Mercurial > repos > iuc > trinity_align_and_estimate_abundance

comparison align_and_estimate_abundance.xml @ 10:afd41a430a76 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
author iuc
date Thu, 14 Jun 2018 03:11:22 -0400
parents 3baf18bcf03e
children aed859a021c0
comparison
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9:cb5f0dde2aa8 10:afd41a430a76
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>