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annotate run_DE_analysis.xml @ 7:1b7800489efb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 6dad4ca6483946af64f484feaff78ac9d1d87352
author iuc
date Mon, 20 Jun 2016 11:44:50 -0400
parents e4a9e0798360
children 258c64019e50
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1 <tool id="run_DE_analysis" name="Differential expression analysis" version="2.1.1.1">
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2 <description>using a Trinity assembly</description>
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3 <requirements>
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4 <requirement type="package" version="2.1.1">trinity</requirement>
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5 <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 -->
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6 <requirement type="package" version="1.10.0">deseq2</requirement>
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7 <requirement type="package" version="1.10.0">bioconductor-deseq2</requirement>
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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 </requirements>
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11 <stdio>
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12 <exit_code range="1:"/>
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13 </stdio>
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14 <command><![CDATA[
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16 ln -s "${matrix}" "input.matrix"
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18 &&
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20 run_DE_analysis.pl
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22 --matrix "input.matrix"
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24 --samples_file "${samples}"
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26 --method ${method_choice.method}
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28 #if $method_choice.method == "edgeR":
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29 --dispersion ${method_choice.edger_dispersion}
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30 #end if
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32 #if $method_choice.method == "ROTS":
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33 --ROTS_B ${method_choice.rots_b}
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34 --ROTS_K ${method_choice.rots_k}
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35 #end if
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36
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37 --min_rowSum_counts ${additional_params.min_rowSum_counts}
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39 #if $additional_params.reference_sample:
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40 --reference_sample ${additional_params.reference_sample}
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41 #end if
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42
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43 #if $additional_params.contrasts:
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44 --contrasts ${additional_params.contrasts}
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45 #end if
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46
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47 --output results
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48
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49 ]]></command>
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50 <inputs>
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51 <param format="tabular" name="matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/>
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52 <param format="tabular" name="samples" type="data" label="Sample description" help="file describing samples and replicates"/>
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53
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54 <conditional name="method_choice">
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55 <param type="select" name="method" label="Differential analysis method">
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56 <option value="edgeR">edgeR</option>
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57 <option value="DESeq2">DESeq2</option>
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58 <option value="voom">voom</option>
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59 <option value="ROTS">ROTS</option>
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60 </param>
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61 <when value="edgeR">
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62 <param name="edger_dispersion" type="float" value="0.1" label="edgeR dispersion value" help="Read edgeR manual to guide your value choice" />
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63 </when>
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64 <when value="ROTS">
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65 <param name="rots_b" type="integer" value="500" label="number of bootstraps and permutation resampling" />
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66 <param name="rots_k" type="integer" value="5000" label="largest top genes size" />
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67 </when>
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68 <when value="voom">
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69 </when>
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70 <when value="DESeq2">
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71 </when>
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72 </conditional>
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73
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74 <section name="additional_params" title="Additional Options" expanded="False">
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75 <param name="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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76 <param name="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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77 <param format="tabular" name="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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78 </section>
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79 </inputs>
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80 <outputs>
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81 <collection name="DE_results" type="list" label="Differential expression results on ${on_string}">
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82 <discover_datasets pattern="(?P&lt;name&gt;.+)\.DE_results" ext="tabular" directory="results" visible="true" />
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83 </collection>
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84 <collection name="PDF_results" type="list" label="Differential expression plots on ${on_string}">
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85 <discover_datasets pattern="(?P&lt;name&gt;.+)\.pdf" ext="pdf" directory="results" visible="true" />
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86 </collection>
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87 </outputs>
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88 <tests>
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89 <test>
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90 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
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91 <param name="samples" value="count/samples.txt"/>
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92 <param name="method" value="DESeq2"/>
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93 <output_collection name="DE_results">
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94 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results"/>
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95 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results"/>
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96 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/matrix.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results"/>
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97 </output_collection>
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98 <output_collection name="PDF_results">
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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/matrix.counts.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf"/>
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100 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/matrix.counts.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/>
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101 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/matrix.counts.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/>
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102 </output_collection>
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103 </test>
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104 </tests>
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105 <help>
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106 <![CDATA[
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107 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
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108 This tool performs differential expression analyses on a transcriptome assembled with Trinity.
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109
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110 **Inputs**
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111
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112 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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113
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114 You must describe your samples and replicates with a tabular file looking like this:
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115
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116 =========== ================
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117 ConditionA CondA_replicate1
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118 ----------- ----------------
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119 ConditionA CondA_replicate2
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120 ----------- ----------------
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121 ConditionB CondB_replicate1
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122 ----------- ----------------
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123 ConditionB CondB_replicate2
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124 ----------- ----------------
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125 ConditionC CondC_replicate1
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126 ----------- ----------------
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127 ConditionC CondC_replicate2
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128 ----------- ----------------
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129 ConditionC CondC_replicate3
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130 =========== ================
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131
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132 It will probably be the same file as used in the tool 'RNASeq samples quality check for transcript quantification'.
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133 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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134
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135
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136 .. _Trinity: http://trinityrnaseq.github.io
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137 ]]>
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138 </help>
4
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139
2
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140 <citations>
5
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141 <citation type="doi">10.1038/nbt.1883</citation>
2
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142 </citations>
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143 </tool>
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144