Mercurial > repos > iuc > trinity_analyze_diff_expr
diff analyze_diff_expr.xml @ 3:24d072085816 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
| author | iuc |
|---|---|
| date | Fri, 31 Mar 2017 11:37:35 -0400 |
| parents | d4128a4e49ca |
| children | 63030102d46e |
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--- a/analyze_diff_expr.xml Thu Mar 23 10:18:48 2017 -0400 +++ b/analyze_diff_expr.xml Fri Mar 31 11:37:35 2017 -0400 @@ -4,19 +4,21 @@ <import>macros.xml</import> </macros> <expand macro="requirements"> - <requirement type="package" version="2.30.0">bioconductor-biobase</requirement> - <requirement type="package" version="2.2.2">bioconductor-qvalue</requirement> - <requirement type="package" version="1.22.0">bioconductor-goseq</requirement> - <requirement type="package" version="3.3.0">bioconductor-go.db</requirement> + <requirement type="package" version="2.6.0">bioconductor-qvalue</requirement> + <requirement type="package" version="1.26.0">bioconductor-goseq</requirement> + <requirement type="package" version="3.4.0">bioconductor-go.db</requirement> </expand> - <expand macro="stdio"/> - <command><![CDATA[ + <command detect_errors="aggressive"><![CDATA[ ## DE results input files must be in the working directory and have suffix .DE_results #import re #for $input in $DE_results ln -s "${input}" "${re.sub('[^\w\-_.]', '_', input.element_identifier)}.DE_results" && #end for + #for $DE_matrix in $DE_matrices + ln -s "${DE_matrix}" "${re.sub('[^\w\-_.]', '_', DE_matrix.element_identifier)}.count_matrix" + && + #end for analyze_diff_expr.pl --matrix "${matrix}" @@ -45,7 +47,8 @@ <inputs> <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"/> <param format="tabular" name="samples" argument="--samples" type="data" label="Sample description" help="File describing samples and replicates"/> - <param format="tabular" name="DE_results" type="data_collection" collection_type="list" label="Differential expression results"/> + <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"/> + <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"/> <param name="p" type="float" argument="-P" value="0.001" label="p-value cutoff for FDR"/> <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"/> <section name="additional_params" title="Additional Options" expanded="False"> @@ -63,7 +66,7 @@ <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,..."/> <param format="tabular" name="gene_lengths" argument="--gene_lengths" type="data" label="Gene length file" help="Must have 2 columns: feature_id length"/> </when> - </conditional> + </conditional> </section> </inputs> <outputs> @@ -94,6 +97,13 @@ <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" /> </collection> </param> + <param name="DE_matrices"> + <collection type="list"> + <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" /> + <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" /> + <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" /> + </collection> + </param> <output_collection name="extracted_DE_genes"> <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"/> <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"/> @@ -122,6 +132,13 @@ <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" /> </collection> </param> + <param name="DE_matrices"> + <collection type="list"> + <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" /> + <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" /> + <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" /> + </collection> + </param> <section name="additional_params"> <conditional name="GO_enrichment"> <param name="examine_GO_enrichment" value="yes"/> @@ -142,7 +159,7 @@ <help> <![CDATA[ Trinity_ assembles transcript sequences from Illumina RNA-Seq data. -This tool extracts the transcripts that are most differentially expressed (most significant FDR and fold-changes), once differential expression analyses have been runned. +This tool extracts the transcripts that are most differentially expressed (most significant FDR and fold-changes), once differential expression analyses have been runned. **Inputs**