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comparison analyze_diff_expr.xml @ 19:c0096052b35b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
author iuc
date Tue, 11 Apr 2023 19:55:15 +0000
parents 2a89673cec86
children 9871e84c26ee
comparison
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18:3f4094b6a565 19:c0096052b35b
1 <tool id="trinity_analyze_diff_expr" name="Extract and cluster differentially expressed transcripts" version="@WRAPPER_VERSION@"> 1 <tool id="trinity_analyze_diff_expr" name="Extract and cluster differentially expressed transcripts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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="bio_tools"/> 6 <expand macro="bio_tools"/>
7 <expand macro="requirements"> 7 <expand macro="requirements"/>
8 <requirement type="package" version="2.18.0">bioconductor-qvalue</requirement>
9 <requirement type="package" version="1.36.0">bioconductor-goseq</requirement>
10 <requirement type="package" version="2.0.8">r-cluster</requirement>
11 <requirement type="package" version="1.1.25">r-fastcluster</requirement>
12 </expand>
13 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
14 ## DE results input files must be in the working directory and have suffix .DE_results 9 ## DE results input files must be in the working directory and have suffix .DE_results
15 #import re 10 #import re
16 #for $input in $DE_results 11 #for $input in $DE_results
17 #if re.search('.DE_results$',input.element_identifier) 12 #if re.search('.DE_results$',input.element_identifier)
33 #end if 28 #end if
34 29
35 analyze_diff_expr.pl 30 analyze_diff_expr.pl
36 --matrix '${matrix}' 31 --matrix '${matrix}'
37 --samples '${samples}' 32 --samples '${samples}'
38 -P ${p} 33 -P ${P}
39 -C ${c} 34 -C ${C}
40 35
41 #if str( $additional_params.max_DE_genes_per_comparison ): 36 #if str( $additional_params.max_DE_genes_per_comparison ):
42 --max_DE_genes_per_comparison ${additional_params.max_DE_genes_per_comparison} 37 --max_DE_genes_per_comparison ${additional_params.max_DE_genes_per_comparison}
43 #end if 38 #end if
44 39
55 #end if 50 #end if
56 51
57 --output results 52 --output results
58 ]]></command> 53 ]]></command>
59 <inputs> 54 <inputs>
60 <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"/> 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"/>
61 <param format="tabular" name="samples" argument="--samples" type="data" label="Sample description" help="File describing samples and replicates"/> 56 <param argument="--samples" format="tabular" type="data" label="Sample description" help="File describing samples and replicates"/>
62 <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"/> 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"/>
63 <param name="p" type="float" argument="-P" value="0.001" label="p-value cutoff for FDR"/> 58 <param argument="-P" type="float" value="0.001" label="p-value cutoff for FDR"/>
64 <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"/> 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"/>
65 <section name="additional_params" title="Additional Options" expanded="False"> 60 <section name="additional_params" title="Additional Options" expanded="False">
66 <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."/> 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."/>
67 <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."/> 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."/>
68 <param name="max_genes_clust" 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"/> 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"/>
69 <conditional name="GO_enrichment"> 64 <conditional name="GO_enrichment">
70 <param type="select" name="examine_GO_enrichment" argument="--examine_GO_enrichment" 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"> 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">
71 <option value="no">No</option> 66 <option value="no">No</option>
72 <option value="yes">Yes</option> 67 <option value="yes">Yes</option>
73 </param> 68 </param>
74 <when value="no"> 69 <when value="no">
75 </when> 70 </when>
76 <when value="yes"> 71 <when value="yes">
77 <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'."/> 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'."/>
78 <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,..."/> 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,..."/>
79 <param format="tabular" name="gene_lengths" argument="--gene_lengths" type="data" label="Gene length file" help="Must have 2 columns: feature_id length"/> 74 <param argument="--gene_lengths" format="tabular" type="data" label="Gene length file" help="Must have 2 columns: feature_id length"/>
80 </when> 75 </when>
81 </conditional> 76 </conditional>
82 </section> 77 </section>
83 </inputs> 78 </inputs>
84 <outputs> 79 <outputs>
91 <data format="pdf" name="results_matrix_log2_centered_heatmap" from_work_dir="results.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/> 86 <data format="pdf" name="results_matrix_log2_centered_heatmap" from_work_dir="results.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/>
92 <data format="tabular" name="results_matrix_log2" from_work_dir="results.matrix.log2.dat"/> 87 <data format="tabular" name="results_matrix_log2" from_work_dir="results.matrix.log2.dat"/>
93 <data format="tabular" name="results_matrix_log2_sample_cor" from_work_dir="results.matrix.log2.sample_cor.dat"/> 88 <data format="tabular" name="results_matrix_log2_sample_cor" from_work_dir="results.matrix.log2.sample_cor.dat"/>
94 <data format="pdf" name="results_matrix_log2_sample_cor_matrix" from_work_dir="results.matrix.log2.sample_cor_matrix.pdf"/> 89 <data format="pdf" name="results_matrix_log2_sample_cor_matrix" from_work_dir="results.matrix.log2.sample_cor_matrix.pdf"/>
95 </collection> 90 </collection>
96 <data format="rdata" name="rdata" label="${tool.name} on ${on_string}: RData file" from_work_dir="results.matrix.RData"/> 91 <data name="rdata" format="rdata" label="${tool.name} on ${on_string}: RData file" from_work_dir="results.matrix.RData"/>
97 <collection name="GOseq_enrichment" type="list" label="${tool.name} on ${on_string}: GOseq enriched and depleted categories"> 92 <collection name="GOseq_enrichment" type="list" label="${tool.name} on ${on_string}: GOseq enriched and depleted categories">
98 <filter>additional_params['GO_enrichment']['examine_GO_enrichment'] == 'yes'</filter> 93 <filter>additional_params['GO_enrichment']['examine_GO_enrichment'] == 'yes'</filter>
99 <discover_datasets pattern="(?P&lt;name&gt;.+\.subset\.GOseq\.(enriched|depleted))$" ext="tabular" /> 94 <discover_datasets pattern="(?P&lt;name&gt;.+\.subset\.GOseq\.(enriched|depleted))$" ext="tabular" />
100 </collection> 95 </collection>
101 </outputs> 96 </outputs>