Mercurial > repos > iuc > trinity_align_and_estimate_abundance
comparison align_and_estimate_abundance.xml @ 22:2fb4ee002432 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 14:53:59 +0000 |
| parents | b2bbe9a7f1b8 |
| children |
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| 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	.*" /> | 201 <has_line_matching expression="TRINITY_DN0_c0_g1	.*" /> |
| 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	.*" /> | 224 <has_line_matching expression="TRINITY_DN0_c0_g1	.*" /> |
| 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"/> |