Mercurial > repos > iuc > trinity_align_and_estimate_abundance

comparison align_and_estimate_abundance.xml @ 22:2fb4ee002432 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 14:53:59 +0000
parents b2bbe9a7f1b8
children
comparison
equal deleted inserted replaced
21:b2bbe9a7f1b8 22:2fb4ee002432
178 <data format="tabular" name="genes_counts_kallisto" label="${tool.name} on ${on_string}: genes counts (Kallisto)" from_work_dir="output/abundance.tsv.genes"> 178 <data format="tabular" name="genes_counts_kallisto" label="${tool.name} on ${on_string}: genes counts (Kallisto)" from_work_dir="output/abundance.tsv.genes">
179 <filter>method['est_method'] == "kallisto"</filter> 179 <filter>method['est_method'] == "kallisto"</filter>
180 </data> 180 </data>
181 </outputs> 181 </outputs>
182 <tests> 182 <tests>
183 <test> 183 <test expect_num_outputs="2">
184 <param name="paired_or_single" value="paired"/> 184 <param name="paired_or_single" value="paired"/>
185 <param name="left_input" value="reads.left.fq.gz"/> 185 <param name="left_input" value="reads.left.fq.gz"/>
186 <param name="right_input" value="reads.right.fq.gz"/> 186 <param name="right_input" value="reads.right.fq.gz"/>
187 <param name="transcripts" value="raw/Trinity.fasta"/> 187 <param name="transcripts" value="raw/Trinity.fasta"/>
188 <param name="library_type" value="RF"/> 188 <param name="library_type" value="RF"/>
201 <has_line_matching expression="TRINITY_DN0_c0_g1&#009;.*" /> 201 <has_line_matching expression="TRINITY_DN0_c0_g1&#009;.*" />
202 <has_n_columns n="7" /> 202 <has_n_columns n="7" />
203 </assert_contents> 203 </assert_contents>
204 </output> 204 </output>
205 </test> 205 </test>
206 <test> 206 <test expect_num_outputs="2">
207 <param name="paired_or_single" value="paired"/> 207 <param name="paired_or_single" value="paired"/>
208 <param name="left_input" value="reads.left.fq"/> 208 <param name="left_input" value="reads.left.fq"/>
209 <param name="right_input" value="reads.right.fq"/> 209 <param name="right_input" value="reads.right.fq"/>
210 <param name="transcripts" value="raw/Trinity.fasta"/> 210 <param name="transcripts" value="raw/Trinity.fasta"/>
211 <param name="library_type" value="RF"/> 211 <param name="library_type" value="RF"/>
224 <has_line_matching expression="TRINITY_DN0_c0_g1&#009;.*" /> 224 <has_line_matching expression="TRINITY_DN0_c0_g1&#009;.*" />
225 <has_n_columns n="7" /> 225 <has_n_columns n="7" />
226 </assert_contents> 226 </assert_contents>
227 </output> 227 </output>
228 </test> 228 </test>
229 <test> 229 <test expect_num_outputs="2">
230 <param name="paired_or_single" value="paired"/> 230 <param name="paired_or_single" value="paired"/>
231 <param name="left_input" value="reads.left.fq"/> 231 <param name="left_input" value="reads.left.fq"/>
232 <param name="right_input" value="reads.right.fq"/> 232 <param name="right_input" value="reads.right.fq"/>
233 <param name="transcripts" value="raw/Trinity.fasta"/> 233 <param name="transcripts" value="raw/Trinity.fasta"/>
234 <param name="library_type" value="RF"/> 234 <param name="library_type" value="RF"/>
247 <has_line_matching expression="TRINITY_DN3_c0_g1.*" /> 247 <has_line_matching expression="TRINITY_DN3_c0_g1.*" />
248 <has_n_columns n="5" /> 248 <has_n_columns n="5" />
249 </assert_contents> 249 </assert_contents>
250 </output> 250 </output>
251 </test> 251 </test>
252 <test> 252 <test expect_num_outputs="2">
253 <param name="paired_or_single" value="paired"/> 253 <param name="paired_or_single" value="paired"/>
254 <param name="left_input" value="reads.left.fq"/> 254 <param name="left_input" value="reads.left.fq"/>
255 <param name="right_input" value="reads.right.fq"/> 255 <param name="right_input" value="reads.right.fq"/>
256 <param name="transcripts" value="raw/Trinity.fasta"/> 256 <param name="transcripts" value="raw/Trinity.fasta"/>
257 <param name="library_type" value="RF"/> 257 <param name="library_type" value="RF"/>