Mercurial > repos > iuc > trinity_analyze_diff_expr

comparison analyze_diff_expr.xml @ 21:9ff3765e7172 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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&lt;name&gt;.+\.subset\.GOseq\.(enriched|depleted))$" ext="tabular" /> 94 <discover_datasets pattern="(?P&lt;name&gt;.+\.subset\.GOseq\.(enriched|depleted))$" 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" />