Mercurial > repos > iuc > trinity_align_and_estimate_abundance

comparison align_and_estimate_abundance.xml @ 18:00719b8004c9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c468d2b9613f88cc5f96f77ab1e0592d3c9ce707"
author iuc
date Sat, 27 Nov 2021 10:13:50 +0000
parents 6c20d62180af
children 75f4e1859ed7
comparison
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17:6c20d62180af 18:00719b8004c9
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&#009;.*" /> 200 <has_line_matching expression="TRINITY_DN0_c0_g1_i1&#009;.*" />
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&#009;.*" /> 223 <has_line_matching expression="TRINITY_DN0_c0_g1_i1&#009;.*" />
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&#009;.*" /> 246 <has_line_matching expression="TRINITY_DN2_c3_g1_i1&#009;.*" />
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&#009;.*" /> 268 <has_line_matching expression="TRINITY_DN1_c0_g1_i1&#009;.*" />
269 <has_n_columns n="5" /> 269 <has_n_columns n="5" />
270 </assert_contents> 270 </assert_contents>