Mercurial > repos > iuc > trinity_align_and_estimate_abundance
comparison align_and_estimate_abundance.xml @ 10:afd41a430a76 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
author | iuc |
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date | Thu, 14 Jun 2018 03:11:22 -0400 |
parents | 3baf18bcf03e |
children | aed859a021c0 |
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9:cb5f0dde2aa8 | 10:afd41a430a76 |
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1 <tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@.3"> | 1 <tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@"> |
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 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements"> | 6 <expand macro="requirements"> |
10 <requirement type="package" version="0.43.1">kallisto</requirement> | 10 <requirement type="package" version="0.43.1">kallisto</requirement> |
11 </expand> | 11 </expand> |
12 <command detect_errors="aggressive"><![CDATA[ | 12 <command detect_errors="aggressive"><![CDATA[ |
13 ln -f -s '$transcripts' input.fa && | 13 ln -f -s '$transcripts' input.fa && |
14 | 14 |
15 #if $additional_params.gene_map.has_gene_map == "yes": | |
16 get_Trinity_gene_to_trans_map.pl input.fa > gene_to_trans.map && | |
17 #else: | |
18 ln -f -s '$additional_params.gene_map.gene_trans_map' gene_to_trans.map && | |
19 #end if | |
20 | |
15 #if $inputs.paired_or_single == "paired": | 21 #if $inputs.paired_or_single == "paired": |
16 #if $inputs.left_input.is_of_type('fasta'): | 22 #if $inputs.left_input.is_of_type('fasta'): |
17 ln -s '$inputs.left_input' paired_left.fa && | 23 ln -s '$inputs.left_input' paired_left.fa && |
18 ln -s '$inputs.right_input' paired_right.fa | 24 ln -s '$inputs.right_input' paired_right.fa |
19 #else: | 25 #else: |
66 --SS_lib_type $inputs.strand.library_type | 72 --SS_lib_type $inputs.strand.library_type |
67 #end if | 73 #end if |
68 #end if | 74 #end if |
69 | 75 |
70 ## Additional parameters. | 76 ## Additional parameters. |
71 #if $additional_params.gene_map.has_gene_map == "no": | 77 --gene_trans_map gene_to_trans.map |
72 --gene_trans_map $additional_params.gene_map.gene_trans_map | |
73 #else | |
74 --trinity_mode | |
75 #end if | |
76 | 78 |
77 --prep_reference | 79 --prep_reference |
78 | 80 |
79 --output_dir output | 81 --output_dir output |
80 | 82 |
197 <test> | 199 <test> |
198 <param name="paired_or_single" value="paired"/> | 200 <param name="paired_or_single" value="paired"/> |
199 <param name="left_input" value="reads.left.fq"/> | 201 <param name="left_input" value="reads.left.fq"/> |
200 <param name="right_input" value="reads.right.fq"/> | 202 <param name="right_input" value="reads.right.fq"/> |
201 <param name="transcripts" value="raw/Trinity.fasta"/> | 203 <param name="transcripts" value="raw/Trinity.fasta"/> |
204 <param name="gene_to_trans" value="raw/Trinity.map" /> | |
202 <param name="library_type" value="RF"/> | 205 <param name="library_type" value="RF"/> |
203 <param name="est_method" value="RSEM"/> | 206 <param name="est_method" value="RSEM"/> |
204 <param name="aln_method" value="bowtie"/> | 207 <param name="aln_method" value="bowtie"/> |
205 <param name="has_gene_map" value="yes"/> | 208 <param name="has_gene_map" value="yes"/> |
206 <output name="isoforms_counts_rsem"> | 209 <output name="isoforms_counts_rsem"> |
219 <test> | 222 <test> |
220 <param name="paired_or_single" value="paired"/> | 223 <param name="paired_or_single" value="paired"/> |
221 <param name="left_input" value="reads.left.fq"/> | 224 <param name="left_input" value="reads.left.fq"/> |
222 <param name="right_input" value="reads.right.fq"/> | 225 <param name="right_input" value="reads.right.fq"/> |
223 <param name="transcripts" value="raw/Trinity.fasta"/> | 226 <param name="transcripts" value="raw/Trinity.fasta"/> |
227 <param name="gene_to_trans" value="raw/Trinity.map" /> | |
224 <param name="library_type" value="RF"/> | 228 <param name="library_type" value="RF"/> |
225 <param name="est_method" value="RSEM"/> | 229 <param name="est_method" value="RSEM"/> |
226 <param name="aln_method" value="bowtie2"/> | 230 <param name="aln_method" value="bowtie2"/> |
227 <param name="has_gene_map" value="yes"/> | 231 <param name="has_gene_map" value="yes"/> |
228 <output name="isoforms_counts_rsem"> | 232 <output name="isoforms_counts_rsem"> |
241 <test> | 245 <test> |
242 <param name="paired_or_single" value="paired"/> | 246 <param name="paired_or_single" value="paired"/> |
243 <param name="left_input" value="reads.left.fq"/> | 247 <param name="left_input" value="reads.left.fq"/> |
244 <param name="right_input" value="reads.right.fq"/> | 248 <param name="right_input" value="reads.right.fq"/> |
245 <param name="transcripts" value="raw/Trinity.fasta"/> | 249 <param name="transcripts" value="raw/Trinity.fasta"/> |
250 <param name="gene_to_trans" value="raw/Trinity.map" /> | |
246 <param name="library_type" value="RF"/> | 251 <param name="library_type" value="RF"/> |
247 <param name="est_method" value="eXpress"/> | 252 <param name="est_method" value="eXpress"/> |
248 <param name="aln_method" value="bowtie"/> | 253 <param name="aln_method" value="bowtie"/> |
249 <param name="has_gene_map" value="yes"/> | 254 <param name="has_gene_map" value="yes"/> |
250 <output name="isoforms_counts_express"> | 255 <output name="isoforms_counts_express"> |
263 <test> | 268 <test> |
264 <param name="paired_or_single" value="paired"/> | 269 <param name="paired_or_single" value="paired"/> |
265 <param name="left_input" value="reads.left.fq"/> | 270 <param name="left_input" value="reads.left.fq"/> |
266 <param name="right_input" value="reads.right.fq"/> | 271 <param name="right_input" value="reads.right.fq"/> |
267 <param name="transcripts" value="raw/Trinity.fasta"/> | 272 <param name="transcripts" value="raw/Trinity.fasta"/> |
273 <param name="gene_to_trans" value="raw/Trinity.map" /> | |
268 <param name="library_type" value="RF"/> | 274 <param name="library_type" value="RF"/> |
269 <param name="est_method" value="salmon"/> | 275 <param name="est_method" value="salmon"/> |
270 <param name="aln_method" value="bowtie"/> | 276 <param name="aln_method" value="bowtie"/> |
271 <param name="has_gene_map" value="yes"/> | 277 <param name="has_gene_map" value="yes"/> |
272 <output name="isoforms_counts_salmon"> | 278 <output name="isoforms_counts_salmon"> |
285 <test> | 291 <test> |
286 <param name="paired_or_single" value="paired"/> | 292 <param name="paired_or_single" value="paired"/> |
287 <param name="left_input" value="reads.left.fq"/> | 293 <param name="left_input" value="reads.left.fq"/> |
288 <param name="right_input" value="reads.right.fq"/> | 294 <param name="right_input" value="reads.right.fq"/> |
289 <param name="transcripts" value="raw/Trinity.fasta"/> | 295 <param name="transcripts" value="raw/Trinity.fasta"/> |
296 <param name="gene_to_trans" value="raw/Trinity.map" /> | |
290 <param name="library_type" value="RF"/> | 297 <param name="library_type" value="RF"/> |
291 <param name="est_method" value="kallisto"/> | 298 <param name="est_method" value="kallisto"/> |
292 <param name="has_gene_map" value="yes"/> | 299 <param name="has_gene_map" value="yes"/> |
293 <output name="isoforms_counts_kallisto"> | 300 <output name="isoforms_counts_kallisto"> |
294 <assert_contents> | 301 <assert_contents> |