Mercurial > repos > iuc > trinity_align_and_estimate_abundance
comparison align_and_estimate_abundance.xml @ 18:00719b8004c9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c468d2b9613f88cc5f96f77ab1e0592d3c9ce707"
author | iuc |
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date | Sat, 27 Nov 2021 10:13:50 +0000 |
parents | 6c20d62180af |
children | 75f4e1859ed7 |
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17:6c20d62180af | 18:00719b8004c9 |
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1 <tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@+galaxy1"> | 1 <tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@+galaxy1"> |
2 <description>on a de novo assembly of RNA-Seq data</description> | 2 <description>on a de novo assembly of RNA-Seq data</description> |
3 <expand macro="bio_tools"/> | |
4 <macros> | 3 <macros> |
5 <import>macros.xml</import> | 4 <import>macros.xml</import> |
6 </macros> | 5 </macros> |
6 <expand macro="bio_tools"/> | |
7 <expand macro="requirements"> | 7 <expand macro="requirements"> |
8 <requirement type="package" version="1.3.2">rsem</requirement> | 8 <requirement type="package" version="1.3.2">rsem</requirement> |
9 <requirement type="package" version="0.46.0">kallisto</requirement> | 9 <requirement type="package" version="0.46.0">kallisto</requirement> |
10 </expand> | 10 </expand> |
11 <command detect_errors="aggressive"><![CDATA[ | 11 <command detect_errors="aggressive"><![CDATA[ |
188 <test> | 188 <test> |
189 <param name="paired_or_single" value="paired"/> | 189 <param name="paired_or_single" value="paired"/> |
190 <param name="left_input" value="reads.left.fq.gz"/> | 190 <param name="left_input" value="reads.left.fq.gz"/> |
191 <param name="right_input" value="reads.right.fq.gz"/> | 191 <param name="right_input" value="reads.right.fq.gz"/> |
192 <param name="transcripts" value="raw/Trinity.fasta"/> | 192 <param name="transcripts" value="raw/Trinity.fasta"/> |
193 <param name="gene_to_trans" value="raw/Trinity.map" /> | |
194 <param name="library_type" value="RF"/> | 193 <param name="library_type" value="RF"/> |
195 <param name="est_method" value="RSEM"/> | 194 <param name="est_method" value="RSEM"/> |
196 <param name="aln_method" value="bowtie"/> | 195 <param name="aln_method" value="bowtie"/> |
197 <param name="has_gene_map" value="yes"/> | 196 <param name="has_gene_map" value="yes"/> |
197 <param name="gene_trans_map" value="raw/Trinity.map" /> | |
198 <output name="isoforms_counts_rsem"> | 198 <output name="isoforms_counts_rsem"> |
199 <assert_contents> | 199 <assert_contents> |
200 <has_line_matching expression="TRINITY_DN0_c0_g1_i1	.*" /> | 200 <has_line_matching expression="TRINITY_DN0_c0_g1_i1	.*" /> |
201 <has_n_columns n="8" /> | 201 <has_n_columns n="8" /> |
202 </assert_contents> | 202 </assert_contents> |
211 <test> | 211 <test> |
212 <param name="paired_or_single" value="paired"/> | 212 <param name="paired_or_single" value="paired"/> |
213 <param name="left_input" value="reads.left.fq"/> | 213 <param name="left_input" value="reads.left.fq"/> |
214 <param name="right_input" value="reads.right.fq"/> | 214 <param name="right_input" value="reads.right.fq"/> |
215 <param name="transcripts" value="raw/Trinity.fasta"/> | 215 <param name="transcripts" value="raw/Trinity.fasta"/> |
216 <param name="gene_to_trans" value="raw/Trinity.map" /> | |
217 <param name="library_type" value="RF"/> | 216 <param name="library_type" value="RF"/> |
218 <param name="est_method" value="RSEM"/> | 217 <param name="est_method" value="RSEM"/> |
219 <param name="aln_method" value="bowtie2"/> | 218 <param name="aln_method" value="bowtie2"/> |
220 <param name="has_gene_map" value="yes"/> | 219 <param name="has_gene_map" value="yes"/> |
220 <param name="gene_trans_map" value="raw/Trinity.map" /> | |
221 <output name="isoforms_counts_rsem"> | 221 <output name="isoforms_counts_rsem"> |
222 <assert_contents> | 222 <assert_contents> |
223 <has_line_matching expression="TRINITY_DN0_c0_g1_i1	.*" /> | 223 <has_line_matching expression="TRINITY_DN0_c0_g1_i1	.*" /> |
224 <has_n_columns n="8" /> | 224 <has_n_columns n="8" /> |
225 </assert_contents> | 225 </assert_contents> |
234 <test> | 234 <test> |
235 <param name="paired_or_single" value="paired"/> | 235 <param name="paired_or_single" value="paired"/> |
236 <param name="left_input" value="reads.left.fq"/> | 236 <param name="left_input" value="reads.left.fq"/> |
237 <param name="right_input" value="reads.right.fq"/> | 237 <param name="right_input" value="reads.right.fq"/> |
238 <param name="transcripts" value="raw/Trinity.fasta"/> | 238 <param name="transcripts" value="raw/Trinity.fasta"/> |
239 <param name="gene_to_trans" value="raw/Trinity.map" /> | |
240 <param name="library_type" value="RF"/> | 239 <param name="library_type" value="RF"/> |
241 <param name="est_method" value="salmon"/> | 240 <param name="est_method" value="salmon"/> |
242 <param name="aln_method" value="bowtie"/> | 241 <param name="aln_method" value="bowtie"/> |
243 <param name="has_gene_map" value="yes"/> | 242 <param name="has_gene_map" value="yes"/> |
243 <param name="gene_trans_map" value="raw/Trinity.map" /> | |
244 <output name="isoforms_counts_salmon"> | 244 <output name="isoforms_counts_salmon"> |
245 <assert_contents> | 245 <assert_contents> |
246 <has_line_matching expression="TRINITY_DN2_c3_g1_i1	.*" /> | 246 <has_line_matching expression="TRINITY_DN2_c3_g1_i1	.*" /> |
247 <has_n_columns n="5" /> | 247 <has_n_columns n="5" /> |
248 </assert_contents> | 248 </assert_contents> |
257 <test> | 257 <test> |
258 <param name="paired_or_single" value="paired"/> | 258 <param name="paired_or_single" value="paired"/> |
259 <param name="left_input" value="reads.left.fq"/> | 259 <param name="left_input" value="reads.left.fq"/> |
260 <param name="right_input" value="reads.right.fq"/> | 260 <param name="right_input" value="reads.right.fq"/> |
261 <param name="transcripts" value="raw/Trinity.fasta"/> | 261 <param name="transcripts" value="raw/Trinity.fasta"/> |
262 <param name="gene_to_trans" value="raw/Trinity.map" /> | |
263 <param name="library_type" value="RF"/> | 262 <param name="library_type" value="RF"/> |
264 <param name="est_method" value="kallisto"/> | 263 <param name="est_method" value="kallisto"/> |
265 <param name="has_gene_map" value="yes"/> | 264 <param name="has_gene_map" value="yes"/> |
265 <param name="gene_trans_map" value="raw/Trinity.map" /> | |
266 <output name="isoforms_counts_kallisto"> | 266 <output name="isoforms_counts_kallisto"> |
267 <assert_contents> | 267 <assert_contents> |
268 <has_line_matching expression="TRINITY_DN1_c0_g1_i1	.*" /> | 268 <has_line_matching expression="TRINITY_DN1_c0_g1_i1	.*" /> |
269 <has_n_columns n="5" /> | 269 <has_n_columns n="5" /> |
270 </assert_contents> | 270 </assert_contents> |