Mercurial > repos > iuc > trinity_abundance_estimates_to_matrix

comparison abundance_estimates_to_matrix.xml @ 22:ba3720d7e68b draft default tip

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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&#009;.*" /> 110 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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&#009;.*" /> 133 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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&#009;.*" /> 156 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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&#009;.*" /> 179 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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&#009;.*" /> 195 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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&#009;.*" /> 212 <has_line_matching expression="TRINITY_DN3_c0_g1&#009;.*" />
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>