Mercurial > repos > iuc > trinity_abundance_estimates_to_matrix
comparison abundance_estimates_to_matrix.xml @ 22:ba3720d7e68b 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 14:55:49 +0000 |
parents | 400691c87530 |
children |
comparison
equal
deleted
inserted
replaced
21:400691c87530 | 22:ba3720d7e68b |
---|---|
87 <data format="tabular" name="norm_UQ_gene" label="${tool.name} on ${on_string}: Matrix of UpperQuartile-normalized expression values (gene)"> | 87 <data format="tabular" name="norm_UQ_gene" label="${tool.name} on ${on_string}: Matrix of UpperQuartile-normalized expression values (gene)"> |
88 <filter>additional_params['cross_sample_norm'] == "UpperQuartile" and gene_trans_map</filter> | 88 <filter>additional_params['cross_sample_norm'] == "UpperQuartile" and gene_trans_map</filter> |
89 </data> | 89 </data> |
90 </outputs> | 90 </outputs> |
91 <tests> | 91 <tests> |
92 <test> | 92 <test expect_num_outputs="3"> |
93 <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/> | 93 <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/> |
94 <param name="est_method" value="RSEM"/> | 94 <param name="est_method" value="RSEM"/> |
95 <param name="cross_sample_norm" value="TMM"/> | 95 <param name="cross_sample_norm" value="TMM"/> |
96 <output name="trans_counts"> | 96 <output name="trans_counts"> |
97 <assert_contents> | 97 <assert_contents> |
110 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> | 110 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
111 <has_n_columns n="3" /> | 111 <has_n_columns n="3" /> |
112 </assert_contents> | 112 </assert_contents> |
113 </output> | 113 </output> |
114 </test> | 114 </test> |
115 <test> | 115 <test expect_num_outputs="3"> |
116 <param name="samples" ftype="tabular" value="count/rsem_bowtie2/sample_A,count/rsem_bowtie2/sample_B"/> | 116 <param name="samples" ftype="tabular" value="count/rsem_bowtie2/sample_A,count/rsem_bowtie2/sample_B"/> |
117 <param name="est_method" value="RSEM"/> | 117 <param name="est_method" value="RSEM"/> |
118 <param name="cross_sample_norm" value="TMM"/> | 118 <param name="cross_sample_norm" value="TMM"/> |
119 <output name="trans_counts"> | 119 <output name="trans_counts"> |
120 <assert_contents> | 120 <assert_contents> |
133 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> | 133 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
134 <has_n_columns n="3" /> | 134 <has_n_columns n="3" /> |
135 </assert_contents> | 135 </assert_contents> |
136 </output> | 136 </output> |
137 </test> | 137 </test> |
138 <test> | 138 <test expect_num_outputs="3"> |
139 <param name="samples" ftype="tabular" value="count/express_bowtie/sample_A,count/express_bowtie/sample_B"/> | 139 <param name="samples" ftype="tabular" value="count/express_bowtie/sample_A,count/express_bowtie/sample_B"/> |
140 <param name="est_method" value="eXpress"/> | 140 <param name="est_method" value="eXpress"/> |
141 <param name="cross_sample_norm" value="TMM"/> | 141 <param name="cross_sample_norm" value="TMM"/> |
142 <output name="trans_counts"> | 142 <output name="trans_counts"> |
143 <assert_contents> | 143 <assert_contents> |
156 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> | 156 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
157 <has_n_columns n="3" /> | 157 <has_n_columns n="3" /> |
158 </assert_contents> | 158 </assert_contents> |
159 </output> | 159 </output> |
160 </test> | 160 </test> |
161 <test> | 161 <test expect_num_outputs="3"> |
162 <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/> | 162 <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/> |
163 <param name="est_method" value="RSEM"/> | 163 <param name="est_method" value="RSEM"/> |
164 <param name="cross_sample_norm" value="UpperQuartile"/> | 164 <param name="cross_sample_norm" value="UpperQuartile"/> |
165 <output name="trans_counts"> | 165 <output name="trans_counts"> |
166 <assert_contents> | 166 <assert_contents> |
178 <assert_contents> | 178 <assert_contents> |
179 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> | 179 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
180 </assert_contents> | 180 </assert_contents> |
181 </output> | 181 </output> |
182 </test> | 182 </test> |
183 <test> | 183 <test expect_num_outputs="2"> |
184 <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/> | 184 <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/> |
185 <param name="est_method" value="RSEM"/> | 185 <param name="est_method" value="RSEM"/> |
186 <param name="cross_sample_norm" value="none"/> | 186 <param name="cross_sample_norm" value="none"/> |
187 <output name="trans_counts"> | 187 <output name="trans_counts"> |
188 <assert_contents> | 188 <assert_contents> |
195 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> | 195 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
196 <has_n_columns n="3" /> | 196 <has_n_columns n="3" /> |
197 </assert_contents> | 197 </assert_contents> |
198 </output> | 198 </output> |
199 </test> | 199 </test> |
200 <test> | 200 <test expect_num_outputs="2"> |
201 <param name="samples" ftype="tabular" value="count/salmon/sample_A,count/salmon/sample_B"/> | 201 <param name="samples" ftype="tabular" value="count/salmon/sample_A,count/salmon/sample_B"/> |
202 <param name="est_method" value="salmon"/> | 202 <param name="est_method" value="salmon"/> |
203 <param name="cross_sample_norm" value="none"/> | 203 <param name="cross_sample_norm" value="none"/> |
204 <output name="trans_counts"> | 204 <output name="trans_counts"> |
205 <assert_contents> | 205 <assert_contents> |
212 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> | 212 <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> |
213 <has_n_columns n="3" /> | 213 <has_n_columns n="3" /> |
214 </assert_contents> | 214 </assert_contents> |
215 </output> | 215 </output> |
216 </test> | 216 </test> |
217 <test> | 217 <test expect_num_outputs="3"> |
218 <param name="samples" ftype="tabular" value="count/kallisto/abundance.tsv.genes,count/kallisto/abundance_B.tsv.genes"/> | 218 <param name="samples" ftype="tabular" value="count/kallisto/abundance.tsv.genes,count/kallisto/abundance_B.tsv.genes"/> |
219 <param name="est_method" value="kallisto"/> | 219 <param name="est_method" value="kallisto"/> |
220 <param name="cross_sample_norm" value="TMM"/> | 220 <param name="cross_sample_norm" value="TMM"/> |
221 <output name="trans_counts"> | 221 <output name="trans_counts"> |
222 <assert_contents> | 222 <assert_contents> |