Mercurial > repos > iuc > trinity_run_de_analysis

annotate run_de_analysis.xml @ 4:36b2700b604d draft

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author iuc
date Thu, 23 Mar 2017 10:16:19 -0400
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1 <tool id="trinity_run_de_analysis" name="Differential expression analysis" version="@WRAPPER_VERSION@.1">
0
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2 <description>using a Trinity assembly</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="requirements">
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7 <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 -->
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8 <requirement type="package" version="3.14.0">bioconductor-edger</requirement>
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9 <requirement type="package" version="3.28.10">bioconductor-limma</requirement>
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10 <requirement type="package" version="1.10.0">bioconductor-deseq2</requirement>
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11 </expand>
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12 <expand macro="stdio"/>
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13 <command><![CDATA[
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15 ln -s "${matrix}" "input.matrix"
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17 &&
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19 run_DE_analysis.pl
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21 --matrix "input.matrix"
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23 --samples_file "${samples}"
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25 --method ${method_choice.method}
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27 #if $method_choice.method == "edgeR":
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28 --dispersion ${method_choice.edger_dispersion}
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29 #end if
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31 #if $method_choice.method == "ROTS":
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32 --ROTS_B ${method_choice.rots_b}
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33 --ROTS_K ${method_choice.rots_k}
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34 #end if
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36 --min_rowSum_counts ${additional_params.min_rowSum_counts}
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38 #if $additional_params.reference_sample:
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39 --reference_sample ${additional_params.reference_sample}
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40 #end if
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42 #if $additional_params.contrasts:
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43 --contrasts ${additional_params.contrasts}
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44 #end if
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46 --output results
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47
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48 ]]></command>
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49 <inputs>
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50 <param format="tabular" name="matrix" argument="--matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/>
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51 <param format="tabular" name="samples" argument="--samples_file" type="data" label="Sample description" help="file describing samples and replicates"/>
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52
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53 <conditional name="method_choice">
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54 <param type="select" name="method" argument="--method" label="Differential analysis method">
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55 <option value="edgeR">edgeR</option>
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56 <option value="DESeq2">DESeq2</option>
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57 <option value="voom">voom</option>
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58 <option value="ROTS">ROTS</option>
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59 </param>
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60 <when value="edgeR">
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61 <param name="edger_dispersion" argument="--dispersion" type="float" value="0.1" label="edgeR dispersion value" help="Read edgeR manual to guide your value choice" />
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62 </when>
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63 <when value="ROTS">
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64 <param name="rots_b" argument="--ROTS_B" type="integer" value="500" label="number of bootstraps and permutation resampling" />
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65 <param name="rots_k" argument="--ROTS_K" type="integer" value="5000" label="largest top genes size" />
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66 </when>
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67 <when value="voom">
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68 </when>
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69 <when value="DESeq2">
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70 </when>
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71 </conditional>
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72
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73 <section name="additional_params" title="Additional Options" expanded="False">
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74 <param name="min_rowSum_counts" argument="--min_rowSum_counts" type="integer" value="2" label="Minimum count" help="Only those rows of matrix meeting requirement will be tested"/>
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75 <param name="reference_sample" argument="--reference_sample" type="text" optional="true" value="" label="Name of a sample to which all other samples should be compared" help="default is doing all pairwise-comparisons among samples"/>
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76 <param format="tabular" name="contrasts" argument="--contrasts" optional="true" type="data" label="Pairs of sample comparisons to perform" help="A 2-column tabular with lists of pairs of samples to compare"/>
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77 </section>
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78 </inputs>
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79 <outputs>
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80 <collection name="DE_results" type="list" label="Differential expression results on ${on_string}">
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81 <discover_datasets pattern="(?P&lt;name&gt;.+)\.DE_results$" ext="tabular" directory="results" />
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82 </collection>
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83 <collection name="PDF_results" type="list" label="Differential expression plots on ${on_string}">
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84 <discover_datasets pattern="(?P&lt;name&gt;.+)\.pdf$" ext="pdf" directory="results" />
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85 </collection>
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86 </outputs>
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87 <tests>
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88 <test>
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89 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
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90 <param name="samples" value="count/samples.txt"/>
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91 <param name="method" value="DESeq2"/>
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92 <output_collection name="DE_results">
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93 <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results"/>
1563554bb3f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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94 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results"/>
1563554bb3f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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95 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results"/>
1563554bb3f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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96 </output_collection>
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97 <output_collection name="PDF_results">
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98 <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf"/>
1563554bb3f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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99 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/>
1563554bb3f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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100 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/>
1563554bb3f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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101 </output_collection>
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102 </test>
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103 <test>
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104 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
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105 <param name="samples" value="count/samples.txt"/>
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106 <param name="method" value="edgeR"/>
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107 <output_collection name="DE_results">
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108 <element name="input.matrix.wt_37_vs_wt_GSNO.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results"/>
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109 <element name="input.matrix.wt_37_vs_wt_ph8.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results"/>
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110 <element name="input.matrix.wt_GSNO_vs_wt_ph8.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results"/>
1563554bb3f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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111 </output_collection>
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112 <output_collection name="PDF_results">
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113 <element name="input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano.pdf"/>
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114 <element name="input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf"/>
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115 <element name="input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf"/>
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116 </output_collection>
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117 </test>
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118 <test>
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119 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
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120 <param name="samples" value="count/samples.txt"/>
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121 <param name="method" value="voom"/>
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122 <output_collection name="DE_results">
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123 <element name="input.matrix.wt_37_vs_wt_GSNO.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results"/>
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124 <element name="input.matrix.wt_37_vs_wt_ph8.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results"/>
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125 <element name="input.matrix.wt_GSNO_vs_wt_ph8.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results"/>
1563554bb3f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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126 </output_collection>
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127 <output_collection name="PDF_results">
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128 <element name="input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano.pdf"/>
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129 <element name="input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf"/>
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130 <element name="input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf"/>
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131 </output_collection>
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132 </test>
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133 </tests>
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134 <help>
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135 <![CDATA[
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136 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
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137 This tool performs differential expression analyses on a transcriptome assembled with Trinity.
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138
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139 **Inputs**
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140
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141 This tool uses the matrix produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool.
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142
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143 You must describe your samples and replicates with a tabular file looking like this:
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144
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145 =========== ================
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146 ConditionA CondA_replicate1
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147 ----------- ----------------
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148 ConditionA CondA_replicate2
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149 ----------- ----------------
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150 ConditionB CondB_replicate1
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151 ----------- ----------------
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152 ConditionB CondB_replicate2
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153 ----------- ----------------
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154 ConditionC CondC_replicate1
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155 ----------- ----------------
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156 ConditionC CondC_replicate2
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157 ----------- ----------------
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158 ConditionC CondC_replicate3
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159 =========== ================
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160
1
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161
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162 This file can be generated with the 'Describe samples and replicates' tool.
0
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163 It will probably be the same file as used in the tool 'RNASeq samples quality check for transcript quantification'.
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164 The names in column 2 must match the names given in the tool 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity'.
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165
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166
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167 .. _Trinity: http://trinityrnaseq.github.io
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168 ]]>
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169 </help>
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170
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171 <expand macro="citation" />
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172 </tool>