out" format="tabular" label="Size Factors on ${on_string}">
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255 <filter>output_options['output_selector'] and 'sizefactors' in output_options['output_selector']</filter>
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256 </data>
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257 <data name="counts_out" format="tabular" label="Normalized counts file on ${on_string}">
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258 <filter>output_options['output_selector'] and 'normCounts' in output_options['output_selector']</filter>
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259 </data>
19
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260 <data name="rlog_out" format="tabular" label="rLog-Normalized counts file on ${on_string}">
27
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261 <filter>output_options['output_selector'] and 'normRLog' in output_options['output_selector']</filter>
18
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262 </data>
19
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263 <data name="vst_out" format="tabular" label="VST-Normalized counts file on ${on_string}">
27
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264 <filter>output_options['output_selector'] and 'normVST' in output_options['output_selector']</filter>
18
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265 </data>
0
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266 </outputs>
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267 <tests>
15
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268 <!--Ensure counts files with header works -->
18
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269 <test expect_num_outputs="4">
0
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270 <repeat name="rep_factorName">
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271 <param name="factorName" value="Treatment"/>
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272 <repeat name="rep_factorLevel">
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273 <param name="factorLevel" value="Treated"/>
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274 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
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275 </repeat>
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276 <repeat name="rep_factorLevel">
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277 <param name="factorLevel" value="Untreated"/>
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278 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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279 </repeat>
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280 </repeat>
31
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281 <section name="advanced_options">
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282 <param name="use_beta_priors" value="1"/>
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283 </section>
27
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284 <section name="output_options">
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285 <param name="output_selector" value="normCounts,normRLog,normVST"/>
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286 </section>
15
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287 <output name="counts_out">
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288 <assert_contents>
31
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289 <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"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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290 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0"/>
15
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291 </assert_contents>
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292 </output>
18
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293 <output name="rlog_out">
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294 <assert_contents>
31
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295 <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"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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296 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0"/>
18
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297 </assert_contents>
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298 </output>
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299 <output name="vst_out">
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300 <assert_contents>
31
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301 <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"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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diff changeset
302 <has_text_matching expression="FBgn0000003\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*"/>
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
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diff changeset
303 </assert_contents>
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304 </output>
15
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305 <output name="deseq_out" >
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306 <assert_contents>
31
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diff changeset
307 <has_text_matching expression="FBgn0003360\t1933\.9504.*\t-2\.8399.*\t0\.1309.*\t-21\.68.*\t.*e-104\t.*e-101"/>
30
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diff changeset
308 <has_n_lines n="3999"/>
15
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diff changeset
309 </assert_contents>
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310 </output>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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311 </test>
17
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312 <!--Ensure additional batch factor correction works -->
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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313 <test expect_num_outputs="2">
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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314 <repeat name="rep_factorName">
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315 <param name="factorName" value="Treatment"/>
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316 <repeat name="rep_factorLevel">
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317 <param name="factorLevel" value="Treated"/>
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318 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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319 </repeat>
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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320 <repeat name="rep_factorLevel">
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321 <param name="factorLevel" value="Untreated"/>
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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322 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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diff changeset
323 </repeat>
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
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324 </repeat>
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325 <param name="batch_factors" value="batch_factors.tab"/>
31
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326 <section name="advanced_options">
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327 <param name="use_beta_priors" value="1"/>
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328 </section>
27
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329 <section name="output_options">
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330 <param name="output_selector" value="normCounts"/>
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331 </section>
17
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332 <output name="deseq_out">
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333 <assert_contents>
31
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334 <has_text_matching expression="FBgn0003360\t1933.*\t-2.9.*\t0.1.*\t-26.*\t1.*-152\t4.*-149"/>
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335 </assert_contents>
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336 </output>
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diff changeset
337 </test>
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338 <!-- Same as above, but without beta priors -->
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iuc
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diff changeset
339 <test expect_num_outputs="2">
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diff changeset
340 <repeat name="rep_factorName">
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diff changeset
341 <param name="factorName" value="Treatment"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
342 <repeat name="rep_factorLevel">
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
343 <param name="factorLevel" value="Treated"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
344 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
345 </repeat>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
346 <repeat name="rep_factorLevel">
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
347 <param name="factorLevel" value="Untreated"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
348 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
349 </repeat>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
350 </repeat>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
351 <param name="batch_factors" value="batch_factors.tab"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
352 <section name="advanced_options">
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
353 <param name="use_beta_priors" value="0"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
354 </section>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
355 <section name="output_options">
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
356 <param name="output_selector" value="normCounts"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
357 </section>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
358 <output name="deseq_out">
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
359 <assert_contents>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
360 <has_text_matching expression="FBgn0003360\t1933.*\t-3.*\t0.1.*\t-26.*\t6.*-151\t1.*-147"/>
17
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 16
diff changeset
361 </assert_contents>
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 16
diff changeset
362 </output>
d9e5cadc7f0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
iuc
parents: 16
diff changeset
363 </test>
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
364 <!--Ensure counts files without header works -->
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
365 <test expect_num_outputs="4">
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
366 <repeat name="rep_factorName">
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
367 <param name="factorName" value="Treatment"/>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
368 <repeat name="rep_factorLevel">
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
369 <param name="factorLevel" value="Treated"/>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
370 <param name="countsFile" value="GSM461179_treat_single.counts.noheader,GSM461180_treat_paired.counts.noheader,GSM461181_treat_paired.counts.noheader"/>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
371 </repeat>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
372 <repeat name="rep_factorLevel">
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
373 <param name="factorLevel" value="Untreated"/>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
374 <param name="countsFile" value="GSM461176_untreat_single.counts.noheader,GSM461177_untreat_paired.counts.noheader,GSM461178_untreat_paired.counts.noheader,GSM461182_untreat_single.counts.noheader"/>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
375 </repeat>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
376 </repeat>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
377 <param name="header" value="False"/>
31
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
378 <section name="advanced_options">
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
379 <param name="use_beta_priors" value="1"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
380 </section>
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
381 <section name="output_options">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
382 <param name="output_selector" value="normCounts,normRLog,normVST"/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
383 </section>
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
384 <output name="counts_out">
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
385 <assert_contents>
31
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
386 <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"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
387 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0"/>
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
388 </assert_contents>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
389 </output>
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
390 <output name="rlog_out">
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
391 <assert_contents>
31
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
392 <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"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
393 <has_text_matching expression="FBgn0000003\t0\t0\t0\t0\t0\t0\t0"/>
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
394 </assert_contents>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
395 </output>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
396 <output name="vst_out">
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
397 <assert_contents>
31
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
398 <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"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
399 <has_text_matching expression="FBgn0000003\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*\t5.*"/>
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
400 </assert_contents>
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
401 </output>
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
402 <output name="deseq_out" >
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
403 <assert_contents>
31
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
404 <has_text_matching expression="FBgn0003360\t1933\.9504.*\t-2\.8399.*\t0\.1309.*\t-21\.68.*\t.*e-104\t.*e-101"/>
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
405 </assert_contents>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
406 </output>
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
407 </test>
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
408 <!--Ensure Sailfish/Salmon input with tx2gene table works-->
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
409 <test expect_num_outputs="1">
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
410 <repeat name="rep_factorName">
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
411 <param name="factorName" value="Treatment"/>
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
412 <repeat name="rep_factorLevel">
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
413 <param name="factorLevel" value="Treated"/>
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
414 <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/>
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
415 </repeat>
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
416 <repeat name="rep_factorLevel">
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
417 <param name="factorLevel" value="Untreated"/>
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
418 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/>
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
419 </repeat>
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents: 5
diff changeset
420 </repeat>
31
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
421 <section name="advanced_options">
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
422 <param name="use_beta_priors" value="1"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
423 </section>
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
424 <section name="output_options">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
425 <param name="output_selector" value=""/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
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parents: 26
diff changeset
426 </section>
6
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parents: 5
diff changeset
427 <param name="tximport_selector" value="tximport"/>
11
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parents: 10
diff changeset
428 <param name="txtype" value="sailfish"/>
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
429 <param name="mapping_format_selector" value="tabular"/>
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
430 <param name="tabular_file" value="tx2gene.tab"/>
15
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iuc
parents: 14
diff changeset
431 <output name="deseq_out" >
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
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parents: 14
diff changeset
432 <assert_contents>
31
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parents: 30
diff changeset
433 <has_text_matching expression="UGT3A2\t1.8841.*\t-0.1329.*\t0.6936.*\t-0.1917.*\t0.8479.*\t0.9999.*"/>
19
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iuc
parents: 18
diff changeset
434 </assert_contents>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
435 </output>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
436 </test>
20
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parents: 19
diff changeset
437 <!--Ensure Sailfish/Salmon input with GFF3 annotation from NCBI works-->
19
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iuc
parents: 18
diff changeset
438 <test expect_num_outputs="1">
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
439 <repeat name="rep_factorName">
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
440 <param name="factorName" value="Treatment"/>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
441 <repeat name="rep_factorLevel">
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
442 <param name="factorLevel" value="Treated"/>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
443 <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
444 </repeat>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
445 <repeat name="rep_factorLevel">
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
446 <param name="factorLevel" value="Untreated"/>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
447 <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
448 </repeat>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
449 </repeat>
31
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diff changeset
450 <section name="advanced_options">
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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parents: 30
diff changeset
451 <param name="use_beta_priors" value="1"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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parents: 30
diff changeset
452 </section>
27
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iuc
parents: 26
diff changeset
453 <section name="output_options">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
454 <param name="output_selector" value=""/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
455 </section>
19
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
456 <param name="tximport_selector" value="tximport"/>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
457 <param name="txtype" value="sailfish"/>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
458 <param name="mapping_format_selector" value="gtf"/>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
459 <param name="gtf_file" value="GRCh38_latest_genomic.gff"/>
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
460 <output name="deseq_out" >
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents: 18
diff changeset
461 <assert_contents>
31
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diff changeset
462 <has_text_matching expression="UGT3A2\t1.8841.*\t-0.1329.*\t0.6936.*\t-0.1917.*\t0.8479.*\t0.9999.*"/>
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
463 </assert_contents>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
464 </output>
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
465 </test>
20
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iuc
parents: 19
diff changeset
466 <!--Ensure Sailfish/Salmon input with GTF annotation from Ensembl works-->
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
467 <test expect_num_outputs="1">
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
468 <repeat name="rep_factorName">
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
469 <param name="factorName" value="Treatment"/>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
470 <repeat name="rep_factorLevel">
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
471 <param name="factorLevel" value="Treated"/>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
472 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
473 </repeat>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
474 <repeat name="rep_factorLevel">
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
475 <param name="factorLevel" value="Untreated"/>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
476 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
477 </repeat>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
478 </repeat>
31
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iuc
parents: 30
diff changeset
479 <section name="advanced_options">
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
480 <param name="use_beta_priors" value="1"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
481 </section>
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
482 <section name="output_options">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
483 <param name="output_selector" value=""/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
484 </section>
20
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iuc
parents: 19
diff changeset
485 <param name="tximport_selector" value="tximport"/>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
486 <param name="txtype" value="sailfish"/>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
487 <param name="mapping_format_selector" value="gtf"/>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
488 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
489 <output name="deseq_out" >
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
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parents: 19
diff changeset
490 <assert_contents>
31
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diff changeset
491 <has_text_matching expression="ENSG00000168671\t1.8841.*\t-0.1180.*\t0.7429.*\t-0.1589.*\t0.8737.*\t0.9999.*"/>
20
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parents: 19
diff changeset
492 </assert_contents>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
493 </output>
89d26b11d452 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 82fc6e1098b8af8b769ff07689704c5275b76459
iuc
parents: 19
diff changeset
494 </test>
22
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
495 <!--Ensure group tags can be used to select factor levels -->
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
496 <test expect_num_outputs="1">
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
497 <param name="select_data|how" value="group_tags"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
498 <param name="select_data|countsFile">
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
499 <collection type="list">
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
500 <element name="1" value="sailfish/sailfish_quant.sf1.tab" tags="group:primary:treated"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
501 <element name="2" value="sailfish/sailfish_quant.sf2.tab" tags="group:primary:treated"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
502 <element name="3" value="sailfish/sailfish_quant.sf3.tab" tags="group:primary:treated"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
503 <element name="4" value="sailfish/sailfish_quant.sf4.tab" tags="group:primary:untreated"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
504 <element name="5" value="sailfish/sailfish_quant.sf5.tab" tags="group:primary:untreated"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
505 <element name="6" value="sailfish/sailfish_quant.sf6.tab" tags="group:primary:untreated"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
506 </collection>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
507 </param>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
508 <repeat name="rep_factorName">
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
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parents: 21
diff changeset
509 <param name="factorName" value="Treatment"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
510 <repeat name="rep_factorLevel">
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
511 <param name="factorLevel" value="Treated"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
512 <param name="groups" value="primary:treated"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
513 </repeat>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
514 <repeat name="rep_factorLevel">
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
515 <param name="factorLevel" value="Untreated"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
516 <param name="groups" value="primary:untreated"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
517 </repeat>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
518 </repeat>
31
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
519 <section name="advanced_options">
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
520 <param name="use_beta_priors" value="1"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
521 </section>
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
522 <section name="output_options">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
523 <param name="output_selector" value=""/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
524 </section>
22
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
525 <param name="tximport_selector" value="tximport"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
526 <param name="txtype" value="sailfish"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
527 <param name="mapping_format_selector" value="tabular"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
528 <param name="tabular_file" value="tx2gene.tab"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
529 <output name="deseq_out" >
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
530 <assert_contents>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
531 <has_text_matching expression="HOXC11\t0.557.*\t0.324.*\t0.437.*\t0.741.*\t0.458.*\t0.999.*"/>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
532 </assert_contents>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
533 </output>
e5c8afac22a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 1b60ee0faa1291f08620cd03d0f6647700daf862
iuc
parents: 21
diff changeset
534 </test>
24
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
535 <!--Ensure many_contrasts produces output collection -->
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
536 <test expect_num_outputs="1">
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
537 <param name="select_data|how" value="group_tags"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
538 <param name="select_data|countsFile">
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
539 <collection type="list">
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
540 <element name="1" value="sailfish/sailfish_quant.sf1.tab" tags="group:primary:treated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
541 <element name="2" value="sailfish/sailfish_quant.sf2.tab" tags="group:primary:treated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
542 <element name="3" value="sailfish/sailfish_quant.sf3.tab" tags="group:primary:treated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
543 <element name="4" value="sailfish/sailfish_quant.sf4.tab" tags="group:primary:untreated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
544 <element name="5" value="sailfish/sailfish_quant.sf5.tab" tags="group:primary:untreated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
545 <element name="6" value="sailfish/sailfish_quant.sf6.tab" tags="group:primary:untreated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
546 </collection>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
547 </param>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
548 <repeat name="rep_factorName">
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
549 <param name="factorName" value="Treatment"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
550 <repeat name="rep_factorLevel">
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
551 <param name="factorLevel" value="Treated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
552 <param name="groups" value="primary:treated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
553 </repeat>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
554 <repeat name="rep_factorLevel">
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
555 <param name="factorLevel" value="Untreated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
556 <param name="groups" value="primary:untreated"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
557 </repeat>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
558 </repeat>
31
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
559 <section name="advanced_options">
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
560 <param name="use_beta_priors" value="1"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
561 </section>
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
562 <section name="output_options">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
563 <param name="output_selector" value="many_contrasts"/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
564 </section>
24
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
565 <param name="tximport_selector" value="tximport"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
566 <param name="txtype" value="sailfish"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
567 <param name="mapping_format_selector" value="tabular"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
568 <param name="tabular_file" value="tx2gene.tab"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
569 <output_collection name="split_output" type="list" count="1">
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
570 <element name="Treatment_Treated_vs_Untreated">
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
571 <assert_contents>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
572 <has_text_matching expression="HOXC11\t0.557.*\t0.324.*\t0.437.*\t0.741.*\t0.458.*\t0.999.*"/>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
573 </assert_contents>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
574 </element>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
575 </output_collection>
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
iuc
parents: 22
diff changeset
576 </test>
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
577 <!--Test alpha_ma option-->
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
578 <test expect_num_outputs="1">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
579 <repeat name="rep_factorName">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
580 <param name="factorName" value="Treatment"/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
581 <repeat name="rep_factorLevel">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
582 <param name="factorLevel" value="Treated"/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
583 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
584 </repeat>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
585 <repeat name="rep_factorLevel">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
586 <param name="factorLevel" value="Untreated"/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
587 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
588 </repeat>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
589 </repeat>
31
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
590 <section name="advanced_options">
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
591 <param name="use_beta_priors" value="1"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
592 </section>
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
593 <section name="output_options">
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
594 <param name="output_selector" value=""/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
595 <param name="alpha_ma" value="0.05"/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
596 </section>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
597 <param name="tximport_selector" value="tximport"/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
598 <param name="txtype" value="sailfish"/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
599 <param name="mapping_format_selector" value="gtf"/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
600 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
601 <output name="deseq_out" >
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
602 <assert_contents>
31
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
603 <has_text_matching expression="ENSG00000168671\t1.8841.*\t-0.1180.*\t0.7429.*\t-0.1589.*\t0.8737.*\t0.9999.*"/>
27
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
604 </assert_contents>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
605 </output>
d027d1f4984e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit c8e7020d39d581d7374a13cf94c64998a6481e05"
iuc
parents: 26
diff changeset
606 </test>
29
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
607 <!-- Same as above alpha_ma test, but with size factors -->
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
608 <test expect_num_outputs="2">
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
609 <repeat name="rep_factorName">
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
610 <param name="factorName" value="Treatment"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
611 <repeat name="rep_factorLevel">
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
612 <param name="factorLevel" value="Treated"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
613 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
614 </repeat>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
615 <repeat name="rep_factorLevel">
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
616 <param name="factorLevel" value="Untreated"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
617 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
618 </repeat>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
619 </repeat>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
620 <section name="output_options">
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
621 <param name="output_selector" value="sizefactors"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
622 <param name="alpha_ma" value="0.05"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
623 </section>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
624 <param name="tximport_selector" value="tximport"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
625 <param name="txtype" value="sailfish"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
626 <param name="mapping_format_selector" value="gtf"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
627 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
628 <output name="sizefactors_out">
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
629 <assert_contents>
31
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
630 <has_text_matching expression="sailfish_quant\.sf4\.tab\t0\.8\d+"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
631 <has_text_matching expression="sailfish_quant\.sf3\.tab\t1\.0\d+"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
632 </assert_contents>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
633 </output>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
634 </test>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
635 <!--Test alpha_ma option, but with user-provided size factors -->
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
636 <test expect_num_outputs="1">
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
637 <repeat name="rep_factorName">
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
638 <param name="factorName" value="Treatment"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
639 <repeat name="rep_factorLevel">
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
640 <param name="factorLevel" value="Treated"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
641 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
642 </repeat>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
643 <repeat name="rep_factorLevel">
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
644 <param name="factorLevel" value="Untreated"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
645 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
646 </repeat>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
647 </repeat>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
648 <section name="advanced_options">
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
649 <param name="use_beta_priors" value="1"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
650 <conditional name="esf_cond">
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
651 <param name="esf" value="user"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
652 <param name="size_factor_input" value="size_factors_out.tsv"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
653 </conditional>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
654 </section>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
655 <section name="output_options">
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
656 <param name="output_selector" value=""/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
657 <param name="alpha_ma" value="0.05"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
658 </section>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
659 <param name="tximport_selector" value="tximport"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
660 <param name="txtype" value="sailfish"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
661 <param name="mapping_format_selector" value="gtf"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
662 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
663 <output name="deseq_out">
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
664 <assert_contents>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
665 <has_text_matching expression="ENSG00000168671\t1.90.*\t-0.05.*\t0.75.*\t-0.07.*\t0.94.*\t0.95.*"/>
29
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
666 </assert_contents>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
667 </output>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
668 </test>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
669 <!-- Same as above alpha_ma size factor test, but with a non-default estimator-->
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
670 <test expect_num_outputs="2">
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
671 <repeat name="rep_factorName">
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
672 <param name="factorName" value="Treatment"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
673 <repeat name="rep_factorLevel">
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
674 <param name="factorLevel" value="Treated"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
675 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf1.tab,sailfish_ensembl/sailfish_quant.sf2.tab,sailfish_ensembl/sailfish_quant.sf3.tab"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
676 </repeat>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
677 <repeat name="rep_factorLevel">
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
678 <param name="factorLevel" value="Untreated"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
679 <param name="countsFile" value="sailfish_ensembl/sailfish_quant.sf4.tab,sailfish_ensembl/sailfish_quant.sf5.tab,sailfish_ensembl/sailfish_quant.sf6.tab"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
680 </repeat>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
681 </repeat>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
682 <section name="advanced_options">
31
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diff changeset
683 <param name="esf" value="poscounts"/>
29
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diff changeset
684 </section>
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diff changeset
685 <section name="output_options">
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
686 <param name="output_selector" value="sizefactors"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
687 <param name="alpha_ma" value="0.05"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
688 </section>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
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diff changeset
689 <param name="tximport_selector" value="tximport"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
690 <param name="txtype" value="sailfish"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
691 <param name="mapping_format_selector" value="gtf"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
692 <param name="gtf_file" value="Homo_sapiens.GRCh38.94.gtf" ftype="gtf"/>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
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diff changeset
693 <output name="sizefactors_out" >
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
694 <assert_contents>
31
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parents: 30
diff changeset
695 <has_text_matching expression="sailfish_quant\.sf4\.tab\t0\.8\d+"/>
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
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parents: 30
diff changeset
696 <has_text_matching expression="sailfish_quant\.sf3\.tab\t1\.0\d+"/>
29
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parents: 28
diff changeset
697 </assert_contents>
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
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diff changeset
698 </output>
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diff changeset
699 </test>
30
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diff changeset
700 <!--Test prefilter parameter -->
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iuc
parents: 29
diff changeset
701 <test expect_num_outputs="2">
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
702 <repeat name="rep_factorName">
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
703 <param name="factorName" value="Treatment"/>
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
704 <repeat name="rep_factorLevel">
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
705 <param name="factorLevel" value="Treated"/>
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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parents: 29
diff changeset
706 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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parents: 29
diff changeset
707 </repeat>
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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parents: 29
diff changeset
708 <repeat name="rep_factorLevel">
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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parents: 29
diff changeset
709 <param name="factorLevel" value="Untreated"/>
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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parents: 29
diff changeset
710 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
711 </repeat>
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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parents: 29
diff changeset
712 </repeat>
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 29
diff changeset
713 <section name="advanced_options">
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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parents: 29
diff changeset
714 <conditional name="prefilter_conditional">
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
715 <param name="prefilter" value="-P"/>
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 29
diff changeset
716 <param name="prefilter_value" value="10"/>
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 29
diff changeset
717 </conditional>
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 29
diff changeset
718 </section>
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 29
diff changeset
719 <section name="output_options">
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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parents: 29
diff changeset
720 <param name="output_selector" value="normCounts"/>
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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parents: 29
diff changeset
721 </section>
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
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diff changeset
722 <output name="counts_out">
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 29
diff changeset
723 <assert_contents>
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
iuc
parents: 29
diff changeset
724 <has_n_lines n="2922"/>
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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parents: 29
diff changeset
725 </assert_contents>
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
726 </output>
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
727 <output name="deseq_out" >
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
728 <assert_contents>
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
729 <has_n_lines n="2921"/> <!-- Smallen value when compared with the first test-->
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
730 </assert_contents>
8fe98f7094de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 6868b66f73ddbe947986d1a20b546873cbd515a9
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diff changeset
731 </output>
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diff changeset
732 </test>
0
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diff changeset
733 </tests>
11
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diff changeset
734 <help><![CDATA[
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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735 .. class:: infomark
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diff changeset
736
3
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diff changeset
737 **What it does**
0
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738
31
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diff changeset
739 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
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diff changeset
740
11
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diff changeset
741 -----
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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diff changeset
742
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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diff changeset
743 **Inputs**
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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diff changeset
744
11
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parents: 10
diff changeset
745 **Count Files**
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746
15
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diff changeset
747 DESeq2_ takes count tables generated from **featureCounts**, **HTSeq-count** or **StringTie** as input. Count tables must be generated for each sample individually. One header row is assumed, but files with no header (e.g from HTSeq) can be input with the *Files have header?* option set to No. DESeq2 is capable of handling multiple factors that affect your experiment. The first factor you input is considered as the primary factor that affects gene expressions. Optionally, you can input one or more secondary factors that might influence your experiment. But the final output will be changes in genes due to primary factor in presence of secondary factors. Each factor has two levels/states. You need to select appropriate count table from your history for each factor level.
0
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diff changeset
748
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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diff changeset
749 The following table gives some examples of factors and their levels:
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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750
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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751 ========= ============== ===============
3
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diff changeset
752 Factor Factor level 1 Factor level 2
0
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753 --------- -------------- ---------------
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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diff changeset
754 Treatment Treated Untreated
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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755 --------- -------------- ---------------
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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diff changeset
756 Condition Knockdown Wildtype
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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757 --------- -------------- ---------------
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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diff changeset
758 TimePoint Day4 Day1
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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diff changeset
759 --------- -------------- ---------------
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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diff changeset
760 SeqType SingleEnd PairedEnd
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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761 --------- -------------- ---------------
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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diff changeset
762 Gender Female Male
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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763 ========= ============== ===============
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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764
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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765 *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.
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
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diff changeset
766
15
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diff changeset
767 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.
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diff changeset
768
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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diff changeset
769 **Salmon or Sailfish Files**
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
770
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
771 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.
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
772
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
773 Example:
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
774
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
775 ============ ========== =============== =========== ===========
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
776 Name Length EffectiveLength TPM NumReads
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
777 ------------ ---------- --------------- ----------- -----------
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
778 NR_001526 164 20.4518 0 0
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
779 NR_001526_1 164 20.4518 0 0
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
780 NR_001526_2 164 20.4518 0 0
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
781 NM_130786 1764 1956.04 2.47415 109.165
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
782 NR_015380 2129 2139.53 1.77331 85.5821
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
783 NM_001198818 9360 7796.58 2.38616e-07 4.19648e-05
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
784 NM_001198819 9527 7964.62 0 0
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
785 NM_001198820 9410 7855.78 0 0
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
786 NM_014576 9267 7714.88 0.0481114 8.37255
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
787 ============ ========== =============== =========== ===========
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
788
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
789 **kallisto Files**
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
790
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
791 kallisto ``abundance.tsv`` files can be imported by setting type to *kallisto* above. An example of the format is shown below.
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
792
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
793 Example:
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
794
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
795 ============ ========== =============== =========== ===========
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
796 target_id length eff_length est_counts tpm
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
797 ------------ ---------- --------------- ----------- -----------
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
798 NR_001526 164 20.4518 0 0
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
799 NR_001526_1 164 20.4518 0 0
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
800 NR_001526_2 164 20.4518 0 0
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
801 NM_130786 1764 1956.04 109.165 2.47415
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
802 NR_015380 2129 2139.53 85.5821 1.77331
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
803 NM_001198818 9360 7796.58 4.19648e-05 2.38616e-07
15
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
804 NM_001198819 9527 7964.62 0 0
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
805 NM_001198820 9410 7855.78 0 0
9a616afdbda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 83eb5b2665d87c02b270596f8175499e69061032
iuc
parents: 14
diff changeset
806 NM_014576 9267 7714.88 8.37255 0.0481114
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
807 ============ ========== =============== =========== ===========
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
808
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
809 -----
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
810
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
811 **Output**
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
812
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
813 DESeq2_ generates a tabular file containing the different columns and optional visualized results as PDF.
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
814
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
815 ====== ==========================================================
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
816 Column Description
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
817 ------ ----------------------------------------------------------
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
818 1 Gene Identifiers
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
819 2 mean normalised counts, averaged over all samples from both conditions
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
820 3 the logarithm (to basis 2) of the fold change (See the note in inputs section)
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
821 4 standard error estimate for the log2 fold change estimate
2
afe2a77c5900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit e0f819a2fd56eb5ee30a7fd772780693e1f085fa
iuc
parents: 1
diff changeset
822 5 Wald statistic
afe2a77c5900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit e0f819a2fd56eb5ee30a7fd772780693e1f085fa
iuc
parents: 1
diff changeset
823 6 p value for the statistical significance of this change
afe2a77c5900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit e0f819a2fd56eb5ee30a7fd772780693e1f085fa
iuc
parents: 1
diff changeset
824 7 p value adjusted for multiple testing with the Benjamini-Hochberg procedure
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
825 which controls false discovery rate (FDR)
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
826 ====== ==========================================================
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
827
29
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
828 By selecting ``Output sample size factors`` in the "Output options"
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
829 selection box, the size factors used to normalize the samples can also
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
830 be output as a tabular file.
cd9874cb9019 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit cbeb1c4c436be04323bd9a809a6393d00b168d07"
iuc
parents: 28
diff changeset
831
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
832 .. _DESeq2: http://master.bioconductor.org/packages/release/bioc/html/DESeq2.html
11
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
833 .. _tximport: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html
25204a860b79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 0a56599c36b4968095ec5a3cb589f94fb139466c
iuc
parents: 10
diff changeset
834 ]]></help>
31
9a882d108833 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
iuc
parents: 30
diff changeset
835 <expand macro="citations"/>
0
d983d19fbbab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 625a9632df44b1b623941e35c22f71f0e55ee371
iuc
parents:
diff changeset
836 </tool>