Mercurial > repos > vandelj > giant_factor_generator

annotate galaxy/wrappers/FactorFileGenerator.xml @ 2:1f4a30d19264 draft default tip

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"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit 89b7d0e8812f53222691cffe29bd48be6519829d"
author vandelj
date Fri, 25 Sep 2020 08:53:02 +0000
parents 7a520f7169e1
children
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1 <tool name="GIANT-Factor file generator" id="giant_factor_generator" version="0.1.3">
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2 <description>Generate factor file used by other GIANT tools</description>
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3 <requirements>
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4 </requirements>
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5 <code file="../../src/General_functions.py"/>
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6 <!--<code file="./src/General_functions.py"/> change for Planemo test-->
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7 <stdio>
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8 <regex match="Execution halted"
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9 source="both"
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10 level="fatal"
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11 description="Execution halted, please contact tool developer or administrators." />
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12 <regex match="Error in"
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13 source="both"
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14 level="fatal"
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15 description="An error occured during R execution, please contact tool developer." />
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16 <exit_code range="1:9" level="fatal" description="Error during factor file generation, see log file for more information." />
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17 </stdio>
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18 <command> <![CDATA[
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20 #import imp
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21 #set $general_functions=$imp.load_source('General_functions', $__tool_directory__+'/../../src/General_functions.py')
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22 ##change for Planemo test
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23 ##set $general_functions=$imp.load_source('General_functions', $__tool_directory__+'/src/General_functions.py')
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24
1
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25 #if $inputCondition.selection == "CELcollection" and $inputCondition.selectCollectionStrat.how=="group_tags":
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26 #set $temp_factor_names = list()
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27 #for $factor in $inputCondition.selectCollectionStrat.factorListBis:
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28 #set $temp_factor = list()
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29 #for $level in $factor.valueList:
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30 #set $temp_level = ''
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31 #for $group in $level.valueConditions.value:
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32 #for $file in $inputCondition.inputData.get_datasets_for_group($group):
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33 printf "$group\t $file.element_identifier\n" >> ./TAGmatching.csv;
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34 #if $temp_level == '':
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35 #set $temp_level = str($file.element_identifier)
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36 #else:
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37 #set $temp_level += ','+str($file.element_identifier)
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38 #end if
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39 #end for
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40 #end for
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41 $temp_factor.append( {'valueName':str($level.valueName), 'valueConditions':$temp_level} )
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42 #end for
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43 $temp_factor.reverse()
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44 $temp_factor_names.append( {'factorName':str($factor.factorName), 'valueList':$temp_factor} )
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45 #end for
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46 #end if
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48 #if $inputCondition.selection == "CELcollection":
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49 #if $inputCondition.selectCollectionStrat.how=="group_tags":
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50 #set $ret_code=$general_functions.generateFactorFile($inputCondition.inputData.collection,$temp_factor_names,$outputData.file_name,$log.file_name)
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51 #else:
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52 #set $ret_code=$general_functions.generateFactorFile($inputCondition.inputData.collection,$inputCondition.selectCollectionStrat.factorListBis,$outputData.file_name,$log.file_name)
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53 #end if
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54 #else:
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55 #set $ret_code=$general_functions.generateFactorFile($inputCondition.inputData,$inputCondition.factorList,$outputData.file_name,$log.file_name)
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56 #end if
0
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57
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58 if [ $ret_code != 0 ]; then
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59 printf "[ERROR]Error during factor file generation\n" >> $log;
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60 exit $ret_code;
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61 fi;
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62
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63 printf "[INFO]End of tool script" >> $log;
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64 ]]>
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65 </command>
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66 <inputs>
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67 <param type="text" name="title" value="ConditionsGenerator_toPersonalize" label="Title for output"/>
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68
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69 <conditional name="inputCondition">
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70 <param name="selection" type="select" label="Input data type for sample names" force_select="true">
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71 <option value="normalizedData">Expression tabular file</option>
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72 <option value="CELfiles">.CEL files</option>
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73 <option value="CELcollection">.CEL file collection</option>
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74 </param>
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75 <when value="normalizedData">
1
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76 <param type="data" name="inputData" format="tabular" label="Select a single dataset" optional="false" multiple="false"/>
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77
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78 <repeat name="factorList" title="Factor">
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79 <param type="text" name="factorName" value="" label="Factor name"/>
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80 <repeat name="valueList" title="Value">
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81 <param type="text" name="valueName" value="" label="Value name"/>
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82 <param name="valueConditions" type="select" optional="false" multiple="true" label="Select sample sharing this value"
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83 refresh_on_change="true" dynamic_options="get_condition_file_names(inputCondition['inputData'],0)">
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84 </param>
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85 </repeat>
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86 </repeat>
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87
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88 </when>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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89 <when value="CELfiles">
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90 <param type="data" name="inputData" format="cel" label="Select multiple files" optional="false" multiple="true">
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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91 <validator type="empty_field" message="At least two data files should be selected"></validator>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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92 </param>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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93
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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94 <repeat name="factorList" title="Factor">
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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95 <param type="text" name="factorName" value="" label="Factor name"/>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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96 <repeat name="valueList" title="Value">
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97 <param type="text" name="valueName" value="" label="Value name"/>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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98 <param name="valueConditions" type="select" optional="false" multiple="true" label="Select sample sharing this value"
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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99 refresh_on_change="true" dynamic_options="get_condition_file_names(inputCondition['inputData'])">
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100 </param>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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101 </repeat>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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102 </repeat>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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103
0
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104 </when>
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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105 <when value="CELcollection">
1
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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106 <param type="data_collection" name="inputData" format="cel" label="Select a single dataset collection" optional="false" multiple="true">
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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107 <validator type="empty_field" message="One data collection should be selected"></validator>
0
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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108 </param>
1
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109
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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110 <conditional name="selectCollectionStrat">
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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111 <param name="how" type="select" label="Select how .CEL files will be assigned to factor values">
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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112 <option value="individualSelection">Select individually each .CEL file from the collection</option>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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113 <option value="group_tags">Use associated .CEL file tags</option>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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114 </param>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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115 <when value="individualSelection">
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116
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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117 <repeat name="factorListBis" title="Factor">
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118 <param type="text" name="factorName" value="" label="Factor name"/>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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119 <repeat name="valueList" title="Value">
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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120 <param type="text" name="valueName" value="" label="Value name"/>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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121 <param name="valueConditions" type="select" optional="false" multiple="true" label="Select sample sharing this value"
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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122 refresh_on_change="true" dynamic_options="get_condition_file_names(inputCondition['inputData'])">
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123 </param>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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124 </repeat>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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125 </repeat>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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126
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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127 </when>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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128 <when value="group_tags">
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129
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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130 <repeat name="factorListBis" title="Factor">
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131 <param type="text" name="factorName" value="" label="Factor name"/>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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132 <repeat name="valueList" title="Value">
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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133 <param type="text" name="valueName" value="" label="Value name"/>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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134 <param name="valueConditions" type="group_tag" data_ref="inputData" multiple="true" label="Select groups sharing this value"/>
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135 </repeat>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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136 </repeat>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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137
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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138 </when>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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139 </conditional>
0
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140 </when>
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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141 </conditional>
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142 </inputs>
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143
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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144 <outputs>
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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145 <data format="tabular" name="outputData" label="${title}_conditionsFile"/>
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146 <data format="txt" name="log" label="${title}_Log" />
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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147 </outputs>
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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148
1
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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149
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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150
0
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151 <tests>
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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152 <test maxseconds="3600">
1
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153 <conditional name="inputCondition">
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154 <param name="selection" value="normalizedData" />
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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155 <param name="inputData" value="./NormalizedData.tabular" />
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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156 <repeat name="factorList">
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157 <param name="factorName" value="Strain" />
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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158 <repeat name="valueList">
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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159 <param name="valueName" value="WT" />
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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160 <param name="valueConditions" value="GSM205769.CEL,GSM205772.CEL,GSM205768.CEL,GSM205767.CEL,GSM205766.CEL,GSM205771.CEL,GSM205770.CEL"/>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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161 </repeat>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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162 <repeat name="valueList">
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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163 <param name="valueName" value="KO" />
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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164 <param name="valueConditions" value="GSM205777.CEL,GSM205776.CEL,GSM205781.CEL,GSM205773.CEL,GSM205780.CEL,GSM205779.CEL,GSM205782.CEL,GSM205775.CEL,GSM205774.CEL,GSM205778.CEL"/>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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165 </repeat>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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166 </repeat>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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167 <repeat name="factorList">
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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168 <param name="factorName" value="Treatment" />
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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169 <repeat name="valueList">
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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170 <param name="valueName" value="Control" />
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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171 <param name="valueConditions" value="GSM205777.CEL,GSM205776.CEL,GSM205773.CEL,GSM205775.CEL,GSM205774.CEL,GSM205768.CEL,GSM205767.CEL,GSM205766.CEL"/>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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172 </repeat>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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173 <repeat name="valueList">
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174 <param name="valueName" value="Treat" />
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175 <param name="valueConditions" value="GSM205781.CEL,GSM205769.CEL,GSM205772.CEL,GSM205780.CEL,GSM205779.CEL,GSM205782.CEL,GSM205778.CEL,GSM205771.CEL,GSM205770.CEL"/>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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176 </repeat>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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177 </repeat>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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178 </conditional>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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179 <output name="outputData" file="./FactorFileGenerator/output/conditionsFile.csv" />
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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180 <output name="log" file="./FactorFileGenerator/output/outputLog.txt" />
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181 </test>
1
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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182 </tests>
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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183
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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184
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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185
0
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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186 <help>
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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187 <![CDATA[
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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188 **What it does ?**
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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189
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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190 This tool generates factor information file used by other tools of GIANT tool suite.
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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191
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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192 -----
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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193
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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194 **Parameters**
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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195
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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196 \- **Title** to personalize output file names (please avoid special characters and spaces).
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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197
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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198 \- **Input Data** used only to extract sample names
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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199
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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200 - **Expression tabular file** with samples as columns and genes as rows (only the header row will be used to extract sample names).
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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201
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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202 ::
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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203
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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204 Conditions 157_(HuGene-2_0-st).CEL 156_(HuGene-2_0-st).CEL 155_(HuGene-2_0-st).CEL 154_(HuGene-2_0-st).CEL
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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205 DDX11L2 4.500872 4.429759 4.780281 4.996189
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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206 MIR1302-2 3.415065 3.520472 3.471503 3.567988
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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207 OR4F5 3.737956 3.011586 3.424494 3.497545
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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208 VWA1 5.189621 5.129595 4.806793 5.227014
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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209
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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210 OR
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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211
1
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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212 - **.CEL files** of your study (you should select multiple .CEL files).
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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213
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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214 OR
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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215
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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216 - **.CEL file collection** of your study (you should select a unique collection file).
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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217
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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218 \- **Individual selection** of files to associate to factor values.
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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219
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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220 or
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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221
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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222 \- **Tag selection** to associate samples sharing the same tag to factor values.
0
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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223
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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224 \- **Factor definition**
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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225
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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226 - **Factor name** to discriminate between samples as 'Treatments', 'Year', 'Strain' (please avoid special characters)
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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227
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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228 - **Value name** of different states for the current factor as 'KO' or 'WT' for 'Strain' factor (please avoid special characters)
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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229
1
7a520f7169e1 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
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230 - **Select sample/tag** to assign to current value
0
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231
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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232 -----
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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233
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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234 **Outputs**
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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235
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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236 - **Factor information tabular file** with factors as columns and samples as rows (header row contains factor names and first column sample names).
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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237
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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238 ::
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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239
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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240 Conditions Sex Treatment Reaction
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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241 138_(HuGene-2_0-st).CEL 1 TreatA Pos
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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242 148_(HuGene-2_0-st).CEL 0 NoTreat Pos
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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243 139_(HuGene-2_0-st).CEL 0 TreatB Neg
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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244 149_(HuGene-2_0-st).CEL 0 NoTreat Neg
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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245
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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246 - **LOG file** for job log. If you see errors, please attached this in the bug report
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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247
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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248 ]]> </help>
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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249
4764dc6a1019 "planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit cb276a594444c8f32e9819fefde3a21f121d35df"
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250 </tool>