| Previous changeset 3:24d072085816 (2017-03-31) Next changeset 5:96be11bb913d (2017-12-15) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686 |
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modified:
analyze_diff_expr.xml |
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added:
test-data/count/kallisto/abundance.tsv test-data/count/kallisto/abundance.tsv.genes test-data/count/kallisto/abundance_B.tsv test-data/count/kallisto/abundance_B.tsv.genes |
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| diff -r 24d072085816 -r 63030102d46e analyze_diff_expr.xml --- a/analyze_diff_expr.xml Fri Mar 31 11:37:35 2017 -0400 +++ b/analyze_diff_expr.xml Mon Aug 28 16:53:59 2017 -0400 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="trinity_analyze_diff_expr" name="Extract and cluster differentially expressed transcripts" version="@WRAPPER_VERSION@.0">\n+<tool id="trinity_analyze_diff_expr" name="Extract and cluster differentially expressed transcripts" version="@WRAPPER_VERSION@.2">\n <description>from a Trinity assembly</description>\n <macros>\n <import>macros.xml</import>\n@@ -6,19 +6,29 @@\n <expand macro="requirements">\n <requirement type="package" version="2.6.0">bioconductor-qvalue</requirement>\n <requirement type="package" version="1.26.0">bioconductor-goseq</requirement>\n- <requirement type="package" version="3.4.0">bioconductor-go.db</requirement>\n+ <requirement type="package" version="2.0.6">r-cluster</requirement>\n </expand>\n <command detect_errors="aggressive"><![CDATA[\n ## DE results input files must be in the working directory and have suffix .DE_results\n #import re\n #for $input in $DE_results\n- ln -s "${input}" "${re.sub(\'[^\\w\\-_.]\', \'_\', input.element_identifier)}.DE_results"\n+ #if re.search(\'.DE_results$\',input.element_identifier)\n+ ##\xc2\xa0General case, where DE results files have been previously generated by run_de_analysis.pl\n+ ln -s "${input}" "${re.sub(\'[^\\w\\-_.]\', \'_\', input.element_identifier)}"\n+ #else\n+ ##\xc2\xa0Particular case, where DE results files have non-standard names\n+ ln -s "${input}" "${re.sub(\'[^\\w\\-_.]\', \'_\', input.element_identifier)}.DE_results"\n+ #end if\n &&\n #end for\n- #for $DE_matrix in $DE_matrices\n- ln -s "${DE_matrix}" "${re.sub(\'[^\\w\\-_.]\', \'_\', DE_matrix.element_identifier)}.count_matrix"\n- &&\n- #end for\n+ #if str( $additional_params.GO_enrichment.examine_GO_enrichment ) == "yes":\n+ ## 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\n+ #for $DE_matrix in $additional_params.GO_enrichment.DE_matrices\n+ ##\xc2\xa0Handle general case, where DE results files and DE matrix files have been previously generated by run_de_analysis.pl\n+ ln -s "${DE_matrix}" "${re.sub(\'[^\\w\\-_.]\', \'_\', DE_matrix.element_identifier)}"\n+ &&\n+ #end for\n+ #end if\n \n analyze_diff_expr.pl\n --matrix "${matrix}"\n@@ -48,7 +58,6 @@\n <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"/>\n <param format="tabular" name="samples" argument="--samples" type="data" label="Sample description" help="File describing samples and replicates"/>\n <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"/>\n- <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"/>\n <param name="p" type="float" argument="-P" value="0.001" label="p-value cutoff for FDR"/>\n <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"/>\n <section name="additional_params" title="Additional Options" expanded="False">\n@@ -63,6 +72,7 @@\n <when value="no">\n </when>\n <when value="yes">\n+ <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 t'..b'are="sim_size" file="count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset"/>\n+ <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"/>\n+ </output_collection>\n+ <output_collection name="summary_files">\n+ <element name="results_matrix" compare="sim_size" file="count/analyze_diff_expr/results.matrix"/>\n+ <element name="results_matrix_log2_centered" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.centered.dat"/>\n+ <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"/>\n+ <element name="results_matrix_log2" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.dat"/>\n+ <element name="results_matrix_log2_sample_cor" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.sample_cor.dat"/>\n+ <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"/>\n+ </output_collection>\n+ <output name="rdata" compare="sim_size" file="count/analyze_diff_expr/results.matrix.RData"/>\n+ </test>\n+ <!-- Test with GO enrichment analysis -->\n+ <test>\n+ <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>\n+ <param name="samples" value="count/samples.txt"/>\n+ <param name="DE_results">\n <collection type="list">\n- <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" />\n- <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" />\n- <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" />\n+ <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" />\n+ <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" />\n+ <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" />\n </collection>\n </param>\n <section name="additional_params">\n <conditional name="GO_enrichment">\n <param name="examine_GO_enrichment" value="yes"/>\n+ <param name="DE_matrices">\n+ <collection type="list">\n+ <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" />\n+ <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" />\n+ <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" />\n+ </collection>\n+ </param>\n <param name="GO_annots" value="count/trinotate/go_annotations.txt"/>\n <param name="gene_lengths" value="count/trinotate/genes.lengths.txt"/>\n </conditional>\n' |
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| diff -r 24d072085816 -r 63030102d46e test-data/count/kallisto/abundance.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/kallisto/abundance.tsv Mon Aug 28 16:53:59 2017 -0400 |
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| @@ -0,0 +1,8 @@ +target_id length eff_length est_counts tpm +TRINITY_DN1_c0_g1_i1 380 133.091 13 114025 +TRINITY_DN0_c0_g1_i1 229 31.75 7 257370 +TRINITY_DN2_c0_g1_i1 279 55.7143 1 20952.6 +TRINITY_DN2_c1_g1_i1 541 279.667 15 62611.6 +TRINITY_DN2_c2_g1_i1 240 42.75 4 109227 +TRINITY_DN2_c3_g1_i1 202 19 0 0 +TRINITY_DN3_c0_g1_i1 216 18.75 7 435814 |
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| diff -r 24d072085816 -r 63030102d46e test-data/count/kallisto/abundance.tsv.genes --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/kallisto/abundance.tsv.genes Mon Aug 28 16:53:59 2017 -0400 |
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| @@ -0,0 +1,8 @@ +target_id length eff_length est_counts tpm +TRINITY_DN3_c0_g1 216.00 18.75 7.00 435814.00 +TRINITY_DN2_c2_g1 240.00 42.75 4.00 109227.00 +TRINITY_DN2_c3_g1 202.00 19.00 0.00 0.00 +TRINITY_DN0_c0_g1 229.00 31.75 7.00 257370.00 +TRINITY_DN2_c0_g1 279.00 55.71 1.00 20952.60 +TRINITY_DN1_c0_g1 380.00 133.09 13.00 114025.00 +TRINITY_DN2_c1_g1 541.00 279.67 15.00 62611.60 |
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| diff -r 24d072085816 -r 63030102d46e test-data/count/kallisto/abundance_B.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/kallisto/abundance_B.tsv Mon Aug 28 16:53:59 2017 -0400 |
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| @@ -0,0 +1,8 @@ +target_id length eff_length est_counts tpm +TRINITY_DN1_c0_g1_i1 229 31.75 7 257370 +TRINITY_DN0_c0_g1_i1 380 133.091 13 114025 +TRINITY_DN2_c0_g1_i1 279 55.7143 1 20952.6 +TRINITY_DN2_c2_g1_i1 541 279.667 15 62611.6 +TRINITY_DN2_c1_g1_i1 240 42.75 4 109227 +TRINITY_DN2_c3_g1_i1 202 19 0 0 +TRINITY_DN3_c0_g1_i1 216 18.75 7 435814 |
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| diff -r 24d072085816 -r 63030102d46e test-data/count/kallisto/abundance_B.tsv.genes --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/kallisto/abundance_B.tsv.genes Mon Aug 28 16:53:59 2017 -0400 |
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| @@ -0,0 +1,8 @@ +target_id length eff_length est_counts tpm +TRINITY_DN3_c0_g1 216.00 18.75 7.00 435814.00 +TRINITY_DN2_c1_g1 240.00 42.75 4.00 109227.00 +TRINITY_DN2_c3_g1 202.00 19.00 0.00 0.00 +TRINITY_DN0_c0_g1 380.00 133.09 13.00 114025.00 +TRINITY_DN2_c0_g1 279.00 55.71 1.00 20952.60 +TRINITY_DN1_c0_g1 229.00 31.75 7.00 257370.00 +TRINITY_DN2_c2_g1 541.00 279.67 15.00 62611.60 |