Mercurial > repos > iuc > trinity_analyze_diff_expr

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit ec26c475a013d89b0f973f29250d660e79d4751f
author iuc
date Wed, 20 Sep 2023 14:59:16 +0000
parents 9871e84c26ee
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1 <tool id="trinity_analyze_diff_expr" name="Extract and cluster differentially expressed transcripts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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2 <description>from 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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2a89673cec86 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c468d2b9613f88cc5f96f77ab1e0592d3c9ce707"
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 ## DE results input files must be in the working directory and have suffix .DE_results
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10 #import re
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11 #for $input in $DE_results
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12 #if re.search('.DE_results$',input.element_identifier)
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13 ## General case, where DE results files have been previously generated by run_de_analysis.pl
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14 ln -s '${input}' "${re.sub('[^\w\-_.]', '_', input.element_identifier)}"
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15 #else
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16 ## Particular case, where DE results files have non-standard names
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17 ln -s '${input}' "${re.sub('[^\w\-_.]', '_', input.element_identifier)}.DE_results"
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18 #end if
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19 &&
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20 #end for
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21 #if str( $additional_params.GO_enrichment.examine_GO_enrichment ) == "yes":
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22 ## DE matrix input files must be in the working directory and have the same name as DE results input files, but replacing suffix .DE_results by suffix .count_matrix
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23 #for $DE_matrix in $additional_params.GO_enrichment.DE_matrices
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24 ## Handle general case, where DE results files and DE matrix files have been previously generated by run_de_analysis.pl
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25 ln -s '${DE_matrix}' "${re.sub('[^\w\-_.]', '_', DE_matrix.element_identifier)}"
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26 &&
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27 #end for
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28 #end if
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30 analyze_diff_expr.pl
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31 --matrix '${matrix}'
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32 --samples '${samples}'
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33 -P ${P}
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34 -C ${C}
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36 #if str( $additional_params.max_DE_genes_per_comparison ):
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37 --max_DE_genes_per_comparison ${additional_params.max_DE_genes_per_comparison}
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38 #end if
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40 $additional_params.order_columns_by_samples_file
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42 #if $additional_params.max_genes_clust:
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43 --max_genes_clust ${additional_params.max_genes_clust}
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44 #end if
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46 #if str( $additional_params.GO_enrichment.examine_GO_enrichment ) == "yes":
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47 --examine_GO_enrichment
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48 --GO_annots '${$additional_params.GO_enrichment.GO_annots}'
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49 --gene_lengths '${$additional_params.GO_enrichment.gene_lengths}'
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50 #end if
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51
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52 --output results
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53 ]]></command>
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54 <inputs>
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55 <param argument="--matrix" format="tabular" type="data" label="Expression matrix" help="Raw counts matrix produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool"/>
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56 <param argument="--samples" format="tabular" type="data" label="Sample description" help="File describing samples and replicates"/>
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57 <param name="DE_results" format="tabular" type="data_collection" collection_type="list" label="Differential expression results" help="Generated by 'Differential expression analysis using a Trinity assembly' tool"/>
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58 <param argument="-P" type="float" value="0.001" label="p-value cutoff for FDR"/>
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59 <param argument="-C" type="float" value="2" label="min abs(log2(a/b)) fold change" help="Default: 2 (meaning 2^(2) or 4-fold"/>
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60 <section name="additional_params" title="Additional Options" expanded="False">
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61 <param argument="--max_DE_genes_per_comparison" type="integer" value="" optional="true" label="Maximum differential expression genes per comparison" help="Extract only up to the top number of DE features within each pairwise comparison. This is useful when you have massive numbers of DE features but still want to make useful heatmaps and other plots with more manageable numbers of data points."/>
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62 <param argument="--order_columns_by_samples_file" type="boolean" checked="false" truevalue="--order_columns_by_samples_file" falsevalue="" label="Order columns by samples file" help="Instead of clustering samples or replicates hierarchically based on gene expression patterns, order columns according to order in the --samples file."/>
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63 <param argument="--max_genes_clust" type="integer" value="10000" label="Maximum genes in cluster" help="If more than 10000, heatmaps are not generated, since too time consuming"/>
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64 <conditional name="GO_enrichment">
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65 <param argument="--examine_GO_enrichment" type="select" label="Run GO enrichment analysis" help="To examine GO enrichment, you must first run Trinotate and then extract all GO assignments for each gene feature, with the Trinotate script extract_GO_assignments_from_Trinotate_xls.pl">
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66 <option value="no">No</option>
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67 <option value="yes">Yes</option>
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68 </param>
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69 <when value="no">
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70 </when>
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71 <when value="yes">
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72 <param name="DE_matrices" format="tabular" type="data_collection" collection_type="list" label="Differential expression count matrices" help="Generated by 'Differential expression analysis using a Trinity assembly' tool. If not, be careful that the file names are identical to the file names of differential expression results, with extension '.count_matrix' instead of '.DE_results'."/>
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73 <param argument="--GO_annots" format="tabular" type="data" label="Extracted GO assignments file" help="Generated by the Trinotate script extract_GO_assignments_from_Trinotate_xls.pl. Must have 2 columns: feature_id GO:000001,GO:00002,..."/>
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74 <param argument="--gene_lengths" format="tabular" type="data" label="Gene length file" help="Must have 2 columns: feature_id length"/>
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75 </when>
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76 </conditional>
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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="extracted_DE_genes" type="list" label="${tool.name} on ${on_string}: extracted differentially expressed genes">
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81 <discover_datasets pattern="(?P&lt;name&gt;.+\.subset)$" ext="tabular" />
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82 </collection>
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83 <collection name="summary_files" type="list" label="${tool.name} on ${on_string}: summary files">
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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84 <data format="tabular" name="results_matrix" from_work_dir="results.matrix"/>
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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85 <data format="tabular" name="results_matrix_log2_centered" from_work_dir="results.matrix.log2.centered.dat"/>
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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86 <data format="pdf" name="results_matrix_log2_centered_heatmap" from_work_dir="results.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/>
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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87 <data format="tabular" name="results_matrix_log2" from_work_dir="results.matrix.log2.dat"/>
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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88 <data format="tabular" name="results_matrix_log2_sample_cor" from_work_dir="results.matrix.log2.sample_cor.dat"/>
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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89 <data format="pdf" name="results_matrix_log2_sample_cor_matrix" from_work_dir="results.matrix.log2.sample_cor_matrix.pdf"/>
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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90 </collection>
19
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parents: 17
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91 <data name="rdata" format="rdata" label="${tool.name} on ${on_string}: RData file" from_work_dir="results.matrix.RData"/>
0
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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92 <collection name="GOseq_enrichment" type="list" label="${tool.name} on ${on_string}: GOseq enriched and depleted categories">
4
63030102d46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
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93 <filter>additional_params['GO_enrichment']['examine_GO_enrichment'] == 'yes'</filter>
0
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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94 <discover_datasets pattern="(?P&lt;name&gt;.+\.subset\.GOseq\.(enriched|depleted))$" ext="tabular" />
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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95 </collection>
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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96 </outputs>
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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97 <tests>
4
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98 <!-- Test without GO enrichment analysis -->
21
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parents: 20
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99 <test expect_num_outputs="9">
0
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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100 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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101 <param name="samples" value="count/samples.txt"/>
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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102 <param name="DE_results">
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103 <collection type="list">
4
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104 <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results" value="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results" ftype="tabular" />
63030102d46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
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105 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results" value="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" />
63030102d46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
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106 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results" value="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" />
3
24d072085816 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
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parents: 0
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107 </collection>
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108 </param>
0
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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109 <output_collection name="extracted_DE_genes">
4
63030102d46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
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110 <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.0.wt_37-UP.subset" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset"/>
63030102d46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
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111 <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.0.wt_GSNO-UP.subset" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset"/>
63030102d46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
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112 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_37-UP.subset" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset"/>
63030102d46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
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113 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_ph8-UP.subset" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset"/>
63030102d46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
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114 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_GSNO-UP.subset" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset"/>
63030102d46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
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115 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_ph8-UP.subset" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset"/>
0
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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116 </output_collection>
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117 <output_collection name="summary_files">
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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118 <element name="results_matrix" compare="sim_size" file="count/analyze_diff_expr/results.matrix"/>
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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119 <element name="results_matrix_log2_centered" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.centered.dat"/>
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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120 <element name="results_matrix_log2_centered_heatmap" delta="100" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/>
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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121 <element name="results_matrix_log2" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.dat"/>
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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122 <element name="results_matrix_log2_sample_cor" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.sample_cor.dat"/>
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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123 <element name="results_matrix_log2_sample_cor_matrix" delta="100" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.sample_cor_matrix.pdf"/>
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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124 </output_collection>
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125 <output name="rdata" compare="sim_size" file="count/analyze_diff_expr/results.matrix.RData"/>
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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126 </test>
4
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127 <!-- Test without GO enrichment analysis, test name of DE_results input files different from those generated by tool run_de_analysis.pl -->
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128 <test expect_num_outputs="9">
0
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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129 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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130 <param name="samples" value="count/samples.txt"/>
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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131 <param name="DE_results">
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132 <collection type="list">
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133 <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2" value="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results" ftype="tabular" />
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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134 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" />
d4128a4e49ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
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135 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" />
4
63030102d46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
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136 </collection>
0
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137 </param>
4
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138 <output_collection name="extracted_DE_genes">
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139 <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.0.wt_37-UP.subset" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset"/>
63030102d46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
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140 <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.0.wt_GSNO-UP.subset" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset"/>
63030102d46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
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141 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_37-UP.subset" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset"/>
63030102d46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
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142 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_ph8-UP.subset" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset"/>
63030102d46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
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143 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_GSNO-UP.subset" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset"/>
63030102d46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
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144 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_ph8-UP.subset" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset"/>
63030102d46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
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145 </output_collection>
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146 <output_collection name="summary_files">
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147 <element name="results_matrix" compare="sim_size" file="count/analyze_diff_expr/results.matrix"/>
63030102d46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
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148 <element name="results_matrix_log2_centered" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.centered.dat"/>
63030102d46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
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149 <element name="results_matrix_log2_centered_heatmap" delta="100" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/>
63030102d46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
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150 <element name="results_matrix_log2" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.dat"/>
63030102d46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686
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151 <element name="results_matrix_log2_sample_cor" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.sample_cor.dat"/>
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152 <element name="results_matrix_log2_sample_cor_matrix" delta="100" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.sample_cor_matrix.pdf"/>
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153 </output_collection>
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154 <output name="rdata" compare="sim_size" file="count/analyze_diff_expr/results.matrix.RData"/>
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155 </test>
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156 <!-- Test with GO enrichment analysis -->
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157 <test expect_num_outputs="10">
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158 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
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159 <param name="samples" value="count/samples.txt"/>
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160 <param name="DE_results">
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161 <collection type="list">
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162 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results" value="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" />
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163 </collection>
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164 </param>
0
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165 <section name="additional_params">
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166 <conditional name="GO_enrichment">
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167 <param name="examine_GO_enrichment" value="yes"/>
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168 <param name="DE_matrices">
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169 <collection type="list">
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170 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix" value="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix" ftype="tabular" />
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171 </collection>
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172 </param>
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173 <param name="GO_annots" value="count/trinotate/go_annotations.txt"/>
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174 <param name="gene_lengths" value="count/trinotate/genes.lengths.txt"/>
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175 </conditional>
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176 </section>
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177 <assert_command>
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178 <has_text text="--examine_GO_enrichment" />
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179 <has_text text="--GO_annots" />
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180 <has_text text="--gene_lengths" />
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181 </assert_command>
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182 <output_collection name="GOseq_enrichment">
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183 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.DE.subset.GOseq.enriched" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.DE.subset.GOseq.enriched"/>
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184 </output_collection>
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185 </test>
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186 </tests>
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187 <help>
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188 <![CDATA[
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189 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
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190 This tool extracts the transcripts that are most differentially expressed (most significant FDR and fold-changes), once differential expression analyses have been runned.
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191
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192 **Inputs**
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193
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194 This tool uses the raw counts matrix produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool.
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195
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196 You must describe your samples and replicates with a tabular file looking like this:
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197
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198 =========== ================
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199 ConditionA CondA_replicate1
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200 ----------- ----------------
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201 ConditionA CondA_replicate2
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202 ----------- ----------------
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203 ConditionB CondB_replicate1
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204 ----------- ----------------
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205 ConditionB CondB_replicate2
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206 ----------- ----------------
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207 ConditionC CondC_replicate1
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208 ----------- ----------------
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209 ConditionC CondC_replicate2
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210 ----------- ----------------
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211 ConditionC CondC_replicate3
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212 =========== ================
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213
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214 This file can be generated with the 'Describe samples and replicates' tool.
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215 It will probably be the same file as used in the tool 'RNASeq samples quality check for transcript quantification' or in the tool 'Differential expression analysis'.
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216 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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217
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218 You must also provide as a data collection the files resulting from the differential expression analysis (outputs of tool 'Differential expression analysis').
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219
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220 .. _Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki
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221 ]]>
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222 </help>
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223 <expand macro="citation" />
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224 </tool>