Mercurial > repos > iuc > trinity_analyze_diff_expr
comparison analyze_diff_expr.xml @ 21:9ff3765e7172 draft default tip
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 |
| children |
comparison
equal
deleted
inserted
replaced
| 20:9871e84c26ee | 21:9ff3765e7172 |
|---|---|
| 94 <discover_datasets pattern="(?P<name>.+\.subset\.GOseq\.(enriched|depleted))$" ext="tabular" /> | 94 <discover_datasets pattern="(?P<name>.+\.subset\.GOseq\.(enriched|depleted))$" ext="tabular" /> |
| 95 </collection> | 95 </collection> |
| 96 </outputs> | 96 </outputs> |
| 97 <tests> | 97 <tests> |
| 98 <!-- Test without GO enrichment analysis --> | 98 <!-- Test without GO enrichment analysis --> |
| 99 <test> | 99 <test expect_num_outputs="9"> |
| 100 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> | 100 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> |
| 101 <param name="samples" value="count/samples.txt"/> | 101 <param name="samples" value="count/samples.txt"/> |
| 102 <param name="DE_results"> | 102 <param name="DE_results"> |
| 103 <collection type="list"> | 103 <collection type="list"> |
| 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" /> | 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" /> |
| 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"/> | 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"/> |
| 124 </output_collection> | 124 </output_collection> |
| 125 <output name="rdata" compare="sim_size" file="count/analyze_diff_expr/results.matrix.RData"/> | 125 <output name="rdata" compare="sim_size" file="count/analyze_diff_expr/results.matrix.RData"/> |
| 126 </test> | 126 </test> |
| 127 <!-- Test without GO enrichment analysis, test name of DE_results input files different from those generated by tool run_de_analysis.pl --> | 127 <!-- Test without GO enrichment analysis, test name of DE_results input files different from those generated by tool run_de_analysis.pl --> |
| 128 <test> | 128 <test expect_num_outputs="9"> |
| 129 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> | 129 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> |
| 130 <param name="samples" value="count/samples.txt"/> | 130 <param name="samples" value="count/samples.txt"/> |
| 131 <param name="DE_results"> | 131 <param name="DE_results"> |
| 132 <collection type="list"> | 132 <collection type="list"> |
| 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" /> | 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" /> |
| 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"/> | 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"/> |
| 153 </output_collection> | 153 </output_collection> |
| 154 <output name="rdata" compare="sim_size" file="count/analyze_diff_expr/results.matrix.RData"/> | 154 <output name="rdata" compare="sim_size" file="count/analyze_diff_expr/results.matrix.RData"/> |
| 155 </test> | 155 </test> |
| 156 <!-- Test with GO enrichment analysis --> | 156 <!-- Test with GO enrichment analysis --> |
| 157 <test> | 157 <test expect_num_outputs="10"> |
| 158 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> | 158 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> |
| 159 <param name="samples" value="count/samples.txt"/> | 159 <param name="samples" value="count/samples.txt"/> |
| 160 <param name="DE_results"> | 160 <param name="DE_results"> |
| 161 <collection type="list"> | 161 <collection type="list"> |
| 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" /> | 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" /> |