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comparison analyze_diff_expr.xml @ 5:74aa3fb94330 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 22687c0338822c4be3c389141cf1de4133b27235
author iuc
date Wed, 17 May 2017 05:40:20 -0400
parents ce471a02397f
children 83a4bace3a2c
comparison
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4:ce471a02397f 5:74aa3fb94330
1 <tool id="trinity_analyze_diff_expr" name="Extract and cluster differentially expressed transcripts" version="@WRAPPER_VERSION@.1"> 1 <tool id="trinity_analyze_diff_expr" name="Extract and cluster differentially expressed transcripts" version="@WRAPPER_VERSION@.2">
2 <description>from a Trinity assembly</description> 2 <description>from a Trinity assembly</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <expand macro="requirements">
7 <requirement type="package" version="2.6.0">bioconductor-qvalue</requirement> 7 <requirement type="package" version="2.6.0">bioconductor-qvalue</requirement>
8 <requirement type="package" version="1.26.0">bioconductor-goseq</requirement> 8 <requirement type="package" version="1.26.0">bioconductor-goseq</requirement>
9 <requirement type="package" version="3.4.0">bioconductor-go.db</requirement>
10 </expand> 9 </expand>
11 <command detect_errors="aggressive"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
12 ## DE results input files must be in the working directory and have suffix .DE_results 11 ## DE results input files must be in the working directory and have suffix .DE_results
13 #import re 12 #import re
14 #for $input in $DE_results 13 #for $input in $DE_results
15 ln -s "${input}" "${re.sub('[^\w\-_.]', '_', input.element_identifier)}.DE_results" 14 #if re.search('.DE_results$',input.element_identifier)
15 ## General case, where DE results files have been previously generated by run_de_analysis.pl
16 ln -s "${input}" "${re.sub('[^\w\-_.]', '_', input.element_identifier)}"
17 #else
18 ## Particular case, where DE results files have non-standard names
19 ln -s "${input}" "${re.sub('[^\w\-_.]', '_', input.element_identifier)}.DE_results"
20 #end if
16 && 21 &&
17 #end for 22 #end for
18 #for $DE_matrix in $DE_matrices 23 #if str( $additional_params.GO_enrichment.examine_GO_enrichment ) == "yes":
19 ln -s "${DE_matrix}" "${re.sub('[^\w\-_.]', '_', DE_matrix.element_identifier)}.count_matrix" 24 ## 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
20 && 25 #for $DE_matrix in $additional_params.GO_enrichment.DE_matrices
21 #end for 26 ## Handle general case, where DE results files and DE matrix files have been previously generated by run_de_analysis.pl
27 ln -s "${DE_matrix}" "${re.sub('[^\w\-_.]', '_', DE_matrix.element_identifier)}"
28 &&
29 #end for
30 #end if
22 31
23 analyze_diff_expr.pl 32 analyze_diff_expr.pl
24 --matrix "${matrix}" 33 --matrix "${matrix}"
25 --samples "${samples}" 34 --samples "${samples}"
26 -P ${p} 35 -P ${p}
46 ]]></command> 55 ]]></command>
47 <inputs> 56 <inputs>
48 <param format="tabular" name="matrix" argument="--matrix" 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"/> 57 <param format="tabular" name="matrix" argument="--matrix" 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"/>
49 <param format="tabular" name="samples" argument="--samples" type="data" label="Sample description" help="File describing samples and replicates"/> 58 <param format="tabular" name="samples" argument="--samples" type="data" label="Sample description" help="File describing samples and replicates"/>
50 <param format="tabular" name="DE_results" type="data_collection" collection_type="list" label="Differential expression results" help="Generated by 'Differential expression analysis using a Trinity assembly' tool"/> 59 <param format="tabular" name="DE_results" type="data_collection" collection_type="list" label="Differential expression results" help="Generated by 'Differential expression analysis using a Trinity assembly' tool"/>
51 <param format="tabular" name="DE_matrices" type="data_collection" collection_type="list" label="Differential expression count matrices" help="Generated by 'Differential expression analysis using a Trinity assembly' tool"/>
52 <param name="p" type="float" argument="-P" value="0.001" label="p-value cutoff for FDR"/> 60 <param name="p" type="float" argument="-P" value="0.001" label="p-value cutoff for FDR"/>
53 <param name="c" type="float" argument="-C" value="2" label="min abs(log2(a/b)) fold change" help="Default: 2 (meaning 2^(2) or 4-fold"/> 61 <param name="c" type="float" argument="-C" value="2" label="min abs(log2(a/b)) fold change" help="Default: 2 (meaning 2^(2) or 4-fold"/>
54 <section name="additional_params" title="Additional Options" expanded="False"> 62 <section name="additional_params" title="Additional Options" expanded="False">
55 <param name="max_DE_genes_per_comparison" 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."/> 63 <param name="max_DE_genes_per_comparison" 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."/>
56 <param name="order_columns_by_samples_file" 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."/> 64 <param name="order_columns_by_samples_file" 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."/>
61 <option value="yes">Yes</option> 69 <option value="yes">Yes</option>
62 </param> 70 </param>
63 <when value="no"> 71 <when value="no">
64 </when> 72 </when>
65 <when value="yes"> 73 <when value="yes">
74 <param format="tabular" name="DE_matrices" 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'."/>
66 <param format="tabular" name="GO_annots" argument="--GO_annots" 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,..."/> 75 <param format="tabular" name="GO_annots" argument="--GO_annots" 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,..."/>
67 <param format="tabular" name="gene_lengths" argument="--gene_lengths" type="data" label="Gene length file" help="Must have 2 columns: feature_id length"/> 76 <param format="tabular" name="gene_lengths" argument="--gene_lengths" type="data" label="Gene length file" help="Must have 2 columns: feature_id length"/>
68 </when> 77 </when>
69 </conditional> 78 </conditional>
70 </section> 79 </section>
71 </inputs> 80 </inputs>
72 <outputs> 81 <outputs>
73 <collection name="extracted_DE_genes" type="list" label="${tool.name} on ${on_string}: extracted differentially expressed genes"> 82 <collection name="extracted_DE_genes" type="list" label="${tool.name} on ${on_string}: extracted differentially expressed genes">
74 <discover_datasets pattern="(?P&lt;name&gt;.+)\.subset$" ext="tabular" /> 83 <discover_datasets pattern="(?P&lt;name&gt;.+\.subset)$" ext="tabular" />
75 </collection> 84 </collection>
76 <collection name="summary_files" type="list" label="${tool.name} on ${on_string}: summary files"> 85 <collection name="summary_files" type="list" label="${tool.name} on ${on_string}: summary files">
77 <data format="tabular" name="results_matrix" from_work_dir="results.matrix"/> 86 <data format="tabular" name="results_matrix" from_work_dir="results.matrix"/>
78 <data format="tabular" name="results_matrix_log2_centered" from_work_dir="results.matrix.log2.centered.dat"/> 87 <data format="tabular" name="results_matrix_log2_centered" from_work_dir="results.matrix.log2.centered.dat"/>
79 <data format="pdf" name="results_matrix_log2_centered_heatmap" from_work_dir="results.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/> 88 <data format="pdf" name="results_matrix_log2_centered_heatmap" from_work_dir="results.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/>
86 <filter>additional_params['GO_enrichment']['examine_GO_enrichment'] == 'yes'</filter> 95 <filter>additional_params['GO_enrichment']['examine_GO_enrichment'] == 'yes'</filter>
87 <discover_datasets pattern="(?P&lt;name&gt;.+\.subset\.GOseq\.(enriched|depleted))$" ext="tabular" /> 96 <discover_datasets pattern="(?P&lt;name&gt;.+\.subset\.GOseq\.(enriched|depleted))$" ext="tabular" />
88 </collection> 97 </collection>
89 </outputs> 98 </outputs>
90 <tests> 99 <tests>
100 <!-- Test without GO enrichment analysis -->
101 <test>
102 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
103 <param name="samples" value="count/samples.txt"/>
104 <param name="DE_results">
105 <collection type="list">
106 <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" />
107 <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" />
108 <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" />
109 </collection>
110 </param>
111 <output_collection name="extracted_DE_genes">
112 <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"/>
113 <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"/>
114 <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"/>
115 <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"/>
116 <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"/>
117 <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"/>
118 </output_collection>
119 <output_collection name="summary_files">
120 <element name="results_matrix" compare="sim_size" file="count/analyze_diff_expr/results.matrix"/>
121 <element name="results_matrix_log2_centered" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.centered.dat"/>
122 <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"/>
123 <element name="results_matrix_log2" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.dat"/>
124 <element name="results_matrix_log2_sample_cor" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.sample_cor.dat"/>
125 <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"/>
126 </output_collection>
127 <output name="rdata" compare="sim_size" file="count/analyze_diff_expr/results.matrix.RData"/>
128 </test>
129 <!-- Test without GO enrichment analysis, test name of DE_results input files different from those generated by tool run_de_analysis.pl -->
91 <test> 130 <test>
92 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> 131 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
93 <param name="samples" value="count/samples.txt"/> 132 <param name="samples" value="count/samples.txt"/>
94 <param name="DE_results"> 133 <param name="DE_results">
95 <collection type="list"> 134 <collection type="list">
96 <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" /> 135 <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" />
97 <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" /> 136 <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" />
98 <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" /> 137 <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" />
99 </collection> 138 </collection>
100 </param> 139 </param>
101 <param name="DE_matrices">
102 <collection type="list">
103 <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2" value="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.count_matrix" ftype="tabular" />
104 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.count_matrix" ftype="tabular" />
105 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix" ftype="tabular" />
106 </collection>
107 </param>
108 <output_collection name="extracted_DE_genes"> 140 <output_collection name="extracted_DE_genes">
109 <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.0.wt_37-UP" 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"/> 141 <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"/>
110 <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.0.wt_GSNO-UP" 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"/> 142 <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"/>
111 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_37-UP" 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"/> 143 <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"/>
112 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_ph8-UP" 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"/> 144 <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"/>
113 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_GSNO-UP" 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"/> 145 <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"/>
114 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_ph8-UP" 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"/> 146 <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"/>
115 </output_collection> 147 </output_collection>
116 <output_collection name="summary_files"> 148 <output_collection name="summary_files">
117 <element name="results_matrix" compare="sim_size" file="count/analyze_diff_expr/results.matrix"/> 149 <element name="results_matrix" compare="sim_size" file="count/analyze_diff_expr/results.matrix"/>
118 <element name="results_matrix_log2_centered" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.centered.dat"/> 150 <element name="results_matrix_log2_centered" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.centered.dat"/>
119 <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"/> 151 <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"/>
121 <element name="results_matrix_log2_sample_cor" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.sample_cor.dat"/> 153 <element name="results_matrix_log2_sample_cor" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.sample_cor.dat"/>
122 <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"/> 154 <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"/>
123 </output_collection> 155 </output_collection>
124 <output name="rdata" compare="sim_size" file="count/analyze_diff_expr/results.matrix.RData"/> 156 <output name="rdata" compare="sim_size" file="count/analyze_diff_expr/results.matrix.RData"/>
125 </test> 157 </test>
158 <!-- Test with GO enrichment analysis -->
126 <test> 159 <test>
127 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> 160 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
128 <param name="samples" value="count/samples.txt"/> 161 <param name="samples" value="count/samples.txt"/>
129 <param name="DE_results"> 162 <param name="DE_results">
130 <collection type="list"> 163 <collection type="list">
131 <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" /> 164 <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" />
132 <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" /> 165 <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" />
133 <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" /> 166 <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" />
134 </collection>
135 </param>
136 <param name="DE_matrices">
137 <collection type="list">
138 <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2" value="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.count_matrix" ftype="tabular" />
139 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.count_matrix" ftype="tabular" />
140 <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix" ftype="tabular" />
141 </collection> 167 </collection>
142 </param> 168 </param>
143 <section name="additional_params"> 169 <section name="additional_params">
144 <conditional name="GO_enrichment"> 170 <conditional name="GO_enrichment">
145 <param name="examine_GO_enrichment" value="yes"/> 171 <param name="examine_GO_enrichment" value="yes"/>
172 <param name="DE_matrices">
173 <collection type="list">
174 <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.count_matrix" value="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.count_matrix" ftype="tabular" />
175 <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.count_matrix" value="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.count_matrix" ftype="tabular" />
176 <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" />
177 </collection>
178 </param>
146 <param name="GO_annots" value="count/trinotate/go_annotations.txt"/> 179 <param name="GO_annots" value="count/trinotate/go_annotations.txt"/>
147 <param name="gene_lengths" value="count/trinotate/genes.lengths.txt"/> 180 <param name="gene_lengths" value="count/trinotate/genes.lengths.txt"/>
148 </conditional> 181 </conditional>
149 </section> 182 </section>
150 <assert_command> 183 <assert_command>